Starting phenix.real_space_refine on Mon Mar 18 05:26:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysi_10898/03_2024/6ysi_10898_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysi_10898/03_2024/6ysi_10898.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysi_10898/03_2024/6ysi_10898_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysi_10898/03_2024/6ysi_10898_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysi_10898/03_2024/6ysi_10898_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysi_10898/03_2024/6ysi_10898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysi_10898/03_2024/6ysi_10898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysi_10898/03_2024/6ysi_10898_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysi_10898/03_2024/6ysi_10898_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 2800 5.49 5 Mg 162 5.21 5 S 68 5.16 5 C 41550 2.51 5 N 15603 2.21 5 O 23671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "B ASP 18": "OD1" <-> "OD2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ASP 203": "OD1" <-> "OD2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 139": "OD1" <-> "OD2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C ASP 175": "OD1" <-> "OD2" Residue "C PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 171": "NH1" <-> "NH2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F ASP 49": "OD1" <-> "OD2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H ARG 43": "NH1" <-> "NH2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H ASP 106": "OD1" <-> "OD2" Residue "H ARG 111": "NH1" <-> "NH2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I GLU 76": "OE1" <-> "OE2" Residue "I GLU 96": "OE1" <-> "OE2" Residue "I ASP 112": "OD1" <-> "OD2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "I PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 2": "NH1" <-> "NH2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J ARG 63": "NH1" <-> "NH2" Residue "J PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 117": "OD1" <-> "OD2" Residue "K TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 44": "OD1" <-> "OD2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ASP 92": "OD1" <-> "OD2" Residue "K GLU 111": "OE1" <-> "OE2" Residue "L ASP 27": "OD1" <-> "OD2" Residue "L ARG 75": "NH1" <-> "NH2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "M ARG 3": "NH1" <-> "NH2" Residue "M ARG 13": "NH1" <-> "NH2" Residue "M ARG 30": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N GLU 16": "OE1" <-> "OE2" Residue "N GLU 18": "OE1" <-> "OE2" Residue "N GLU 28": "OE1" <-> "OE2" Residue "N ASP 36": "OD1" <-> "OD2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N GLU 95": "OE1" <-> "OE2" Residue "O ARG 9": "NH1" <-> "NH2" Residue "O ASP 69": "OD1" <-> "OD2" Residue "O GLU 79": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "P GLU 4": "OE1" <-> "OE2" Residue "P ARG 5": "NH1" <-> "NH2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "P ARG 68": "NH1" <-> "NH2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 71": "NH1" <-> "NH2" Residue "P ARG 75": "NH1" <-> "NH2" Residue "P ASP 78": "OD1" <-> "OD2" Residue "P ASP 91": "OD1" <-> "OD2" Residue "Q ASP 8": "OD1" <-> "OD2" Residue "Q GLU 17": "OE1" <-> "OE2" Residue "Q GLU 35": "OE1" <-> "OE2" Residue "Q GLU 53": "OE1" <-> "OE2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q ASP 79": "OD1" <-> "OD2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q GLU 99": "OE1" <-> "OE2" Residue "R PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "R ARG 23": "NH1" <-> "NH2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "R GLU 47": "OE1" <-> "OE2" Residue "R ARG 49": "NH1" <-> "NH2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R GLU 66": "OE1" <-> "OE2" Residue "S ASP 64": "OD1" <-> "OD2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 41": "OE1" <-> "OE2" Residue "T GLU 43": "OE1" <-> "OE2" Residue "T ARG 48": "NH1" <-> "NH2" Residue "T ARG 57": "NH1" <-> "NH2" Residue "T ASP 70": "OD1" <-> "OD2" Residue "U GLU 12": "OE1" <-> "OE2" Residue "V GLU 57": "OE1" <-> "OE2" Residue "X GLU 24": "OE1" <-> "OE2" Residue "X ASP 30": "OD1" <-> "OD2" Residue "X ASP 45": "OD1" <-> "OD2" Residue "X PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 28": "OE1" <-> "OE2" Residue "Z GLU 9": "OE1" <-> "OE2" Residue "a ARG 29": "NH1" <-> "NH2" Residue "b GLU 30": "OE1" <-> "OE2" Residue "b ARG 36": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 83855 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2109 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1571 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "C" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1485 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 192} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 865 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 6, 'TRANS': 169} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 542 Unresolved non-hydrogen angles: 679 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 10, 'GLU:plan': 8, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 279 Chain: "E" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1327 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "F" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1122 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "G" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "H" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1071 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "I" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1086 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "J" Number of atoms: 950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Conformer: "B" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} bond proxies already assigned to first conformer: 946 Chain: "K" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 864 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain: "L" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "M" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "N" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 806 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "O" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "P" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 717 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "Q" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 761 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "R" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 753 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "S" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 577 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "T" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 631 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "U" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "V" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 453 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "W" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 213 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "X" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "Y" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 426 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "Z" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "1" Number of atoms: 57324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2672, 57324 Classifications: {'RNA': 2672} Modifications used: {'rna2p_pur': 258, 'rna2p_pyr': 148, 'rna3p_pur': 1278, 'rna3p_pyr': 988} Link IDs: {'rna2p': 406, 'rna3p': 2265} Chain breaks: 5 Chain: "5" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 52, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 101} Chain: "6" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 112 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "8" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 169 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 5} Chain: "a" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "b" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 294 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "1" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 201 Unusual residues: {' MG': 159, 'T1C': 1} Classifications: {'undetermined': 160} Link IDs: {None: 159} Chain: "5" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 3, 'T1C': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 83355 SG CYS b 11 180.975 95.182 89.940 1.00 36.50 S ATOM 83371 SG CYS b 14 177.885 95.962 88.286 1.00 35.23 S ATOM 83476 SG CYS b 27 179.459 92.684 87.696 1.00 35.09 S Time building chain proxies: 34.38, per 1000 atoms: 0.41 Number of scatterers: 83855 At special positions: 0 Unit cell: (209.805, 215.13, 184.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 68 16.00 P 2800 15.00 Mg 162 11.99 O 23671 8.00 N 15603 7.00 C 41550 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: 37.79 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 101 " pdb="ZN ZN b 101 " - pdb=" ND1 HIS b 33 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 14 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 11 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 27 " Number of angles added : 3 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 47 sheets defined 24.7% alpha, 19.5% beta 970 base pairs and 1517 stacking pairs defined. Time for finding SS restraints: 41.10 Creating SS restraints... Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.607A pdb=" N ARG A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'C' and resid 24 through 38 Processing helix chain 'C' and resid 97 through 113 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 189 through 198 removed outlier: 3.528A pdb=" N GLU C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 10 Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 48 through 60 removed outlier: 4.856A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 Processing helix chain 'D' and resid 163 through 172 Processing helix chain 'E' and resid 59 through 80 Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.882A pdb=" N TYR E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 37 removed outlier: 4.217A pdb=" N GLU F 31 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 68 through 71 No H-bonds generated for 'chain 'F' and resid 68 through 71' Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 97 through 108 removed outlier: 3.503A pdb=" N GLY F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 121 removed outlier: 3.960A pdb=" N LYS F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 106 No H-bonds generated for 'chain 'G' and resid 104 through 106' Processing helix chain 'G' and resid 112 through 117 Processing helix chain 'H' and resid 59 through 62 No H-bonds generated for 'chain 'H' and resid 59 through 62' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 131 through 139 Processing helix chain 'I' and resid 44 through 58 Processing helix chain 'I' and resid 111 through 124 removed outlier: 3.747A pdb=" N ALA I 123 " --> pdb=" O ALA I 119 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 31 Processing helix chain 'J' and resid 38 through 56 removed outlier: 3.736A pdb=" N ARG J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG J 46 " --> pdb=" O LYS J 42 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL J 47 " --> pdb=" O GLU J 43 " (cutoff:3.500A) Proline residue: J 50 - end of helix Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 81 Processing helix chain 'J' and resid 83 through 86 No H-bonds generated for 'chain 'J' and resid 83 through 86' Processing helix chain 'K' and resid 3 through 22 removed outlier: 4.549A pdb=" N SER K 14 " --> pdb=" O ARG K 10 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N THR K 15 " --> pdb=" O ARG K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 83 Processing helix chain 'K' and resid 101 through 112 Processing helix chain 'L' and resid 6 through 13 Processing helix chain 'L' and resid 57 through 59 No H-bonds generated for 'chain 'L' and resid 57 through 59' Processing helix chain 'L' and resid 101 through 105 Processing helix chain 'L' and resid 108 through 111 Processing helix chain 'M' and resid 8 through 21 removed outlier: 3.516A pdb=" N ALA M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 30 Processing helix chain 'M' and resid 32 through 72 removed outlier: 3.678A pdb=" N GLN M 37 " --> pdb=" O ARG M 33 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG M 51 " --> pdb=" O TYR M 47 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS M 54 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN M 72 " --> pdb=" O GLY M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 85 Processing helix chain 'M' and resid 92 through 101 Processing helix chain 'M' and resid 103 through 117 Processing helix chain 'O' and resid 15 through 25 removed outlier: 3.898A pdb=" N LEU O 20 " --> pdb=" O GLN O 16 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE O 25 " --> pdb=" O VAL O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 38 Processing helix chain 'O' and resid 43 through 63 removed outlier: 3.771A pdb=" N LEU O 47 " --> pdb=" O LYS O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 92 No H-bonds generated for 'chain 'O' and resid 90 through 92' Processing helix chain 'P' and resid 3 through 9 removed outlier: 3.682A pdb=" N GLN P 8 " --> pdb=" O GLU P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 25 Processing helix chain 'P' and resid 39 through 50 Processing helix chain 'Q' and resid 65 through 67 No H-bonds generated for 'chain 'Q' and resid 65 through 67' Processing helix chain 'R' and resid 18 through 26 Processing helix chain 'R' and resid 48 through 56 removed outlier: 3.586A pdb=" N GLU R 56 " --> pdb=" O VAL R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 61 No H-bonds generated for 'chain 'R' and resid 59 through 61' Processing helix chain 'T' and resid 41 through 43 No H-bonds generated for 'chain 'T' and resid 41 through 43' Processing helix chain 'T' and resid 53 through 62 Processing helix chain 'T' and resid 64 through 73 Processing helix chain 'U' and resid 11 through 33 Processing helix chain 'U' and resid 40 through 60 removed outlier: 3.612A pdb=" N VAL U 45 " --> pdb=" O GLU U 42 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA U 46 " --> pdb=" O VAL U 43 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS U 48 " --> pdb=" O VAL U 45 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS U 54 " --> pdb=" O ALA U 51 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU U 57 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR U 58 " --> pdb=" O THR U 55 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS U 60 " --> pdb=" O LEU U 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 26 Processing helix chain 'V' and resid 41 through 49 removed outlier: 3.815A pdb=" N MET V 46 " --> pdb=" O SER V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 53 No H-bonds generated for 'chain 'V' and resid 51 through 53' Processing helix chain 'X' and resid 10 through 19 removed outlier: 4.952A pdb=" N HIS X 19 " --> pdb=" O MET X 15 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 16 Processing helix chain 'Z' and resid 18 through 21 No H-bonds generated for 'chain 'Z' and resid 18 through 21' Processing helix chain 'Z' and resid 25 through 37 Processing helix chain 'a' and resid 8 through 11 No H-bonds generated for 'chain 'a' and resid 8 through 11' Processing helix chain 'a' and resid 37 through 42 Processing helix chain 'a' and resid 54 through 60 Processing helix chain 'b' and resid 31 through 33 No H-bonds generated for 'chain 'b' and resid 31 through 33' Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'A' and resid 34 through 37 removed outlier: 3.662A pdb=" N LYS A 37 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN A 60 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 101 through 105 removed outlier: 3.790A pdb=" N ARG A 80 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS A 95 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL A 78 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 129 through 131 Processing sheet with id= E, first strand: chain 'A' and resid 181 through 185 removed outlier: 6.727A pdb=" N ARG A 175 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU A 164 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 172 through 175 removed outlier: 4.399A pdb=" N GLN B 115 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP B 203 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 27 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N MET B 12 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 25 " --> pdb=" O MET B 12 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG B 14 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 23 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS B 193 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 180 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 79 through 84 removed outlier: 3.893A pdb=" N LEU B 79 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 53 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR B 52 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE B 35 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 118 through 122 removed outlier: 5.670A pdb=" N LEU B 168 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE B 121 " --> pdb=" O GLY B 166 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY B 166 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 117 through 120 removed outlier: 6.323A pdb=" N VAL C 185 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL C 120 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N MET C 187 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASP C 167 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR C 149 " --> pdb=" O ASP C 167 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL C 169 " --> pdb=" O THR C 149 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 127 through 131 removed outlier: 3.952A pdb=" N ILE D 154 " --> pdb=" O MET D 130 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 16 through 18 removed outlier: 3.991A pdb=" N GLY E 31 " --> pdb=" O GLY E 28 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 161 through 164 Processing sheet with id= M, first strand: chain 'E' and resid 95 through 99 Processing sheet with id= N, first strand: chain 'F' and resid 15 through 19 removed outlier: 6.337A pdb=" N TYR F 53 " --> pdb=" O PHE F 16 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL F 18 " --> pdb=" O TYR F 53 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE F 55 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 73 through 77 Processing sheet with id= P, first strand: chain 'G' and resid 7 through 9 removed outlier: 6.638A pdb=" N LYS G 40 " --> pdb=" O ILE G 22 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL G 24 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE G 38 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN G 59 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA G 83 " --> pdb=" O VAL G 63 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 76 through 80 removed outlier: 6.742A pdb=" N ARG H 109 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL H 79 " --> pdb=" O ARG H 109 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG H 111 " --> pdb=" O VAL H 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'H' and resid 123 through 125 removed outlier: 7.145A pdb=" N LYS H 143 " --> pdb=" O VAL H 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'I' and resid 129 through 133 removed outlier: 3.702A pdb=" N TYR I 104 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA I 36 " --> pdb=" O ILE I 102 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE I 102 " --> pdb=" O ALA I 36 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 40 through 43 removed outlier: 6.893A pdb=" N ILE I 74 " --> pdb=" O GLU I 91 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP I 93 " --> pdb=" O LYS I 72 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LYS I 72 " --> pdb=" O TRP I 93 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 33 through 37 Processing sheet with id= V, first strand: chain 'K' and resid 90 through 92 Processing sheet with id= W, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.724A pdb=" N LYS L 86 " --> pdb=" O GLN L 32 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR L 28 " --> pdb=" O LYS L 90 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N GLU L 47 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE L 67 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR L 63 " --> pdb=" O ILE L 51 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS L 53 " --> pdb=" O ALA L 61 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA L 61 " --> pdb=" O LYS L 53 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 11 through 15 removed outlier: 3.868A pdb=" N MET N 40 " --> pdb=" O VAL N 4 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 19 through 23 Processing sheet with id= Z, first strand: chain 'N' and resid 32 through 35 removed outlier: 6.216A pdb=" N GLU N 62 " --> pdb=" O ILE N 98 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE N 98 " --> pdb=" O GLU N 62 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 72 through 78 removed outlier: 3.982A pdb=" N TYR N 83 " --> pdb=" O ARG N 78 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 3 through 8 removed outlier: 6.506A pdb=" N GLY O 109 " --> pdb=" O VAL O 72 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL O 72 " --> pdb=" O GLY O 109 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 83 through 88 Processing sheet with id= AD, first strand: chain 'P' and resid 10 through 13 removed outlier: 5.951A pdb=" N LYS P 32 " --> pdb=" O LYS P 11 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL P 30 " --> pdb=" O PRO P 13 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS P 80 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS P 56 " --> pdb=" O THR P 85 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'P' and resid 66 through 68 Processing sheet with id= AF, first strand: chain 'Q' and resid 21 through 23 Processing sheet with id= AG, first strand: chain 'Q' and resid 39 through 44 Processing sheet with id= AH, first strand: chain 'Q' and resid 81 through 86 Processing sheet with id= AI, first strand: chain 'Q' and resid 24 through 28 removed outlier: 6.430A pdb=" N LYS Q 33 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL Q 27 " --> pdb=" O ARG Q 31 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG Q 31 " --> pdb=" O VAL Q 27 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'R' and resid 5 through 7 removed outlier: 6.111A pdb=" N GLU R 66 " --> pdb=" O LEU R 6 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP R 94 " --> pdb=" O GLN R 79 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU R 81 " --> pdb=" O HIS R 92 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS R 92 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N ALA R 93 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N PHE R 95 " --> pdb=" O PRO R 31 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE R 33 " --> pdb=" O PHE R 95 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ARG R 97 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR R 35 " --> pdb=" O ARG R 97 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'S' and resid 51 through 53 Processing sheet with id= AL, first strand: chain 'S' and resid 66 through 72 Processing sheet with id= AM, first strand: chain 'T' and resid 13 through 18 Processing sheet with id= AN, first strand: chain 'T' and resid 33 through 40 Processing sheet with id= AO, first strand: chain 'V' and resid 34 through 38 Processing sheet with id= AP, first strand: chain 'W' and resid 22 through 26 removed outlier: 6.739A pdb=" N THR W 32 " --> pdb=" O THR W 15 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'X' and resid 27 through 29 Processing sheet with id= AR, first strand: chain 'Y' and resid 16 through 21 Processing sheet with id= AS, first strand: chain 'a' and resid 22 through 24 Processing sheet with id= AT, first strand: chain 'b' and resid 2 through 4 Processing sheet with id= AU, first strand: chain 'b' and resid 14 through 19 754 hydrogen bonds defined for protein. 2094 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2408 hydrogen bonds 3660 hydrogen bond angles 0 basepair planarities 970 basepair parallelities 1517 stacking parallelities Total time for adding SS restraints: 161.79 Time building geometry restraints manager: 40.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8853 1.32 - 1.44: 40106 1.44 - 1.56: 36517 1.56 - 1.69: 5591 1.69 - 1.81: 120 Bond restraints: 91187 Sorted by residual: bond pdb=" C8 T1C 5 205 " pdb=" C9 T1C 5 205 " ideal model delta sigma weight residual 1.024 1.394 -0.370 2.00e-02 2.50e+03 3.43e+02 bond pdb=" C8 T1C 13160 " pdb=" C9 T1C 13160 " ideal model delta sigma weight residual 1.024 1.392 -0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C8 T1C 5 201 " pdb=" C9 T1C 5 201 " ideal model delta sigma weight residual 1.024 1.392 -0.368 2.00e-02 2.50e+03 3.38e+02 bond pdb=" C12 T1C 5 201 " pdb=" C1C T1C 5 201 " ideal model delta sigma weight residual 1.155 1.506 -0.351 2.00e-02 2.50e+03 3.08e+02 bond pdb=" C12 T1C 13160 " pdb=" C1C T1C 13160 " ideal model delta sigma weight residual 1.155 1.506 -0.351 2.00e-02 2.50e+03 3.07e+02 ... (remaining 91182 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.33: 16665 106.33 - 113.52: 54856 113.52 - 120.71: 35906 120.71 - 127.90: 24587 127.90 - 135.09: 5033 Bond angle restraints: 137047 Sorted by residual: angle pdb=" C1A T1C 5 205 " pdb=" C61 T1C 5 205 " pdb=" C7 T1C 5 205 " ideal model delta sigma weight residual 105.85 120.38 -14.53 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C1A T1C 5 201 " pdb=" C61 T1C 5 201 " pdb=" C7 T1C 5 201 " ideal model delta sigma weight residual 105.85 120.32 -14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" C10 T1C 13160 " pdb=" C1A T1C 13160 " pdb=" C61 T1C 13160 " ideal model delta sigma weight residual 105.73 119.73 -14.00 3.00e+00 1.11e-01 2.18e+01 angle pdb=" C1A T1C 13160 " pdb=" C61 T1C 13160 " pdb=" C7 T1C 13160 " ideal model delta sigma weight residual 105.85 119.85 -14.00 3.00e+00 1.11e-01 2.18e+01 angle pdb=" C10 T1C 5 205 " pdb=" C1A T1C 5 205 " pdb=" C61 T1C 5 205 " ideal model delta sigma weight residual 105.73 119.21 -13.48 3.00e+00 1.11e-01 2.02e+01 ... (remaining 137042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 50704 35.85 - 71.70: 6716 71.70 - 107.55: 707 107.55 - 143.40: 15 143.40 - 179.25: 17 Dihedral angle restraints: 58159 sinusoidal: 49353 harmonic: 8806 Sorted by residual: dihedral pdb=" O4' U 12057 " pdb=" C1' U 12057 " pdb=" N1 U 12057 " pdb=" C2 U 12057 " ideal model delta sinusoidal sigma weight residual -160.00 12.34 -172.34 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C 11130 " pdb=" C1' C 11130 " pdb=" N1 C 11130 " pdb=" C2 C 11130 " ideal model delta sinusoidal sigma weight residual -160.00 12.19 -172.19 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U 1 62 " pdb=" C1' U 1 62 " pdb=" N1 U 1 62 " pdb=" C2 U 1 62 " ideal model delta sinusoidal sigma weight residual 200.00 30.03 169.97 1 1.50e+01 4.44e-03 8.47e+01 ... (remaining 58156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 17216 0.113 - 0.226: 412 0.226 - 0.339: 21 0.339 - 0.452: 1 0.452 - 0.565: 3 Chirality restraints: 17653 Sorted by residual: chirality pdb=" C41 T1C 5 201 " pdb=" C1C T1C 5 201 " pdb=" C4 T1C 5 201 " pdb=" C5 T1C 5 201 " both_signs ideal model delta sigma weight residual False 3.12 2.56 0.57 2.00e-01 2.50e+01 7.99e+00 chirality pdb=" C41 T1C 13160 " pdb=" C1C T1C 13160 " pdb=" C4 T1C 13160 " pdb=" C5 T1C 13160 " both_signs ideal model delta sigma weight residual False 3.12 2.56 0.57 2.00e-01 2.50e+01 7.98e+00 chirality pdb=" C41 T1C 5 205 " pdb=" C1C T1C 5 205 " pdb=" C4 T1C 5 205 " pdb=" C5 T1C 5 205 " both_signs ideal model delta sigma weight residual False 3.12 2.65 0.47 2.00e-01 2.50e+01 5.64e+00 ... (remaining 17650 not shown) Planarity restraints: 6959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C9 T1C 5 201 " -0.162 2.00e-02 2.50e+03 1.36e-01 2.30e+02 pdb=" C91 T1C 5 201 " 0.044 2.00e-02 2.50e+03 pdb=" C92 T1C 5 201 " -0.113 2.00e-02 2.50e+03 pdb=" N9 T1C 5 201 " 0.226 2.00e-02 2.50e+03 pdb=" O91 T1C 5 201 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 T1C 13160 " 0.087 2.00e-02 2.50e+03 7.53e-02 8.51e+01 pdb=" C12 T1C 13160 " 0.001 2.00e-02 2.50e+03 pdb=" C1B T1C 13160 " 0.015 2.00e-02 2.50e+03 pdb=" C1C T1C 13160 " 0.088 2.00e-02 2.50e+03 pdb=" C51 T1C 13160 " -0.090 2.00e-02 2.50e+03 pdb=" O12 T1C 13160 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C9 T1C 5 205 " -0.088 2.00e-02 2.50e+03 7.27e-02 6.60e+01 pdb=" C91 T1C 5 205 " 0.026 2.00e-02 2.50e+03 pdb=" C92 T1C 5 205 " -0.064 2.00e-02 2.50e+03 pdb=" N9 T1C 5 205 " 0.118 2.00e-02 2.50e+03 pdb=" O91 T1C 5 205 " 0.008 2.00e-02 2.50e+03 ... (remaining 6956 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 411 2.45 - 3.06: 48385 3.06 - 3.68: 160512 3.68 - 4.29: 255275 4.29 - 4.90: 327456 Nonbonded interactions: 792039 Sorted by model distance: nonbonded pdb=" OP1 A 11769 " pdb="MG MG 13078 " model vdw 1.839 2.170 nonbonded pdb=" OP1 C 11995 " pdb="MG MG 13025 " model vdw 1.873 2.170 nonbonded pdb=" OP2 A 11147 " pdb="MG MG 13022 " model vdw 1.884 2.170 nonbonded pdb=" OP2 A 11772 " pdb="MG MG 13078 " model vdw 1.886 2.170 nonbonded pdb=" OP2 C 11661 " pdb="MG MG 13117 " model vdw 1.887 2.170 ... (remaining 792034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.750 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: 0.060 Extract box with map and model: 15.720 Check model and map are aligned: 0.950 Set scattering table: 0.610 Process input model: 351.020 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.270 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: 0.030 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 386.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 0.370 91187 Z= 0.571 Angle : 0.768 14.530 137047 Z= 0.396 Chirality : 0.046 0.565 17653 Planarity : 0.006 0.136 6959 Dihedral : 23.604 179.253 52495 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 5.75 % Allowed : 16.94 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.34 (0.13), residues: 3057 helix: -1.41 (0.15), residues: 770 sheet: -1.16 (0.18), residues: 687 loop : -1.78 (0.13), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 248 HIS 0.006 0.002 HIS F 47 PHE 0.023 0.003 PHE B 121 TYR 0.019 0.002 TYR F 125 ARG 0.009 0.001 ARG T 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 689 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.8725 (p) cc_final: 0.8474 (m) REVERT: A 102 ARG cc_start: 0.8813 (mtt180) cc_final: 0.8501 (mtt-85) REVERT: B 29 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7373 (pp20) REVERT: B 188 SER cc_start: 0.8581 (t) cc_final: 0.8126 (t) REVERT: E 19 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.7004 (tt0) REVERT: F 12 GLN cc_start: 0.8337 (tp40) cc_final: 0.8081 (tp40) REVERT: F 53 TYR cc_start: 0.9164 (m-80) cc_final: 0.8853 (m-80) REVERT: H 19 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7799 (ttm-80) REVERT: L 12 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6922 (pt0) REVERT: L 44 GLN cc_start: 0.8635 (tt0) cc_final: 0.8421 (tt0) REVERT: N 60 THR cc_start: 0.9079 (p) cc_final: 0.8804 (p) REVERT: O 79 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: P 87 LYS cc_start: 0.7456 (ttmm) cc_final: 0.7245 (mttp) REVERT: Q 48 ARG cc_start: 0.4354 (OUTLIER) cc_final: 0.4065 (mmp-170) REVERT: S 81 LYS cc_start: 0.8928 (pttp) cc_final: 0.8376 (pttp) REVERT: T 40 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8286 (tt) REVERT: V 1 MET cc_start: 0.4928 (OUTLIER) cc_final: 0.4677 (tmt) REVERT: Y 6 ARG cc_start: 0.8583 (mtp-110) cc_final: 0.8336 (mtp-110) REVERT: Y 26 MET cc_start: 0.8047 (ttp) cc_final: 0.7822 (ttp) REVERT: a 42 GLN cc_start: 0.9213 (mt0) cc_final: 0.8853 (mt0) outliers start: 134 outliers final: 76 residues processed: 771 average time/residue: 1.8754 time to fit residues: 1891.3279 Evaluate side-chains 694 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 612 time to evaluate : 3.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 44 LYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 12 GLU Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 98 THR Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 78 ILE Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 20 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 8.9990 chunk 436 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 294 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 451 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 274 optimal weight: 7.9990 chunk 336 optimal weight: 6.9990 chunk 523 optimal weight: 3.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 48 HIS A 117 GLN A 134 ASN A 142 HIS ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN A 260 ASN B 33 ASN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS C 28 HIS C 29 GLN C 40 GLN C 45 HIS E 36 ASN E 51 GLN E 64 GLN E 74 ASN E 104 ASN E 143 GLN F 40 HIS F 58 ASN F 77 HIS F 130 HIS F 138 GLN ** H 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN J 72 ASN J 91 ASN K 18 HIS K 35 HIS L 9 GLN L 44 GLN M 37 GLN M 52 GLN N 89 HIS O 16 GLN O 63 ASN P 8 GLN Q 9 GLN Q 21 GLN Q 59 GLN Q 84 GLN R 75 ASN R 79 GLN R 92 HIS S 29 GLN T 23 ASN U 22 GLN U 25 GLN V 14 HIS V 24 GLN X 25 ASN X 40 HIS Y 22 ASN Y 42 HIS b 37 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.0513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 91187 Z= 0.313 Angle : 0.652 14.931 137047 Z= 0.333 Chirality : 0.040 0.375 17653 Planarity : 0.005 0.055 6959 Dihedral : 23.549 179.966 47034 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 4.20 % Allowed : 22.73 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.37 (0.14), residues: 3057 helix: -0.15 (0.17), residues: 772 sheet: -0.76 (0.19), residues: 675 loop : -1.33 (0.13), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 248 HIS 0.006 0.001 HIS X 40 PHE 0.017 0.002 PHE B 121 TYR 0.015 0.002 TYR J 112 ARG 0.007 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 642 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8305 (mtpm) cc_final: 0.8095 (mtpp) REVERT: A 102 ARG cc_start: 0.8808 (mtt180) cc_final: 0.8489 (mtt-85) REVERT: A 170 SER cc_start: 0.8545 (p) cc_final: 0.8320 (t) REVERT: B 188 SER cc_start: 0.8689 (t) cc_final: 0.8204 (t) REVERT: C 56 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7514 (ptpt) REVERT: E 155 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: F 12 GLN cc_start: 0.8324 (tp40) cc_final: 0.8072 (tp40) REVERT: F 53 TYR cc_start: 0.9144 (m-80) cc_final: 0.8838 (m-80) REVERT: G 120 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: H 19 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7837 (ttm-80) REVERT: H 118 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8118 (pp) REVERT: L 12 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6847 (pt0) REVERT: L 86 LYS cc_start: 0.8360 (tttp) cc_final: 0.8149 (ttpp) REVERT: L 109 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.4624 (mptt) REVERT: M 22 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8628 (ttmm) REVERT: N 60 THR cc_start: 0.8988 (p) cc_final: 0.8695 (p) REVERT: O 23 ASP cc_start: 0.7836 (m-30) cc_final: 0.7628 (m-30) REVERT: O 71 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7931 (tttt) REVERT: a 42 GLN cc_start: 0.9195 (mt0) cc_final: 0.8797 (mt0) REVERT: b 4 GLN cc_start: 0.8643 (mt0) cc_final: 0.8359 (pt0) outliers start: 98 outliers final: 54 residues processed: 702 average time/residue: 1.8218 time to fit residues: 1688.7354 Evaluate side-chains 670 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 609 time to evaluate : 3.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 12 GLU Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain M residue 22 LYS Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 48 LYS Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 78 ILE Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 33 LYS Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 30 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 435 optimal weight: 20.0000 chunk 356 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 524 optimal weight: 6.9990 chunk 566 optimal weight: 10.0000 chunk 466 optimal weight: 20.0000 chunk 519 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 chunk 420 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 HIS ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN C 40 GLN E 51 GLN F 138 GLN ** H 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN J 72 ASN J 91 ASN L 9 GLN L 44 GLN Q 9 GLN Q 21 GLN Q 59 GLN Q 84 GLN R 79 GLN U 25 GLN V 24 GLN X 25 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.122 91187 Z= 0.595 Angle : 0.849 18.758 137047 Z= 0.421 Chirality : 0.050 0.433 17653 Planarity : 0.007 0.059 6959 Dihedral : 23.635 179.798 46971 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.29 % Rotamer: Outliers : 6.09 % Allowed : 22.26 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.25 (0.14), residues: 3057 helix: -0.08 (0.18), residues: 769 sheet: -0.65 (0.19), residues: 696 loop : -1.26 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 248 HIS 0.008 0.002 HIS F 47 PHE 0.027 0.003 PHE B 121 TYR 0.022 0.003 TYR F 125 ARG 0.009 0.001 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 621 time to evaluate : 3.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.8756 (p) cc_final: 0.8475 (m) REVERT: A 102 ARG cc_start: 0.8830 (mtt180) cc_final: 0.8517 (mtt-85) REVERT: B 188 SER cc_start: 0.8645 (t) cc_final: 0.8111 (t) REVERT: C 161 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8484 (mtm180) REVERT: C 194 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8395 (ttpp) REVERT: E 155 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: F 12 GLN cc_start: 0.8352 (tp40) cc_final: 0.8098 (tp40) REVERT: F 53 TYR cc_start: 0.9172 (m-80) cc_final: 0.8875 (m-80) REVERT: G 120 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: H 19 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7875 (ttm-80) REVERT: H 118 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8175 (pp) REVERT: J 1 MET cc_start: 0.8266 (mtm) cc_final: 0.7945 (mtm) REVERT: L 12 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6864 (pt0) REVERT: L 109 LYS cc_start: 0.6822 (OUTLIER) cc_final: 0.4653 (mptt) REVERT: L 115 GLU cc_start: 0.7596 (tt0) cc_final: 0.7376 (tt0) REVERT: M 78 ARG cc_start: 0.8185 (mmt180) cc_final: 0.7945 (mmp80) REVERT: N 60 THR cc_start: 0.9070 (p) cc_final: 0.8781 (p) REVERT: O 23 ASP cc_start: 0.7932 (m-30) cc_final: 0.7653 (m-30) REVERT: O 71 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7948 (tttt) REVERT: R 40 GLU cc_start: 0.6949 (mp0) cc_final: 0.6453 (mp0) REVERT: S 44 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: S 70 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7782 (pm20) REVERT: T 27 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8024 (tmt90) REVERT: T 40 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8287 (tt) REVERT: V 1 MET cc_start: 0.4959 (OUTLIER) cc_final: 0.4561 (tmt) REVERT: a 42 GLN cc_start: 0.9224 (mt0) cc_final: 0.8842 (mt0) outliers start: 142 outliers final: 85 residues processed: 709 average time/residue: 1.8485 time to fit residues: 1728.3238 Evaluate side-chains 710 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 613 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 44 LYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 GLU Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 22 LYS Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 58 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 98 THR Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 48 LYS Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 70 GLU Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 78 ILE Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 20 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 0.6980 chunk 393 optimal weight: 2.9990 chunk 271 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 250 optimal weight: 0.8980 chunk 351 optimal weight: 4.9990 chunk 525 optimal weight: 2.9990 chunk 556 optimal weight: 9.9990 chunk 274 optimal weight: 20.0000 chunk 498 optimal weight: 2.9990 chunk 150 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 117 GLN A 198 GLN B 47 GLN B 153 GLN C 29 GLN C 40 GLN F 88 ASN F 138 GLN H 107 GLN I 17 ASN J 91 ASN L 9 GLN L 44 GLN L 55 ASN Q 9 GLN Q 59 GLN Q 84 GLN R 79 GLN T 20 HIS U 25 GLN V 24 GLN X 25 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 91187 Z= 0.122 Angle : 0.536 14.930 137047 Z= 0.276 Chirality : 0.034 0.324 17653 Planarity : 0.004 0.045 6959 Dihedral : 23.316 179.549 46970 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.82 % Allowed : 24.27 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.57 (0.14), residues: 3057 helix: 0.80 (0.19), residues: 783 sheet: -0.43 (0.19), residues: 697 loop : -0.92 (0.14), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 248 HIS 0.005 0.001 HIS N 82 PHE 0.010 0.001 PHE B 121 TYR 0.016 0.001 TYR J 112 ARG 0.008 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 672 time to evaluate : 3.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8277 (mtpm) cc_final: 0.7986 (mtpp) REVERT: A 40 THR cc_start: 0.8574 (p) cc_final: 0.8358 (m) REVERT: A 102 ARG cc_start: 0.8768 (mtt180) cc_final: 0.8483 (mtt-85) REVERT: A 266 MET cc_start: 0.8267 (mmm) cc_final: 0.8059 (tpp) REVERT: B 188 SER cc_start: 0.8686 (t) cc_final: 0.8205 (t) REVERT: E 122 THR cc_start: 0.8185 (p) cc_final: 0.7955 (m) REVERT: F 12 GLN cc_start: 0.8319 (tp40) cc_final: 0.8093 (tp40) REVERT: H 19 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7695 (ttp-110) REVERT: H 118 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8016 (pp) REVERT: I 39 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8256 (ttm-80) REVERT: N 60 THR cc_start: 0.8827 (p) cc_final: 0.8512 (p) REVERT: O 71 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7985 (tttt) REVERT: O 79 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: R 40 GLU cc_start: 0.6744 (mp0) cc_final: 0.6338 (mp0) REVERT: Z 40 HIS cc_start: 0.8205 (m170) cc_final: 0.8001 (m170) REVERT: a 42 GLN cc_start: 0.9121 (mt0) cc_final: 0.8763 (mt0) REVERT: a 48 MET cc_start: 0.8542 (mmm) cc_final: 0.8138 (mmm) outliers start: 89 outliers final: 49 residues processed: 722 average time/residue: 1.9060 time to fit residues: 1815.4940 Evaluate side-chains 678 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 626 time to evaluate : 3.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 33 LYS Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 30 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 414 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 475 optimal weight: 6.9990 chunk 384 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 284 optimal weight: 8.9990 chunk 499 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 117 GLN B 133 GLN C 29 GLN C 40 GLN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN F 67 ASN F 138 GLN H 6 ASN I 17 ASN J 72 ASN J 91 ASN L 9 GLN L 44 GLN L 55 ASN P 8 GLN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN Q 21 GLN Q 44 GLN Q 59 GLN Q 84 GLN R 79 GLN U 25 GLN Y 22 ASN b 4 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.121 91187 Z= 0.610 Angle : 0.859 18.111 137047 Z= 0.424 Chirality : 0.050 0.433 17653 Planarity : 0.007 0.060 6959 Dihedral : 23.582 179.583 46944 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 5.32 % Allowed : 23.63 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.87 (0.14), residues: 3057 helix: 0.33 (0.18), residues: 774 sheet: -0.44 (0.19), residues: 694 loop : -1.06 (0.14), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP A 248 HIS 0.008 0.002 HIS F 47 PHE 0.028 0.003 PHE B 121 TYR 0.022 0.003 TYR F 125 ARG 0.009 0.001 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 631 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.8835 (mtt180) cc_final: 0.8517 (mtt-85) REVERT: A 266 MET cc_start: 0.8399 (mmm) cc_final: 0.8024 (mmp) REVERT: B 188 SER cc_start: 0.8664 (t) cc_final: 0.8121 (t) REVERT: E 155 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7005 (pm20) REVERT: F 12 GLN cc_start: 0.8381 (tp40) cc_final: 0.8138 (tp40) REVERT: H 19 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7944 (ttm-80) REVERT: H 118 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8164 (pp) REVERT: I 39 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8627 (ttm-80) REVERT: J 1 MET cc_start: 0.8262 (mtm) cc_final: 0.7938 (mtm) REVERT: L 12 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6832 (pt0) REVERT: L 91 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7867 (ttt180) REVERT: L 105 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6947 (m-30) REVERT: L 109 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.4501 (mptt) REVERT: L 116 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8090 (ttpp) REVERT: M 78 ARG cc_start: 0.8186 (mmt180) cc_final: 0.7933 (mmp80) REVERT: N 10 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8892 (mttp) REVERT: N 60 THR cc_start: 0.9055 (p) cc_final: 0.8764 (p) REVERT: O 71 LYS cc_start: 0.8301 (ttpp) cc_final: 0.7963 (tttt) REVERT: O 79 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: S 44 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: S 53 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7667 (ttt) REVERT: S 70 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: T 27 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8043 (tmt90) REVERT: T 40 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8248 (tt) REVERT: Y 26 MET cc_start: 0.8123 (ttp) cc_final: 0.7816 (mtp) REVERT: a 42 GLN cc_start: 0.9221 (mt0) cc_final: 0.8836 (mt0) outliers start: 124 outliers final: 76 residues processed: 697 average time/residue: 1.8514 time to fit residues: 1695.6473 Evaluate side-chains 706 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 615 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 44 LYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 GLU Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 91 ARG Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 48 LYS Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain S residue 53 MET Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 70 GLU Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 78 ILE Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 56 SER Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 20 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 0.7980 chunk 501 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 326 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 557 optimal weight: 5.9990 chunk 462 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 117 GLN A 198 GLN C 29 GLN C 40 GLN E 51 GLN F 63 GLN F 88 ASN F 138 GLN H 107 GLN I 17 ASN J 91 ASN L 9 GLN L 44 GLN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN Q 44 GLN Q 59 GLN Q 84 GLN R 79 GLN T 20 HIS U 25 GLN V 24 GLN X 25 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 91187 Z= 0.177 Angle : 0.562 14.367 137047 Z= 0.290 Chirality : 0.035 0.309 17653 Planarity : 0.004 0.048 6959 Dihedral : 23.334 179.502 46944 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.16 % Allowed : 25.39 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.46 (0.14), residues: 3057 helix: 0.81 (0.19), residues: 782 sheet: -0.24 (0.19), residues: 677 loop : -0.86 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 248 HIS 0.004 0.001 HIS N 82 PHE 0.012 0.001 PHE S 69 TYR 0.016 0.001 TYR J 112 ARG 0.007 0.000 ARG L 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 635 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7713 (tt0) cc_final: 0.7398 (tt0) REVERT: A 102 ARG cc_start: 0.8782 (mtt180) cc_final: 0.8478 (mtt-85) REVERT: B 188 SER cc_start: 0.8647 (t) cc_final: 0.8115 (t) REVERT: C 161 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8439 (mtm180) REVERT: E 107 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8334 (mt) REVERT: E 122 THR cc_start: 0.8266 (p) cc_final: 0.8022 (m) REVERT: H 19 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7736 (ttp-110) REVERT: H 118 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8050 (pp) REVERT: I 39 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8443 (ttm-80) REVERT: L 12 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6849 (pt0) REVERT: L 91 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7729 (tmt170) REVERT: N 60 THR cc_start: 0.8908 (p) cc_final: 0.8591 (p) REVERT: O 71 LYS cc_start: 0.8273 (ttpp) cc_final: 0.7958 (tttt) REVERT: O 79 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: Q 60 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: R 40 GLU cc_start: 0.6932 (mp0) cc_final: 0.6500 (mp0) REVERT: a 42 GLN cc_start: 0.9159 (mt0) cc_final: 0.8781 (mt0) outliers start: 97 outliers final: 63 residues processed: 693 average time/residue: 1.9107 time to fit residues: 1758.2636 Evaluate side-chains 687 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 616 time to evaluate : 3.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 GLU Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 91 ARG Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 33 LYS Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 64 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 317 optimal weight: 10.0000 chunk 406 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 chunk 469 optimal weight: 7.9990 chunk 311 optimal weight: 8.9990 chunk 555 optimal weight: 10.0000 chunk 347 optimal weight: 6.9990 chunk 338 optimal weight: 6.9990 chunk 256 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 117 GLN A 198 GLN C 29 GLN C 40 GLN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN F 61 GLN F 63 GLN F 138 GLN H 6 ASN H 107 GLN I 17 ASN J 72 ASN J 91 ASN L 9 GLN L 44 GLN Q 9 GLN Q 21 GLN Q 44 GLN Q 59 GLN Q 84 GLN R 79 GLN U 25 GLN X 25 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.131 91187 Z= 0.681 Angle : 0.908 18.764 137047 Z= 0.446 Chirality : 0.053 0.465 17653 Planarity : 0.007 0.067 6959 Dihedral : 23.600 179.654 46944 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.29 % Rotamer: Outliers : 5.36 % Allowed : 24.70 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.93 (0.14), residues: 3057 helix: 0.11 (0.18), residues: 791 sheet: -0.43 (0.19), residues: 705 loop : -1.03 (0.14), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP A 248 HIS 0.009 0.002 HIS F 47 PHE 0.029 0.003 PHE B 121 TYR 0.023 0.003 TYR F 125 ARG 0.011 0.001 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 621 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7762 (tt0) cc_final: 0.7553 (tt0) REVERT: A 102 ARG cc_start: 0.8842 (mtt180) cc_final: 0.8513 (mtt-85) REVERT: B 188 SER cc_start: 0.8634 (t) cc_final: 0.8122 (t) REVERT: E 107 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8336 (mt) REVERT: E 155 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: H 19 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7967 (ttm-80) REVERT: H 118 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8178 (pp) REVERT: I 39 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8681 (ttm-80) REVERT: J 1 MET cc_start: 0.8274 (mtm) cc_final: 0.7929 (mtm) REVERT: L 12 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6818 (pt0) REVERT: L 39 ASP cc_start: 0.5039 (OUTLIER) cc_final: 0.4763 (p0) REVERT: L 56 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8225 (mmt90) REVERT: L 91 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7829 (tmt170) REVERT: L 105 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: L 116 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8070 (ttpp) REVERT: M 78 ARG cc_start: 0.8197 (mmt180) cc_final: 0.7936 (mmp80) REVERT: N 10 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8854 (mttt) REVERT: N 60 THR cc_start: 0.9074 (p) cc_final: 0.8785 (p) REVERT: O 71 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7948 (tttt) REVERT: O 79 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: Q 60 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: S 44 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: S 53 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7450 (ttt) REVERT: T 27 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8028 (tmt90) REVERT: T 40 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8255 (tt) REVERT: X 52 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7280 (tm-30) outliers start: 125 outliers final: 79 residues processed: 698 average time/residue: 1.8341 time to fit residues: 1685.3133 Evaluate side-chains 719 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 621 time to evaluate : 3.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 44 LYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 GLU Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 91 ARG Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 48 LYS Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain S residue 53 MET Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 70 GLU Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 78 ILE Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain X residue 52 GLN Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 33 LYS Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 64 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 331 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 352 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 chunk 274 optimal weight: 30.0000 chunk 51 optimal weight: 0.6980 chunk 436 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 117 GLN A 198 GLN A 200 ASN C 29 GLN C 40 GLN E 51 GLN E 106 ASN F 63 GLN F 88 ASN F 138 GLN H 6 ASN H 107 GLN I 17 ASN J 91 ASN L 9 GLN L 44 GLN Q 9 GLN Q 59 GLN Q 84 GLN R 79 GLN U 25 GLN V 24 GLN X 25 ASN a 42 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 91187 Z= 0.177 Angle : 0.568 14.482 137047 Z= 0.293 Chirality : 0.035 0.307 17653 Planarity : 0.004 0.047 6959 Dihedral : 23.346 179.527 46944 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.95 % Allowed : 26.63 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.45 (0.14), residues: 3057 helix: 0.76 (0.19), residues: 782 sheet: -0.20 (0.19), residues: 677 loop : -0.84 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 248 HIS 0.004 0.001 HIS F 47 PHE 0.011 0.001 PHE B 121 TYR 0.017 0.001 TYR J 112 ARG 0.007 0.000 ARG L 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 639 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7994 (mtpp) REVERT: A 40 THR cc_start: 0.8697 (p) cc_final: 0.8405 (p) REVERT: A 102 ARG cc_start: 0.8801 (mtt180) cc_final: 0.8521 (mtt-85) REVERT: B 188 SER cc_start: 0.8615 (t) cc_final: 0.8091 (t) REVERT: E 107 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8354 (mt) REVERT: E 122 THR cc_start: 0.8290 (p) cc_final: 0.8025 (m) REVERT: H 19 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7711 (ttp-110) REVERT: H 118 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8096 (pp) REVERT: I 39 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8483 (ttm-80) REVERT: L 12 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6784 (pt0) REVERT: L 91 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7711 (tmt170) REVERT: L 105 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6766 (m-30) REVERT: N 60 THR cc_start: 0.8884 (p) cc_final: 0.8565 (p) REVERT: O 71 LYS cc_start: 0.8263 (ttpp) cc_final: 0.7940 (tttt) REVERT: O 79 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: R 40 GLU cc_start: 0.6979 (mp0) cc_final: 0.6682 (mp0) REVERT: V 17 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8424 (ttmm) outliers start: 92 outliers final: 61 residues processed: 692 average time/residue: 1.8080 time to fit residues: 1654.2753 Evaluate side-chains 695 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 624 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 GLU Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 91 ARG Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 48 LYS Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain T residue 78 ILE Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 33 LYS Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 64 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 7.9990 chunk 531 optimal weight: 10.0000 chunk 485 optimal weight: 10.0000 chunk 517 optimal weight: 6.9990 chunk 311 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 406 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 467 optimal weight: 20.0000 chunk 489 optimal weight: 6.9990 chunk 515 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 117 GLN A 198 GLN A 250 GLN C 29 GLN C 40 GLN C 165 HIS ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN F 63 GLN F 138 GLN H 107 GLN I 17 ASN J 91 ASN L 9 GLN L 44 GLN P 8 GLN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN Q 21 GLN Q 59 GLN Q 84 GLN R 79 GLN U 25 GLN X 25 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.116 91187 Z= 0.559 Angle : 0.813 17.418 137047 Z= 0.404 Chirality : 0.048 0.404 17653 Planarity : 0.006 0.062 6959 Dihedral : 23.519 179.661 46944 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.58 % Rotamer: Outliers : 4.33 % Allowed : 26.37 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.75 (0.14), residues: 3057 helix: 0.32 (0.18), residues: 785 sheet: -0.33 (0.19), residues: 697 loop : -0.94 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 248 HIS 0.007 0.002 HIS F 47 PHE 0.026 0.003 PHE B 121 TYR 0.020 0.003 TYR F 125 ARG 0.009 0.001 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 610 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8029 (mtpm) REVERT: A 40 THR cc_start: 0.8725 (p) cc_final: 0.8462 (p) REVERT: A 102 ARG cc_start: 0.8839 (mtt180) cc_final: 0.8563 (mtt-85) REVERT: B 188 SER cc_start: 0.8595 (t) cc_final: 0.8069 (t) REVERT: E 107 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8314 (mt) REVERT: E 155 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: H 19 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7961 (ttm-80) REVERT: H 118 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8178 (pp) REVERT: I 39 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8607 (ttm-80) REVERT: J 1 MET cc_start: 0.8245 (mtm) cc_final: 0.7898 (mtm) REVERT: L 12 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6808 (pt0) REVERT: L 39 ASP cc_start: 0.5004 (OUTLIER) cc_final: 0.4729 (p0) REVERT: L 91 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7806 (tmt170) REVERT: L 105 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6912 (m-30) REVERT: L 116 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8061 (ttpp) REVERT: M 78 ARG cc_start: 0.8183 (mmt180) cc_final: 0.7929 (mmp80) REVERT: N 60 THR cc_start: 0.9048 (p) cc_final: 0.8757 (p) REVERT: O 71 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7950 (tttt) REVERT: O 79 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: S 44 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7582 (mp0) outliers start: 101 outliers final: 72 residues processed: 673 average time/residue: 1.8189 time to fit residues: 1616.9627 Evaluate side-chains 693 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 608 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 44 LYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 GLU Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 91 ARG Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 48 LYS Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 78 ILE Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 33 LYS Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 3.9990 chunk 547 optimal weight: 4.9990 chunk 333 optimal weight: 3.9990 chunk 259 optimal weight: 0.8980 chunk 380 optimal weight: 1.9990 chunk 573 optimal weight: 4.9990 chunk 528 optimal weight: 2.9990 chunk 456 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 352 optimal weight: 5.9990 chunk 280 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 117 GLN C 29 GLN C 40 GLN C 165 HIS ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN F 88 ASN F 138 GLN H 107 GLN I 17 ASN J 91 ASN L 9 GLN L 44 GLN P 8 GLN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN Q 59 GLN Q 84 GLN R 79 GLN U 25 GLN X 25 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 91187 Z= 0.234 Angle : 0.604 14.339 137047 Z= 0.311 Chirality : 0.037 0.307 17653 Planarity : 0.005 0.048 6959 Dihedral : 23.379 179.964 46944 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 3.64 % Allowed : 27.27 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.48 (0.14), residues: 3057 helix: 0.71 (0.19), residues: 780 sheet: -0.21 (0.19), residues: 689 loop : -0.84 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 248 HIS 0.005 0.001 HIS F 47 PHE 0.015 0.002 PHE B 121 TYR 0.018 0.002 TYR J 112 ARG 0.007 0.000 ARG L 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 611 time to evaluate : 3.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8002 (mtpm) REVERT: A 40 THR cc_start: 0.8698 (p) cc_final: 0.8419 (p) REVERT: A 100 GLU cc_start: 0.7824 (tt0) cc_final: 0.7597 (tt0) REVERT: A 102 ARG cc_start: 0.8809 (mtt180) cc_final: 0.8494 (mtt-85) REVERT: B 188 SER cc_start: 0.8632 (t) cc_final: 0.8134 (t) REVERT: E 107 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8307 (mt) REVERT: H 19 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7713 (ttp-110) REVERT: H 118 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8076 (pp) REVERT: I 39 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8496 (ttm-80) REVERT: L 12 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6777 (pt0) REVERT: L 105 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6788 (m-30) REVERT: N 60 THR cc_start: 0.8894 (p) cc_final: 0.8576 (p) REVERT: O 71 LYS cc_start: 0.8265 (ttpp) cc_final: 0.7940 (tttt) REVERT: O 79 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: V 17 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8442 (ttmm) outliers start: 85 outliers final: 64 residues processed: 664 average time/residue: 1.8422 time to fit residues: 1620.1410 Evaluate side-chains 680 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 607 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 12 GLU Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 101 VAL Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain T residue 78 ILE Chi-restraints excluded: chain U residue 5 ASP Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 40 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 17 LYS Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 33 LYS Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 6.9990 chunk 486 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 421 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 457 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 469 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 117 GLN C 29 GLN C 40 GLN C 165 HIS ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN F 63 GLN F 138 GLN H 107 GLN I 17 ASN J 91 ASN K 30 ASN L 9 GLN L 44 GLN P 8 GLN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN Q 59 GLN Q 84 GLN R 79 GLN U 25 GLN X 25 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.089576 restraints weight = 90046.998| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 0.78 r_work: 0.2807 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.119 91187 Z= 0.580 Angle : 0.835 17.958 137047 Z= 0.415 Chirality : 0.050 0.420 17653 Planarity : 0.007 0.066 6959 Dihedral : 23.539 179.682 46942 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.29 % Favored : 95.65 % Rotamer: Outliers : 4.20 % Allowed : 26.59 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.78 (0.14), residues: 3057 helix: 0.22 (0.18), residues: 787 sheet: -0.32 (0.19), residues: 692 loop : -0.94 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP A 248 HIS 0.008 0.002 HIS F 47 PHE 0.027 0.003 PHE B 121 TYR 0.022 0.003 TYR F 53 ARG 0.009 0.001 ARG Z 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25509.69 seconds wall clock time: 449 minutes 39.26 seconds (26979.26 seconds total)