Starting phenix.real_space_refine on Mon Feb 19 16:47:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/02_2024/7asn_11901_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/02_2024/7asn_11901.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/02_2024/7asn_11901_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/02_2024/7asn_11901_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/02_2024/7asn_11901_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/02_2024/7asn_11901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/02_2024/7asn_11901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/02_2024/7asn_11901_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/02_2024/7asn_11901_updated.pdb" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2848 5.49 5 S 46 5.16 5 C 39561 2.51 5 N 14939 2.21 5 O 23300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 2": "NH1" <-> "NH2" Residue "1 ASP 14": "OD1" <-> "OD2" Residue "1 ARG 24": "NH1" <-> "NH2" Residue "1 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 20": "NH1" <-> "NH2" Residue "2 ARG 22": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "3 ARG 42": "NH1" <-> "NH2" Residue "3 ARG 57": "NH1" <-> "NH2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F ARG 43": "NH1" <-> "NH2" Residue "F PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ASP 79": "OD1" <-> "OD2" Residue "F ASP 84": "OD1" <-> "OD2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F ASP 229": "OD1" <-> "OD2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ASP 267": "OD1" <-> "OD2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 106": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 160": "OD1" <-> "OD2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "H ARG 28": "NH1" <-> "NH2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 142": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L ASP 80": "OD1" <-> "OD2" Residue "L PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 137": "OD1" <-> "OD2" Residue "Y ARG 10": "NH1" <-> "NH2" Residue "Y ARG 20": "NH1" <-> "NH2" Residue "Y PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ARG 56": "NH1" <-> "NH2" Residue "Y TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 82": "NH1" <-> "NH2" Residue "Y PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 112": "OE1" <-> "OE2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "G PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M ARG 14": "NH1" <-> "NH2" Residue "M ARG 35": "NH1" <-> "NH2" Residue "M ASP 86": "OD1" <-> "OD2" Residue "M ASP 95": "OD1" <-> "OD2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N ARG 23": "NH1" <-> "NH2" Residue "N ASP 26": "OD1" <-> "OD2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 87": "OE1" <-> "OE2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "N TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 48": "NH1" <-> "NH2" Residue "O ASP 89": "OD1" <-> "OD2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "O ASP 102": "OD1" <-> "OD2" Residue "O PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 19": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P GLU 29": "OE1" <-> "OE2" Residue "P PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 67": "NH1" <-> "NH2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 84": "NH1" <-> "NH2" Residue "P TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "Q TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "Q GLU 112": "OE1" <-> "OE2" Residue "R GLU 18": "OE1" <-> "OE2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 43": "OE1" <-> "OE2" Residue "R GLU 44": "OE1" <-> "OE2" Residue "R TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "R PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 7": "OD1" <-> "OD2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S ASP 31": "OD1" <-> "OD2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S GLU 58": "OE1" <-> "OE2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 9": "NH1" <-> "NH2" Residue "T ARG 22": "NH1" <-> "NH2" Residue "T TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 53": "NH1" <-> "NH2" Residue "T ARG 57": "NH1" <-> "NH2" Residue "T ASP 90": "OD1" <-> "OD2" Residue "a ARG 22": "NH1" <-> "NH2" Residue "a GLU 25": "OE1" <-> "OE2" Residue "a ARG 28": "NH1" <-> "NH2" Residue "a ARG 33": "NH1" <-> "NH2" Residue "a ASP 35": "OD1" <-> "OD2" Residue "a ARG 49": "NH1" <-> "NH2" Residue "a PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 37": "NH1" <-> "NH2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "W GLU 23": "OE1" <-> "OE2" Residue "W GLU 24": "OE1" <-> "OE2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 44": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "W ARG 58": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X GLU 24": "OE1" <-> "OE2" Residue "X GLU 38": "OE1" <-> "OE2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "b ARG 6": "NH1" <-> "NH2" Residue "b ARG 7": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 80694 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 58787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2742, 58787 Classifications: {'DNA': 1, 'RNA': 2741} Modifications used: {'rna2p': 1, 'rna2p_pur': 291, 'rna2p_pyr': 173, 'rna3p': 2, 'rna3p_pur': 1277, 'rna3p_pyr': 997} Link IDs: {'rna2p': 465, 'rna3p': 2276} Chain breaks: 11 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 2260 Classifications: {'RNA': 106} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 51, 'rna3p_pyr': 46} Link IDs: {'rna2p': 9, 'rna3p': 96} Chain breaks: 4 Chain: "1" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 367 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "3" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "F" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2094 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain: "D" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1627 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1572 Classifications: {'peptide': 206} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1132 Classifications: {'peptide': 144} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1086 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1071 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 918 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 872 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 115} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "N" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "O" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 790 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 715 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "S" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 770 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "T" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "a" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 597 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 379 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 541 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "b" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 360 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 32.83, per 1000 atoms: 0.41 Number of scatterers: 80694 At special positions: 0 Unit cell: (233.376, 235.95, 202.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 2848 15.00 O 23300 8.00 N 14939 7.00 C 39561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 1 9 " - pdb=" SG CYS 1 12 " distance=2.01 Simple disulfide: pdb=" SG CYS 1 12 " - pdb=" SG CYS 1 36 " distance=2.02 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: 32.21 Conformation dependent library (CDL) restraints added in 3.6 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4628 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 35 sheets defined 20.9% alpha, 15.7% beta 645 base pairs and 1328 stacking pairs defined. Time for finding SS restraints: 36.57 Creating SS restraints... Processing helix chain '2' and resid 10 through 16 removed outlier: 3.538A pdb=" N SER 2 14 " --> pdb=" O LYS 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 23 Processing helix chain '2' and resid 26 through 37 removed outlier: 3.571A pdb=" N VAL 2 31 " --> pdb=" O ASN 2 27 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG 2 36 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) Processing helix chain '3' and resid 38 through 43 removed outlier: 3.657A pdb=" N ARG 3 42 " --> pdb=" O THR 3 38 " (cutoff:3.500A) Processing helix chain '3' and resid 52 through 62 removed outlier: 3.536A pdb=" N LYS 3 56 " --> pdb=" O LYS 3 52 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG 3 57 " --> pdb=" O SER 3 53 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLN 3 60 " --> pdb=" O LYS 3 56 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU 3 61 " --> pdb=" O ARG 3 57 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU 3 62 " --> pdb=" O VAL 3 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 208 through 214 Processing helix chain 'D' and resid 41 through 44 No H-bonds generated for 'chain 'D' and resid 41 through 44' Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 131 through 134 No H-bonds generated for 'chain 'D' and resid 131 through 134' Processing helix chain 'E' and resid 30 through 44 removed outlier: 3.601A pdb=" N GLU E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 136 through 143 Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'E' and resid 196 through 206 Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 90 through 95 Processing helix chain 'H' and resid 98 through 109 removed outlier: 3.645A pdb=" N SER H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 122 removed outlier: 3.763A pdb=" N LYS H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 93 through 98 removed outlier: 3.524A pdb=" N VAL L 97 " --> pdb=" O PRO L 93 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 93 through 98' Processing helix chain 'L' and resid 130 through 139 Processing helix chain 'Y' and resid 44 through 58 Processing helix chain 'Y' and resid 111 through 123 removed outlier: 4.012A pdb=" N ARG Y 119 " --> pdb=" O ARG Y 115 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA Y 121 " --> pdb=" O ALA Y 117 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER Y 122 " --> pdb=" O LEU Y 118 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS Y 123 " --> pdb=" O ARG Y 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 112 through 117 removed outlier: 3.860A pdb=" N SER G 116 " --> pdb=" O MET G 112 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 117' Processing helix chain 'M' and resid 7 through 18 Processing helix chain 'M' and resid 71 through 86 removed outlier: 3.858A pdb=" N LYS M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS M 83 " --> pdb=" O ALA M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 113 Processing helix chain 'N' and resid 5 through 14 removed outlier: 3.599A pdb=" N THR N 11 " --> pdb=" O ILE N 7 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER N 13 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN N 14 " --> pdb=" O VAL N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 58 No H-bonds generated for 'chain 'N' and resid 56 through 58' Processing helix chain 'O' and resid 9 through 20 removed outlier: 3.732A pdb=" N THR O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 29 Processing helix chain 'O' and resid 32 through 72 removed outlier: 3.525A pdb=" N PHE O 47 " --> pdb=" O GLY O 43 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG O 55 " --> pdb=" O ARG O 51 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS O 72 " --> pdb=" O ALA O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 86 Processing helix chain 'O' and resid 92 through 101 Processing helix chain 'O' and resid 103 through 116 removed outlier: 3.552A pdb=" N GLN O 108 " --> pdb=" O LYS O 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 21 removed outlier: 4.074A pdb=" N LEU Q 19 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 38 removed outlier: 3.658A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 3.675A pdb=" N GLU Q 59 " --> pdb=" O LEU Q 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 21 removed outlier: 3.562A pdb=" N ALA R 21 " --> pdb=" O SER R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 46 removed outlier: 3.630A pdb=" N LYS R 39 " --> pdb=" O LYS R 35 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET R 40 " --> pdb=" O THR R 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'T' and resid 15 through 24 removed outlier: 3.942A pdb=" N LYS T 23 " --> pdb=" O LYS T 19 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER T 24 " --> pdb=" O GLN T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 52 Processing helix chain 'V' and resid 51 through 55 Processing helix chain 'W' and resid 6 through 8 No H-bonds generated for 'chain 'W' and resid 6 through 8' Processing helix chain 'W' and resid 13 through 33 removed outlier: 3.809A pdb=" N SER W 20 " --> pdb=" O GLU W 16 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU W 23 " --> pdb=" O LYS W 19 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA W 33 " --> pdb=" O ARG W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 64 removed outlier: 3.550A pdb=" N LYS W 48 " --> pdb=" O ARG W 44 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR W 49 " --> pdb=" O THR W 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 25 Processing helix chain 'X' and resid 41 through 49 removed outlier: 3.720A pdb=" N GLN X 46 " --> pdb=" O ALA X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 53 No H-bonds generated for 'chain 'X' and resid 51 through 53' Processing helix chain 'b' and resid 10 through 18 removed outlier: 3.857A pdb=" N THR b 18 " --> pdb=" O ASN b 14 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '1' and resid 17 through 21 removed outlier: 4.575A pdb=" N TYR 1 17 " --> pdb=" O LEU 1 7 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '3' and resid 14 through 16 Processing sheet with id= C, first strand: chain 'F' and resid 3 through 5 Processing sheet with id= D, first strand: chain 'F' and resid 34 through 36 Processing sheet with id= E, first strand: chain 'F' and resid 101 through 105 removed outlier: 3.737A pdb=" N SER F 80 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL F 95 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL F 78 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 129 through 131 removed outlier: 3.921A pdb=" N LEU F 130 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR F 191 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN F 143 " --> pdb=" O THR F 191 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 180 through 184 removed outlier: 3.719A pdb=" N GLU F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR F 171 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG F 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL F 164 " --> pdb=" O ARG F 175 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 9 through 17 removed outlier: 6.673A pdb=" N VAL D 27 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE D 16 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU D 21 " --> pdb=" O PHE D 16 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN D 187 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS D 198 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL D 185 " --> pdb=" O LYS D 198 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 87 through 91 removed outlier: 4.192A pdb=" N PHE D 87 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL D 35 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 210 through 213 Processing sheet with id= K, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.823A pdb=" N GLY E 15 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 123 through 126 removed outlier: 6.374A pdb=" N LEU E 192 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL E 126 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE E 194 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 16 through 19 removed outlier: 6.663A pdb=" N TYR H 54 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE H 19 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE H 56 " --> pdb=" O ILE H 19 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 74 through 78 Processing sheet with id= O, first strand: chain 'L' and resid 75 through 77 Processing sheet with id= P, first strand: chain 'Y' and resid 131 through 133 removed outlier: 3.955A pdb=" N VAL Y 132 " --> pdb=" O GLY Y 33 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS Y 63 " --> pdb=" O ALA Y 107 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'Y' and resid 40 through 43 removed outlier: 6.899A pdb=" N TYR Y 74 " --> pdb=" O GLU Y 91 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP Y 93 " --> pdb=" O THR Y 72 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR Y 72 " --> pdb=" O TRP Y 93 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 7 through 9 removed outlier: 3.657A pdb=" N ASN G 45 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU G 20 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL G 43 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE G 39 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL G 63 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'M' and resid 29 through 31 Processing sheet with id= T, first strand: chain 'N' and resid 85 through 90 removed outlier: 3.979A pdb=" N LYS N 85 " --> pdb=" O HIS N 31 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR N 27 " --> pdb=" O LYS N 89 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR N 62 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG N 52 " --> pdb=" O THR N 60 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR N 60 " --> pdb=" O ARG N 52 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE N 61 " --> pdb=" O PHE N 76 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 10 through 15 removed outlier: 3.834A pdb=" N PHE P 40 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU P 6 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL P 38 " --> pdb=" O GLU P 6 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 19 through 22 Processing sheet with id= W, first strand: chain 'P' and resid 32 through 35 removed outlier: 3.507A pdb=" N LYS P 99 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR P 61 " --> pdb=" O ILE P 97 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE P 97 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 71 through 76 Processing sheet with id= Y, first strand: chain 'Q' and resid 3 through 7 removed outlier: 6.123A pdb=" N SER Q 108 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL Q 71 " --> pdb=" O SER Q 108 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Q' and resid 82 through 87 Processing sheet with id= AA, first strand: chain 'R' and resid 52 through 58 removed outlier: 4.276A pdb=" N ARG R 76 " --> pdb=" O VAL R 29 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG R 9 " --> pdb=" O ASP R 28 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 20 through 22 Processing sheet with id= AC, first strand: chain 'S' and resid 82 through 84 Processing sheet with id= AD, first strand: chain 'T' and resid 6 through 8 removed outlier: 3.796A pdb=" N VAL T 41 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU T 92 " --> pdb=" O VAL T 74 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL T 74 " --> pdb=" O LEU T 92 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'a' and resid 59 through 61 Processing sheet with id= AF, first strand: chain 'a' and resid 74 through 79 Processing sheet with id= AG, first strand: chain 'V' and resid 13 through 16 removed outlier: 4.295A pdb=" N SER V 13 " --> pdb=" O TRP V 29 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'V' and resid 33 through 39 removed outlier: 3.832A pdb=" N VAL V 36 " --> pdb=" O VAL V 47 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL V 47 " --> pdb=" O VAL V 36 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'X' and resid 3 through 7 471 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1608 hydrogen bonds 2584 hydrogen bond angles 0 basepair planarities 645 basepair parallelities 1328 stacking parallelities Total time for adding SS restraints: 110.08 Time building geometry restraints manager: 34.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6353 1.30 - 1.43: 40753 1.43 - 1.56: 35377 1.56 - 1.69: 5685 1.69 - 1.82: 85 Bond restraints: 88253 Sorted by residual: bond pdb=" C5 5MU A1966 " pdb=" C6 5MU A1966 " ideal model delta sigma weight residual 1.155 1.450 -0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C5 5MU A 792 " pdb=" C6 5MU A 792 " ideal model delta sigma weight residual 1.155 1.443 -0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C4 5MU A 792 " pdb=" C5 5MU A 792 " ideal model delta sigma weight residual 1.802 1.611 0.191 2.00e-02 2.50e+03 9.15e+01 bond pdb=" C4 5MU A1966 " pdb=" C5 5MU A1966 " ideal model delta sigma weight residual 1.802 1.617 0.185 2.00e-02 2.50e+03 8.52e+01 bond pdb=" N1 5MU A1966 " pdb=" C2 5MU A1966 " ideal model delta sigma weight residual 1.436 1.581 -0.145 2.00e-02 2.50e+03 5.28e+01 ... (remaining 88248 not shown) Histogram of bond angle deviations from ideal: 97.79 - 106.18: 17076 106.18 - 114.58: 56352 114.58 - 122.97: 43815 122.97 - 131.37: 15140 131.37 - 139.77: 837 Bond angle restraints: 133220 Sorted by residual: angle pdb=" C1' 2MA A2530 " pdb=" N9 2MA A2530 " pdb=" C8 2MA A2530 " ideal model delta sigma weight residual 135.36 112.85 22.51 3.00e+00 1.11e-01 5.63e+01 angle pdb=" CA CYS 1 12 " pdb=" CB CYS 1 12 " pdb=" SG CYS 1 12 " ideal model delta sigma weight residual 114.40 130.24 -15.84 2.30e+00 1.89e-01 4.74e+01 angle pdb=" N VAL F 224 " pdb=" CA VAL F 224 " pdb=" C VAL F 224 " ideal model delta sigma weight residual 112.83 106.17 6.66 9.90e-01 1.02e+00 4.53e+01 angle pdb=" C1' 2MA A2530 " pdb=" N9 2MA A2530 " pdb=" C4 2MA A2530 " ideal model delta sigma weight residual 116.52 135.43 -18.91 3.00e+00 1.11e-01 3.97e+01 angle pdb=" N ARG E 168 " pdb=" CA ARG E 168 " pdb=" C ARG E 168 " ideal model delta sigma weight residual 114.75 107.45 7.30 1.26e+00 6.30e-01 3.36e+01 ... (remaining 133215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 48372 35.66 - 71.33: 7200 71.33 - 106.99: 811 106.99 - 142.66: 39 142.66 - 178.32: 29 Dihedral angle restraints: 56451 sinusoidal: 49246 harmonic: 7205 Sorted by residual: dihedral pdb=" C5' A A 775 " pdb=" C4' A A 775 " pdb=" C3' A A 775 " pdb=" O3' A A 775 " ideal model delta sinusoidal sigma weight residual 147.00 68.56 78.44 1 8.00e+00 1.56e-02 1.20e+02 dihedral pdb=" CA ILE H 58 " pdb=" C ILE H 58 " pdb=" N ASN H 59 " pdb=" CA ASN H 59 " ideal model delta harmonic sigma weight residual 180.00 128.71 51.29 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" C4' A A 775 " pdb=" C3' A A 775 " pdb=" C2' A A 775 " pdb=" C1' A A 775 " ideal model delta sinusoidal sigma weight residual -35.00 32.82 -67.82 1 8.00e+00 1.56e-02 9.34e+01 ... (remaining 56448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 15572 0.088 - 0.176: 1471 0.176 - 0.265: 134 0.265 - 0.353: 37 0.353 - 0.441: 10 Chirality restraints: 17224 Sorted by residual: chirality pdb=" C3' A A 775 " pdb=" C4' A A 775 " pdb=" O3' A A 775 " pdb=" C2' A A 775 " both_signs ideal model delta sigma weight residual False -2.74 -2.30 -0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" C3' U A1706 " pdb=" C4' U A1706 " pdb=" O3' U A1706 " pdb=" C2' U A1706 " both_signs ideal model delta sigma weight residual False -2.48 -2.06 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C3' C A 572 " pdb=" C4' C A 572 " pdb=" O3' C A 572 " pdb=" C2' C A 572 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 17221 not shown) Planarity restraints: 6263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A 792 " 0.013 2.00e-02 2.50e+03 4.86e-01 5.32e+03 pdb=" C4' 5MU A 792 " 0.398 2.00e-02 2.50e+03 pdb=" O4' 5MU A 792 " 0.477 2.00e-02 2.50e+03 pdb=" C3' 5MU A 792 " -0.571 2.00e-02 2.50e+03 pdb=" O3' 5MU A 792 " -0.413 2.00e-02 2.50e+03 pdb=" C2' 5MU A 792 " -0.260 2.00e-02 2.50e+03 pdb=" O2' 5MU A 792 " 0.793 2.00e-02 2.50e+03 pdb=" C1' 5MU A 792 " 0.256 2.00e-02 2.50e+03 pdb=" N1 5MU A 792 " -0.694 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MA A2530 " -0.665 2.00e-02 2.50e+03 4.83e-01 5.24e+03 pdb=" C4' 2MA A2530 " 0.236 2.00e-02 2.50e+03 pdb=" O4' 2MA A2530 " 0.546 2.00e-02 2.50e+03 pdb=" C3' 2MA A2530 " -0.282 2.00e-02 2.50e+03 pdb=" O3' 2MA A2530 " 0.749 2.00e-02 2.50e+03 pdb=" C2' 2MA A2530 " -0.568 2.00e-02 2.50e+03 pdb=" O2' 2MA A2530 " -0.391 2.00e-02 2.50e+03 pdb=" C1' 2MA A2530 " 0.425 2.00e-02 2.50e+03 pdb=" N9 2MA A2530 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A1966 " 0.166 2.00e-02 2.50e+03 2.99e-01 2.01e+03 pdb=" C4' 5MU A1966 " -0.312 2.00e-02 2.50e+03 pdb=" O4' 5MU A1966 " -0.219 2.00e-02 2.50e+03 pdb=" C3' 5MU A1966 " 0.469 2.00e-02 2.50e+03 pdb=" O3' 5MU A1966 " -0.190 2.00e-02 2.50e+03 pdb=" C2' 5MU A1966 " 0.420 2.00e-02 2.50e+03 pdb=" O2' 5MU A1966 " -0.242 2.00e-02 2.50e+03 pdb=" C1' 5MU A1966 " -0.308 2.00e-02 2.50e+03 pdb=" N1 5MU A1966 " 0.216 2.00e-02 2.50e+03 ... (remaining 6260 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 676 2.54 - 3.13: 55803 3.13 - 3.72: 151152 3.72 - 4.31: 221929 4.31 - 4.90: 293252 Nonbonded interactions: 722812 Sorted by model distance: nonbonded pdb=" O4 U A 163 " pdb=" O2' G A2244 " model vdw 1.953 2.440 nonbonded pdb=" O2' A A1745 " pdb=" OP1 C A1793 " model vdw 1.995 2.440 nonbonded pdb=" N2 G A2866 " pdb=" O6 G A2889 " model vdw 2.024 2.520 nonbonded pdb=" O2' G A1490 " pdb=" OP2 C A1491 " model vdw 2.044 2.440 nonbonded pdb=" OG1 THR D 2 " pdb=" O ASN D 93 " model vdw 2.046 2.440 ... (remaining 722807 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.770 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: 0.100 Extract box with map and model: 10.570 Check model and map are aligned: 0.900 Set scattering table: 0.560 Process input model: 261.280 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 287.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2123 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 : 0.008 0.295 88253 Z= 0.465 Angle : 1.047 22.509 133220 Z= 0.543 Chirality : 0.055 0.441 17224 Planarity : 0.012 0.486 6263 Dihedral : 25.084 178.319 51817 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.26 % Favored : 88.62 % Rotamer: Outliers : 0.48 % Allowed : 0.48 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.27 (0.14), residues: 2496 helix: -1.75 (0.20), residues: 566 sheet: -1.29 (0.24), residues: 413 loop : -2.74 (0.13), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 213 HIS 0.023 0.003 HIS E 49 PHE 0.059 0.004 PHE D 147 TYR 0.030 0.004 TYR N 101 ARG 0.027 0.002 ARG P 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 803 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU Q 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 8 residues processed: 809 average time/residue: 1.8398 time to fit residues: 1925.3753 Evaluate side-chains 417 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 409 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain N residue 113 GLN Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain X residue 58 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 444 optimal weight: 5.9990 chunk 398 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 chunk 136 optimal weight: 30.0000 chunk 268 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 412 optimal weight: 3.9990 chunk 159 optimal weight: 30.0000 chunk 250 optimal weight: 40.0000 chunk 306 optimal weight: 3.9990 chunk 477 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 HIS 3 7 HIS ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN F 153 GLN D 19 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN O 52 GLN ** P 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 HIS Q 61 ASN Q 102 HIS R 54 ASN S 39 ASN V 23 ASN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2818 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 88253 Z= 0.246 Angle : 0.798 15.481 133220 Z= 0.411 Chirality : 0.041 0.354 17224 Planarity : 0.007 0.114 6263 Dihedral : 25.117 177.549 46884 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.29 % Favored : 92.63 % Rotamer: Outliers : 6.35 % Allowed : 20.47 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.60 (0.15), residues: 2496 helix: -0.94 (0.20), residues: 542 sheet: -1.08 (0.24), residues: 410 loop : -2.31 (0.13), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 65 HIS 0.006 0.001 HIS L 35 PHE 0.032 0.003 PHE N 76 TYR 0.021 0.002 TYR F 103 ARG 0.018 0.001 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 552 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU Q 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: F 6 TYR cc_start: 0.5786 (m-80) cc_final: 0.5521 (m-80) outliers start: 131 outliers final: 46 residues processed: 615 average time/residue: 1.7168 time to fit residues: 1391.7181 Evaluate side-chains 447 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 401 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain 2 residue 13 HIS Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 115 ARG Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 113 GLN Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 84 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain P residue 100 ILE Chi-restraints excluded: chain Q residue 28 ASN Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain R residue 73 ASN Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 58 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 265 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 397 optimal weight: 30.0000 chunk 325 optimal weight: 6.9990 chunk 131 optimal weight: 30.0000 chunk 478 optimal weight: 10.0000 chunk 516 optimal weight: 6.9990 chunk 426 optimal weight: 8.9990 chunk 474 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 383 optimal weight: 30.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN F 153 GLN ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN D 176 ASN D 200 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 HIS ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN Y 46 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 GLN ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 HIS M 55 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 HIS ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 ASN S 64 HIS T 85 GLN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 19 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3477 moved from start: 0.8559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 88253 Z= 0.296 Angle : 0.797 14.223 133220 Z= 0.414 Chirality : 0.041 0.318 17224 Planarity : 0.008 0.124 6263 Dihedral : 25.253 179.996 46873 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 7.95 % Allowed : 24.98 % Favored : 67.07 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.77 (0.15), residues: 2496 helix: -1.25 (0.20), residues: 562 sheet: -1.52 (0.22), residues: 492 loop : -2.26 (0.14), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 65 HIS 0.112 0.004 HIS 2 13 PHE 0.031 0.004 PHE D 147 TYR 0.023 0.003 TYR H 141 ARG 0.025 0.002 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 579 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. REVERT: 3 49 LEU cc_start: 0.4884 (OUTLIER) cc_final: 0.4671 (tp) REVERT: E 185 ASP cc_start: 0.4730 (OUTLIER) cc_final: 0.4510 (m-30) REVERT: R 58 TYR cc_start: 0.5254 (OUTLIER) cc_final: 0.4683 (t80) REVERT: a 33 ARG cc_start: 0.5408 (OUTLIER) cc_final: 0.5106 (mpp-170) outliers start: 164 outliers final: 51 residues processed: 655 average time/residue: 1.6751 time to fit residues: 1460.6037 Evaluate side-chains 477 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 422 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 115 ARG Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 119 PHE Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 113 GLN Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 58 TYR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain T residue 9 ARG Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 48 PHE Chi-restraints excluded: chain a residue 33 ARG Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 58 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 472 optimal weight: 30.0000 chunk 359 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 228 optimal weight: 30.0000 chunk 321 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 chunk 508 optimal weight: 30.0000 chunk 250 optimal weight: 50.0000 chunk 455 optimal weight: 8.9990 chunk 137 optimal weight: 40.0000 overall best weight: 11.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 GLN ** P 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN Q 97 ASN ** S 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 45 GLN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3853 moved from start: 1.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 88253 Z= 0.353 Angle : 0.868 14.746 133220 Z= 0.445 Chirality : 0.046 1.276 17224 Planarity : 0.007 0.114 6263 Dihedral : 25.520 179.726 46870 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 27.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 9.51 % Allowed : 27.93 % Favored : 62.56 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.74 (0.15), residues: 2496 helix: -1.48 (0.20), residues: 535 sheet: -1.23 (0.23), residues: 472 loop : -2.23 (0.14), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 65 HIS 0.018 0.002 HIS 2 13 PHE 0.043 0.004 PHE a 77 TYR 0.032 0.003 TYR Q 62 ARG 0.037 0.002 ARG M 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 555 time to evaluate : 3.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: L 39 LYS cc_start: 0.6300 (OUTLIER) cc_final: 0.6008 (ptmt) REVERT: N 42 ILE cc_start: 0.3995 (tp) cc_final: 0.3754 (tp) REVERT: Q 97 ASN cc_start: 0.6764 (OUTLIER) cc_final: 0.6538 (p0) outliers start: 196 outliers final: 62 residues processed: 669 average time/residue: 1.6763 time to fit residues: 1488.1750 Evaluate side-chains 497 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 433 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 115 ARG Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 113 GLN Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 102 ASP Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 97 ASN Chi-restraints excluded: chain Q residue 105 ILE Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 60 VAL Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain X residue 58 GLU Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 21 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 423 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 chunk 7 optimal weight: 30.0000 chunk 378 optimal weight: 8.9990 chunk 209 optimal weight: 20.0000 chunk 433 optimal weight: 50.0000 chunk 351 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 259 optimal weight: 50.0000 chunk 456 optimal weight: 9.9990 chunk 128 optimal weight: 30.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN G 110 ASN ** O 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 GLN P 65 GLN Q 97 ASN R 47 ASN R 57 ASN ** R 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 36 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3852 moved from start: 1.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 88253 Z= 0.237 Angle : 0.707 13.460 133220 Z= 0.366 Chirality : 0.038 0.325 17224 Planarity : 0.006 0.116 6263 Dihedral : 25.223 179.613 46870 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 7.08 % Allowed : 34.14 % Favored : 58.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.26 (0.16), residues: 2496 helix: -0.85 (0.21), residues: 533 sheet: -1.07 (0.23), residues: 491 loop : -1.97 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 213 HIS 0.011 0.001 HIS Y 13 PHE 0.025 0.003 PHE O 25 TYR 0.028 0.002 TYR O 32 ARG 0.016 0.001 ARG T 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 496 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 76 PHE cc_start: 0.5513 (OUTLIER) cc_final: 0.5002 (p90) REVERT: Q 25 ARG cc_start: 0.3903 (mmm160) cc_final: 0.3683 (mtp85) REVERT: Q 73 GLU cc_start: 0.3782 (mm-30) cc_final: 0.3547 (mm-30) outliers start: 146 outliers final: 74 residues processed: 572 average time/residue: 1.6565 time to fit residues: 1261.1452 Evaluate side-chains 491 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 416 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain 2 residue 9 ASN Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain F residue 70 ASN Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 44 SER Chi-restraints excluded: chain Y residue 115 ARG Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 113 GLN Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 64 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain a residue 33 ARG Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain W residue 4 LYS Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain b residue 7 ARG Chi-restraints excluded: chain b residue 11 THR Chi-restraints excluded: chain b residue 21 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 171 optimal weight: 50.0000 chunk 457 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 298 optimal weight: 1.9990 chunk 125 optimal weight: 30.0000 chunk 508 optimal weight: 6.9990 chunk 422 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 42 optimal weight: 40.0000 chunk 168 optimal weight: 30.0000 chunk 267 optimal weight: 20.0000 overall best weight: 11.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 228 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3983 moved from start: 1.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 88253 Z= 0.327 Angle : 0.802 15.840 133220 Z= 0.409 Chirality : 0.042 0.359 17224 Planarity : 0.006 0.113 6263 Dihedral : 25.397 179.717 46867 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 26.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 7.61 % Allowed : 34.92 % Favored : 57.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.15), residues: 2496 helix: -1.04 (0.21), residues: 534 sheet: -1.19 (0.23), residues: 466 loop : -2.05 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 65 HIS 0.014 0.002 HIS Y 13 PHE 0.033 0.003 PHE W 26 TYR 0.036 0.003 TYR O 32 ARG 0.019 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 479 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 16 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6353 (ptt180) REVERT: Y 112 GLU cc_start: 0.3208 (pm20) cc_final: 0.2968 (pm20) REVERT: N 76 PHE cc_start: 0.5665 (OUTLIER) cc_final: 0.5078 (p90) REVERT: Q 73 GLU cc_start: 0.3856 (mm-30) cc_final: 0.3653 (mm-30) REVERT: R 87 ILE cc_start: 0.3606 (OUTLIER) cc_final: 0.3350 (pt) outliers start: 157 outliers final: 83 residues processed: 568 average time/residue: 1.6355 time to fit residues: 1242.4121 Evaluate side-chains 511 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 425 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain 1 residue 41 LYS Chi-restraints excluded: chain 2 residue 9 ASN Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 16 ARG Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 115 ARG Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 113 GLN Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 36 ASP Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 78 ARG Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain W residue 4 LYS Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain b residue 7 ARG Chi-restraints excluded: chain b residue 11 THR Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 41 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 490 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 289 optimal weight: 5.9990 chunk 371 optimal weight: 7.9990 chunk 287 optimal weight: 9.9990 chunk 428 optimal weight: 6.9990 chunk 284 optimal weight: 30.0000 chunk 506 optimal weight: 6.9990 chunk 317 optimal weight: 30.0000 chunk 309 optimal weight: 7.9990 chunk 234 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** H 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 ASN ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 GLN ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN R 47 ASN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 36 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3908 moved from start: 1.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 88253 Z= 0.215 Angle : 0.690 16.753 133220 Z= 0.357 Chirality : 0.037 0.353 17224 Planarity : 0.006 0.114 6263 Dihedral : 25.173 179.567 46867 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.92 % Allowed : 38.02 % Favored : 56.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.14 (0.16), residues: 2496 helix: -0.70 (0.22), residues: 544 sheet: -1.01 (0.24), residues: 450 loop : -1.89 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 65 HIS 0.012 0.001 HIS Y 13 PHE 0.049 0.003 PHE T 48 TYR 0.031 0.002 TYR O 32 ARG 0.014 0.001 ARG R 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 456 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 16 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6282 (ptt180) REVERT: N 76 PHE cc_start: 0.5549 (OUTLIER) cc_final: 0.4949 (p90) REVERT: R 6 ILE cc_start: 0.4149 (OUTLIER) cc_final: 0.3942 (pp) REVERT: S 4 LYS cc_start: 0.5394 (OUTLIER) cc_final: 0.4891 (pmtt) outliers start: 122 outliers final: 79 residues processed: 525 average time/residue: 1.6801 time to fit residues: 1175.3457 Evaluate side-chains 494 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 411 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 CYS Chi-restraints excluded: chain 1 residue 41 LYS Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 16 ARG Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 59 ARG Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 115 ARG Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 36 ASP Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 78 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 108 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain a residue 33 ARG Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain W residue 4 LYS Chi-restraints excluded: chain W residue 36 GLN Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain b residue 7 ARG Chi-restraints excluded: chain b residue 11 THR Chi-restraints excluded: chain b residue 18 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 313 optimal weight: 20.0000 chunk 202 optimal weight: 90.0000 chunk 302 optimal weight: 9.9990 chunk 152 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 322 optimal weight: 0.7980 chunk 345 optimal weight: 0.0060 chunk 250 optimal weight: 50.0000 chunk 47 optimal weight: 30.0000 chunk 398 optimal weight: 8.9990 overall best weight: 7.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 GLN ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 71 GLN a 37 GLN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3935 moved from start: 1.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 88253 Z= 0.232 Angle : 0.703 16.725 133220 Z= 0.363 Chirality : 0.037 0.365 17224 Planarity : 0.006 0.114 6263 Dihedral : 25.134 179.613 46864 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 6.11 % Allowed : 38.85 % Favored : 55.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.15 (0.16), residues: 2496 helix: -0.70 (0.22), residues: 547 sheet: -1.02 (0.24), residues: 445 loop : -1.90 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 16 HIS 0.011 0.001 HIS Y 13 PHE 0.028 0.002 PHE T 48 TYR 0.036 0.002 TYR O 32 ARG 0.012 0.001 ARG N 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 442 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 16 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6191 (ptt180) REVERT: L 59 ARG cc_start: 0.5013 (OUTLIER) cc_final: 0.4792 (mpt180) REVERT: N 76 PHE cc_start: 0.5659 (OUTLIER) cc_final: 0.5006 (p90) REVERT: O 74 MET cc_start: 0.3217 (tpt) cc_final: 0.2955 (tpt) REVERT: Q 1 MET cc_start: 0.4437 (ppp) cc_final: 0.4093 (pp-130) REVERT: R 68 TYR cc_start: 0.2721 (OUTLIER) cc_final: 0.2236 (m-10) REVERT: S 4 LYS cc_start: 0.5504 (OUTLIER) cc_final: 0.4848 (pmtt) outliers start: 126 outliers final: 85 residues processed: 516 average time/residue: 1.7970 time to fit residues: 1240.8964 Evaluate side-chains 508 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 418 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 LYS Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 16 ARG Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 59 ARG Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 52 GLN Chi-restraints excluded: chain O residue 102 ASP Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 36 ASP Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 78 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain Q residue 105 ILE Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 68 TYR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain a residue 33 ARG Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain W residue 4 LYS Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain b residue 7 ARG Chi-restraints excluded: chain b residue 11 THR Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 41 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 461 optimal weight: 5.9990 chunk 485 optimal weight: 9.9990 chunk 443 optimal weight: 2.9990 chunk 472 optimal weight: 20.0000 chunk 284 optimal weight: 9.9990 chunk 205 optimal weight: 50.0000 chunk 370 optimal weight: 5.9990 chunk 144 optimal weight: 30.0000 chunk 426 optimal weight: 9.9990 chunk 446 optimal weight: 5.9990 chunk 470 optimal weight: 40.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 GLN ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3897 moved from start: 1.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 88253 Z= 0.199 Angle : 0.681 17.431 133220 Z= 0.352 Chirality : 0.036 0.365 17224 Planarity : 0.006 0.113 6263 Dihedral : 25.054 178.743 46864 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.80 % Allowed : 40.69 % Favored : 54.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.06 (0.16), residues: 2496 helix: -0.62 (0.22), residues: 537 sheet: -0.99 (0.25), residues: 453 loop : -1.83 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 65 HIS 0.010 0.001 HIS Y 13 PHE 0.036 0.002 PHE D 53 TYR 0.042 0.002 TYR O 32 ARG 0.013 0.001 ARG S 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 445 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 TYR cc_start: 0.4775 (t80) cc_final: 0.4511 (t80) REVERT: N 76 PHE cc_start: 0.5589 (OUTLIER) cc_final: 0.5202 (p90) REVERT: O 58 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5428 (ttt180) REVERT: Q 1 MET cc_start: 0.4403 (OUTLIER) cc_final: 0.3967 (pp-130) REVERT: S 4 LYS cc_start: 0.5432 (OUTLIER) cc_final: 0.4771 (pmtt) outliers start: 99 outliers final: 73 residues processed: 502 average time/residue: 1.6852 time to fit residues: 1132.6941 Evaluate side-chains 492 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 415 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 LYS Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 52 GLN Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 101 SER Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 78 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain X residue 6 ILE Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain b residue 7 ARG Chi-restraints excluded: chain b residue 11 THR Chi-restraints excluded: chain b residue 41 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 310 optimal weight: 9.9990 chunk 499 optimal weight: 6.9990 chunk 304 optimal weight: 9.9990 chunk 236 optimal weight: 30.0000 chunk 347 optimal weight: 0.9990 chunk 524 optimal weight: 50.0000 chunk 482 optimal weight: 20.0000 chunk 417 optimal weight: 8.9990 chunk 43 optimal weight: 40.0000 chunk 322 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 GLN ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 37 GLN b 19 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3930 moved from start: 1.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 88253 Z= 0.223 Angle : 0.701 17.466 133220 Z= 0.361 Chirality : 0.036 0.376 17224 Planarity : 0.006 0.113 6263 Dihedral : 25.070 179.785 46864 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 4.22 % Allowed : 41.42 % Favored : 54.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.03 (0.16), residues: 2496 helix: -0.63 (0.22), residues: 546 sheet: -0.97 (0.25), residues: 438 loop : -1.79 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Y 65 HIS 0.016 0.002 HIS N 31 PHE 0.038 0.002 PHE D 53 TYR 0.046 0.002 TYR O 32 ARG 0.016 0.001 ARG Q 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 436 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 76 PHE cc_start: 0.5655 (OUTLIER) cc_final: 0.5243 (p90) REVERT: Q 1 MET cc_start: 0.4759 (OUTLIER) cc_final: 0.4482 (pp-130) REVERT: S 4 LYS cc_start: 0.5558 (OUTLIER) cc_final: 0.4868 (pmtt) outliers start: 87 outliers final: 65 residues processed: 486 average time/residue: 1.6876 time to fit residues: 1101.8058 Evaluate side-chains 490 residues out of total 2123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 422 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 LYS Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 20 ASP Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 52 GLN Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 78 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain b residue 7 ARG Chi-restraints excluded: chain b residue 41 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 331 optimal weight: 30.0000 chunk 444 optimal weight: 5.9990 chunk 127 optimal weight: 30.0000 chunk 384 optimal weight: 0.0000 chunk 61 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 417 optimal weight: 1.9990 chunk 174 optimal weight: 70.0000 chunk 429 optimal weight: 6.9990 chunk 52 optimal weight: 30.0000 chunk 76 optimal weight: 30.0000 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 GLN ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.078851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.057232 restraints weight = 473717.218| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.43 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 1.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 88253 Z= 0.214 Angle : 0.694 17.440 133220 Z= 0.357 Chirality : 0.036 0.373 17224 Planarity : 0.006 0.113 6263 Dihedral : 25.049 179.210 46864 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.32 % Allowed : 41.56 % Favored : 54.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.03 (0.16), residues: 2496 helix: -0.72 (0.22), residues: 541 sheet: -0.98 (0.25), residues: 446 loop : -1.75 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Y 65 HIS 0.010 0.001 HIS Y 13 PHE 0.042 0.003 PHE E 139 TYR 0.049 0.002 TYR O 32 ARG 0.013 0.001 ARG N 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22048.16 seconds wall clock time: 387 minutes 31.79 seconds (23251.79 seconds total)