Starting phenix.real_space_refine on Tue Feb 20 18:35:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn2_29304/02_2024/8fn2_29304.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn2_29304/02_2024/8fn2_29304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn2_29304/02_2024/8fn2_29304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn2_29304/02_2024/8fn2_29304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn2_29304/02_2024/8fn2_29304.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn2_29304/02_2024/8fn2_29304.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2874 5.49 5 S 96 5.16 5 C 45288 2.51 5 N 16563 2.21 5 O 24919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 54": "OD1" <-> "OD2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E ASP 107": "OD1" <-> "OD2" Residue "E PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 181": "OE1" <-> "OE2" Residue "E PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F ASP 119": "OD1" <-> "OD2" Residue "F PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 160": "OD1" <-> "OD2" Residue "F PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 3": "NH1" <-> "NH2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H ASP 36": "OD1" <-> "OD2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 137": "OD1" <-> "OD2" Residue "H ASP 165": "OD1" <-> "OD2" Residue "I PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 25": "OD1" <-> "OD2" Residue "L ASP 28": "OD1" <-> "OD2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 55": "OD1" <-> "OD2" Residue "L TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 12": "OD1" <-> "OD2" Residue "M ASP 56": "OD1" <-> "OD2" Residue "M TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 88": "OD1" <-> "OD2" Residue "M PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 120": "OE1" <-> "OE2" Residue "N PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 38": "OE1" <-> "OE2" Residue "O PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "O PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 106": "OD1" <-> "OD2" Residue "P GLU 117": "OE1" <-> "OE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 48": "OD1" <-> "OD2" Residue "Q TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 43": "OE1" <-> "OE2" Residue "R TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 49": "OD1" <-> "OD2" Residue "S PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "T GLU 29": "OE1" <-> "OE2" Residue "T TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 26": "OD1" <-> "OD2" Residue "U TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 99": "OD1" <-> "OD2" Residue "U PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 113": "OD1" <-> "OD2" Residue "V TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 14": "OE1" <-> "OE2" Residue "V TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 45": "OE1" <-> "OE2" Residue "V TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 60": "OD1" <-> "OD2" Residue "W GLU 62": "OE1" <-> "OE2" Residue "W PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 66": "OD1" <-> "OD2" Residue "X PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 119": "OE1" <-> "OE2" Residue "X PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 35": "OE1" <-> "OE2" Residue "Y ASP 56": "OD1" <-> "OD2" Residue "Y GLU 68": "OE1" <-> "OE2" Residue "Y PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 11": "OD1" <-> "OD2" Residue "b PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 33": "OE1" <-> "OE2" Residue "c TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 11": "OE1" <-> "OE2" Residue "e GLU 36": "OE1" <-> "OE2" Residue "e GLU 39": "OE1" <-> "OE2" Residue "e TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 15": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 89742 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 59248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2762, 59248 Classifications: {'RNA': 2762} Modifications used: {'rna2p_pur': 288, 'rna2p_pyr': 139, 'rna3p_pur': 1337, 'rna3p_pyr': 998} Link IDs: {'rna2p': 427, 'rna3p': 2334} Chain breaks: 5 Chain: "B" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2398 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 53, 'rna3p_pyr': 40} Link IDs: {'rna2p': 19, 'rna3p': 92} Chain: "D" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2156 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 261} Chain: "E" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1564 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain: "F" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1658 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 203} Chain: "G" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1439 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain: "H" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1405 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 174} Chain: "I" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 411 Classifications: {'peptide': 63} Incomplete info: {'backbone_only': 23} Link IDs: {'PTRANS': 1, 'TRANS': 61} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "J" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 528 Classifications: {'peptide': 132} Incomplete info: {'backbone_only': 125} Link IDs: {'PTRANS': 2, 'TRANS': 129} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 532 Unresolved non-hydrogen angles: 761 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 167 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 6, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 216 Chain: "K" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 272 Classifications: {'peptide': 68} Incomplete info: {'backbone_only': 63} Link IDs: {'TRANS': 67} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "L" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1171 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 136} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 942 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "N" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1129 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "O" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1092 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain: "P" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1004 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "Q" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 968 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain: "R" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 951 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "S" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 943 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'TRANS': 113} Chain: "T" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 859 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 100} Chain: "U" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 918 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "V" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 784 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "W" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 800 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain: "X" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1432 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "Y" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 571 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'TRANS': 73} Chain: "Z" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "a" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 553 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 814 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'TRANS': 99} Chain: "c" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "d" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 484 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain: "e" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "f" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 422 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "g" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 548 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "h" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 305 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "i" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 375 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 87432 SG CYS d 31 90.601 196.647 80.075 1.00 66.40 S ATOM 87452 SG CYS d 34 92.307 196.363 76.612 1.00 78.21 S ATOM 87529 SG CYS d 44 93.978 194.860 79.511 1.00 67.59 S ATOM 87552 SG CYS d 47 93.744 198.614 79.314 1.00 72.45 S ATOM 89145 SG CYS h 11 56.544 108.324 143.679 1.00 72.05 S ATOM 89169 SG CYS h 14 57.774 109.865 140.484 1.00 77.57 S ATOM 89274 SG CYS h 27 55.232 111.803 142.555 1.00 74.97 S Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N ALA I 60 " occ=0.00 ... (2 atoms not shown) pdb=" O ALA I 60 " occ=0.00 residue: pdb=" N LYS I 61 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS I 61 " occ=0.00 residue: pdb=" N LYS I 62 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS I 62 " occ=0.00 residue: pdb=" N GLN I 63 " occ=0.00 ... (2 atoms not shown) pdb=" O GLN I 63 " occ=0.00 residue: pdb=" N ASN L 2 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN L 2 " occ=0.00 residue: pdb=" N LYS L 3 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS L 3 " occ=0.00 residue: pdb=" N ILE L 4 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE L 4 " occ=0.00 residue: pdb=" N THR L 5 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR L 5 " occ=0.00 residue: pdb=" N ASN L 6 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN L 6 " occ=0.00 residue: pdb=" N ASN L 7 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN L 7 " occ=0.00 Time building chain proxies: 36.30, per 1000 atoms: 0.40 Number of scatterers: 89742 At special positions: 0 Unit cell: (245.526, 233.469, 188.529, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 96 16.00 P 2874 15.00 O 24919 8.00 N 16563 7.00 C 45288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS e 17 " - pdb=" SG CYS e 44 " distance=2.05 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: 39.68 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d 101 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 34 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 44 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 47 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 31 " pdb=" ZN h 101 " pdb="ZN ZN h 101 " - pdb=" ND1 HIS h 32 " pdb="ZN ZN h 101 " - pdb=" SG CYS h 14 " pdb="ZN ZN h 101 " - pdb=" SG CYS h 11 " pdb="ZN ZN h 101 " - pdb=" SG CYS h 27 " Number of angles added : 9 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6278 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 53 sheets defined 31.5% alpha, 22.3% beta 732 base pairs and 1647 stacking pairs defined. Time for finding SS restraints: 33.14 Creating SS restraints... Processing helix chain 'D' and resid 12 through 15 removed outlier: 4.079A pdb=" N TYR D 15 " --> pdb=" O SER D 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 12 through 15' Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 209 through 216 removed outlier: 3.543A pdb=" N SER D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 269 removed outlier: 3.593A pdb=" N ASP D 268 " --> pdb=" O ARG D 265 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS D 269 " --> pdb=" O TYR D 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 269' Processing helix chain 'E' and resid 56 through 60 removed outlier: 4.150A pdb=" N VAL E 60 " --> pdb=" O SER E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 68 removed outlier: 3.804A pdb=" N TYR E 68 " --> pdb=" O ILE E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.934A pdb=" N VAL E 99 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE E 100 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 125 Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 28 through 42 Processing helix chain 'F' and resid 101 through 118 Processing helix chain 'F' and resid 136 through 147 Processing helix chain 'F' and resid 161 through 169 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 197 through 209 removed outlier: 4.099A pdb=" N LYS F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 14 Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 44 through 48 Processing helix chain 'G' and resid 49 through 65 removed outlier: 3.789A pdb=" N LEU G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing helix chain 'G' and resid 137 through 141 Processing helix chain 'G' and resid 165 through 176 removed outlier: 3.765A pdb=" N SER G 169 " --> pdb=" O ASN G 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 7 removed outlier: 3.865A pdb=" N ARG H 6 " --> pdb=" O SER H 2 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 82 removed outlier: 3.844A pdb=" N GLY H 66 " --> pdb=" O LYS H 62 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 79 " --> pdb=" O MET H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 152 removed outlier: 3.744A pdb=" N LYS H 152 " --> pdb=" O ILE H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 179 Processing helix chain 'I' and resid 22 through 29 Processing helix chain 'I' and resid 29 through 34 Processing helix chain 'I' and resid 43 through 54 Processing helix chain 'J' and resid 2 through 23 Processing helix chain 'J' and resid 35 through 49 Processing helix chain 'J' and resid 57 through 68 Processing helix chain 'J' and resid 73 through 77 Processing helix chain 'J' and resid 89 through 104 Processing helix chain 'J' and resid 119 through 129 Processing helix chain 'K' and resid 77 through 85 Processing helix chain 'K' and resid 103 through 114 Processing helix chain 'K' and resid 115 through 117 No H-bonds generated for 'chain 'K' and resid 115 through 117' Processing helix chain 'K' and resid 122 through 138 Processing helix chain 'L' and resid 13 through 17 removed outlier: 3.624A pdb=" N VAL L 17 " --> pdb=" O PRO L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 44 removed outlier: 3.733A pdb=" N GLY L 44 " --> pdb=" O LYS L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 68 removed outlier: 4.103A pdb=" N VAL L 68 " --> pdb=" O ALA L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 78 Processing helix chain 'L' and resid 95 through 102 Processing helix chain 'L' and resid 104 through 115 Processing helix chain 'L' and resid 118 through 127 Processing helix chain 'L' and resid 138 through 142 removed outlier: 3.512A pdb=" N ASN L 142 " --> pdb=" O LYS L 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 109 removed outlier: 3.968A pdb=" N ASP M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 118 Processing helix chain 'N' and resid 36 through 40 removed outlier: 3.851A pdb=" N ASN N 40 " --> pdb=" O LYS N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 58 Processing helix chain 'N' and resid 77 through 84 Processing helix chain 'N' and resid 91 through 98 Processing helix chain 'N' and resid 128 through 139 Processing helix chain 'O' and resid 44 through 58 Processing helix chain 'O' and resid 110 through 123 Processing helix chain 'P' and resid 8 through 12 removed outlier: 4.115A pdb=" N SER P 11 " --> pdb=" O ASN P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 32 Processing helix chain 'P' and resid 38 through 55 removed outlier: 3.690A pdb=" N ARG P 50 " --> pdb=" O ARG P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 68 removed outlier: 3.656A pdb=" N LYS P 68 " --> pdb=" O ARG P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 82 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'Q' and resid 2 through 23 Processing helix chain 'Q' and resid 69 through 86 removed outlier: 3.787A pdb=" N GLU Q 86 " --> pdb=" O LYS Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 114 Processing helix chain 'R' and resid 2 through 12 Processing helix chain 'R' and resid 52 through 55 removed outlier: 3.595A pdb=" N GLY R 55 " --> pdb=" O LYS R 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 52 through 55' Processing helix chain 'R' and resid 96 through 101 Processing helix chain 'R' and resid 103 through 108 removed outlier: 3.610A pdb=" N ALA R 106 " --> pdb=" O ILE R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 21 Processing helix chain 'S' and resid 25 through 30 removed outlier: 3.812A pdb=" N LYS S 29 " --> pdb=" O GLY S 26 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER S 30 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 69 removed outlier: 4.494A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 91 through 102 removed outlier: 3.720A pdb=" N ILE S 100 " --> pdb=" O SER S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 115 removed outlier: 3.617A pdb=" N PHE S 106 " --> pdb=" O ASP S 102 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG S 115 " --> pdb=" O LEU S 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 30 Processing helix chain 'U' and resid 17 through 29 Proline residue: U 23 - end of helix removed outlier: 3.545A pdb=" N ILE U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 43 Processing helix chain 'U' and resid 45 through 66 Processing helix chain 'U' and resid 94 through 96 No H-bonds generated for 'chain 'U' and resid 94 through 96' Processing helix chain 'V' and resid 13 through 24 Processing helix chain 'V' and resid 35 through 48 Processing helix chain 'X' and resid 2 through 4 No H-bonds generated for 'chain 'X' and resid 2 through 4' Processing helix chain 'X' and resid 16 through 26 Processing helix chain 'X' and resid 47 through 55 Processing helix chain 'X' and resid 114 through 119 Processing helix chain 'X' and resid 135 through 139 Processing helix chain 'Z' and resid 24 through 28 Processing helix chain 'Z' and resid 66 through 76 Processing helix chain 'Z' and resid 76 through 84 Processing helix chain 'Z' and resid 87 through 91 Processing helix chain 'a' and resid 8 through 33 Processing helix chain 'a' and resid 39 through 61 Processing helix chain 'b' and resid 3 through 18 Processing helix chain 'b' and resid 20 through 39 Processing helix chain 'b' and resid 57 through 68 Processing helix chain 'b' and resid 81 through 91 Processing helix chain 'd' and resid 9 through 21 Processing helix chain 'f' and resid 9 through 17 Processing helix chain 'f' and resid 17 through 23 Processing helix chain 'f' and resid 24 through 38 Processing helix chain 'f' and resid 43 through 47 Processing helix chain 'g' and resid 8 through 13 Processing helix chain 'g' and resid 38 through 47 removed outlier: 3.582A pdb=" N LYS g 47 " --> pdb=" O ARG g 43 " (cutoff:3.500A) Processing helix chain 'g' and resid 55 through 63 Processing helix chain 'h' and resid 29 through 32 Processing helix chain 'i' and resid 50 through 55 Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AA3, first strand: chain 'D' and resid 103 through 107 removed outlier: 6.433A pdb=" N ILE D 93 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE D 83 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU D 95 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 133 removed outlier: 5.713A pdb=" N ILE D 166 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS D 177 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 168 " --> pdb=" O THR D 175 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET D 183 " --> pdb=" O ILE D 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 3 through 15 removed outlier: 5.551A pdb=" N LYS E 8 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU E 28 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 10 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS E 188 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL E 175 " --> pdb=" O LYS E 188 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR E 169 " --> pdb=" O GLY E 110 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLY E 110 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN E 171 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL E 108 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR E 111 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE E 198 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 80 through 84 removed outlier: 3.717A pdb=" N GLY E 36 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY E 51 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE E 34 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN E 32 " --> pdb=" O ILE E 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.402A pdb=" N MET E 163 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE E 117 " --> pdb=" O GLY E 161 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLY E 161 " --> pdb=" O PHE E 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 2 through 6 Processing sheet with id=AA9, first strand: chain 'F' and resid 123 through 126 removed outlier: 6.630A pdb=" N VAL F 153 " --> pdb=" O LYS F 175 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU F 177 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE F 155 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 69 through 72 removed outlier: 3.609A pdb=" N GLY G 89 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS G 36 " --> pdb=" O VAL G 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 120 through 121 removed outlier: 5.596A pdb=" N ILE G 120 " --> pdb=" O SER G 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'H' and resid 9 through 10 Processing sheet with id=AB4, first strand: chain 'H' and resid 16 through 20 Processing sheet with id=AB5, first strand: chain 'H' and resid 121 through 125 Processing sheet with id=AB6, first strand: chain 'H' and resid 95 through 99 Processing sheet with id=AB7, first strand: chain 'I' and resid 18 through 20 Processing sheet with id=AB8, first strand: chain 'J' and resid 52 through 55 removed outlier: 6.487A pdb=" N ASP J 30 " --> pdb=" O VAL J 108 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL J 108 " --> pdb=" O ASP J 30 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 100 through 102 removed outlier: 6.388A pdb=" N GLY K 100 " --> pdb=" O GLU K 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'L' and resid 128 through 130 removed outlier: 6.724A pdb=" N TRP L 21 " --> pdb=" O ILE L 144 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU L 146 " --> pdb=" O TRP L 21 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL L 23 " --> pdb=" O LEU L 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 79 through 83 Processing sheet with id=AC3, first strand: chain 'M' and resid 7 through 10 removed outlier: 5.370A pdb=" N LYS M 17 " --> pdb=" O ILE M 10 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN M 45 " --> pdb=" O LYS M 17 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA M 19 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL M 43 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N CYS M 21 " --> pdb=" O ILE M 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE M 41 " --> pdb=" O CYS M 21 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS M 23 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE M 39 " --> pdb=" O LYS M 23 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS M 59 " --> pdb=" O LEU M 87 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA M 83 " --> pdb=" O VAL M 63 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N CYS M 84 " --> pdb=" O TYR M 7 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR M 9 " --> pdb=" O CYS M 84 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE M 86 " --> pdb=" O THR M 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 76 through 79 removed outlier: 6.333A pdb=" N THR R 57 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE R 49 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU R 59 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE R 63 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N GLU R 43 " --> pdb=" O ILE R 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN R 36 " --> pdb=" O GLU R 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG R 26 " --> pdb=" O VAL R 85 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL R 85 " --> pdb=" O ARG R 26 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL R 28 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL R 83 " --> pdb=" O VAL R 28 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N LYS R 30 " --> pdb=" O GLU R 81 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLU R 81 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 102 through 103 removed outlier: 6.349A pdb=" N VAL M 102 " --> pdb=" O ILE M 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'N' and resid 74 through 76 removed outlier: 6.241A pdb=" N VAL N 75 " --> pdb=" O LEU N 111 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 89 through 90 removed outlier: 6.246A pdb=" N PHE N 122 " --> pdb=" O GLN N 143 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 63 through 65 Processing sheet with id=AC9, first strand: chain 'O' and resid 40 through 43 removed outlier: 6.855A pdb=" N TYR O 74 " --> pdb=" O ASP O 91 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TRP O 93 " --> pdb=" O ILE O 72 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE O 72 " --> pdb=" O TRP O 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 33 through 37 removed outlier: 6.142A pdb=" N MET P 110 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 52 through 58 removed outlier: 5.739A pdb=" N THR Q 53 " --> pdb=" O ASP Q 47 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASP Q 47 " --> pdb=" O THR Q 53 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA Q 55 " --> pdb=" O VAL Q 45 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL Q 34 " --> pdb=" O ASP Q 95 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 10 through 14 removed outlier: 6.756A pdb=" N TYR T 2 " --> pdb=" O ILE T 41 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE T 41 " --> pdb=" O TYR T 2 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU T 4 " --> pdb=" O LEU T 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 18 through 23 removed outlier: 3.978A pdb=" N GLU T 18 " --> pdb=" O VAL T 98 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU T 65 " --> pdb=" O TYR T 95 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU T 97 " --> pdb=" O TYR T 63 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N TYR T 63 " --> pdb=" O LEU T 97 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASP T 99 " --> pdb=" O CYS T 61 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N CYS T 61 " --> pdb=" O ASP T 99 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE T 101 " --> pdb=" O ILE T 59 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE T 59 " --> pdb=" O ILE T 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 72 through 77 Processing sheet with id=AD6, first strand: chain 'U' and resid 8 through 14 removed outlier: 5.995A pdb=" N THR U 8 " --> pdb=" O VAL U 112 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL U 112 " --> pdb=" O THR U 8 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS U 10 " --> pdb=" O VAL U 110 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL U 110 " --> pdb=" O LYS U 10 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LYS U 12 " --> pdb=" O ILE U 108 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE U 108 " --> pdb=" O LYS U 12 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP U 99 " --> pdb=" O ILE U 90 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE U 90 " --> pdb=" O ASP U 99 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU U 101 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS U 88 " --> pdb=" O LEU U 101 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN U 103 " --> pdb=" O ARG U 86 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG U 86 " --> pdb=" O ASN U 103 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN U 105 " --> pdb=" O GLY U 84 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP U 113 " --> pdb=" O VAL U 76 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL U 76 " --> pdb=" O ASP U 113 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 7 through 10 removed outlier: 4.152A pdb=" N LYS V 83 " --> pdb=" O VAL V 30 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER V 53 " --> pdb=" O TYR V 88 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'V' and resid 63 through 67 removed outlier: 6.187A pdb=" N LYS V 64 " --> pdb=" O LYS V 76 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS V 76 " --> pdb=" O LYS V 64 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL V 66 " --> pdb=" O ILE V 74 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'W' and resid 65 through 66 Processing sheet with id=AE1, first strand: chain 'W' and resid 42 through 47 Processing sheet with id=AE2, first strand: chain 'W' and resid 81 through 85 Processing sheet with id=AE3, first strand: chain 'X' and resid 6 through 11 removed outlier: 7.484A pdb=" N SER X 8 " --> pdb=" O LYS X 46 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS X 46 " --> pdb=" O SER X 8 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLU X 28 " --> pdb=" O TYR X 89 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ILE X 91 " --> pdb=" O GLU X 28 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N PHE X 93 " --> pdb=" O PRO X 30 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL X 32 " --> pdb=" O PHE X 93 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLU X 95 " --> pdb=" O VAL X 32 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR X 34 " --> pdb=" O GLU X 95 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE X 88 " --> pdb=" O GLU X 81 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU X 81 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N HIS X 90 " --> pdb=" O ALA X 79 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA X 79 " --> pdb=" O HIS X 90 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP X 92 " --> pdb=" O LYS X 77 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU X 7 " --> pdb=" O ASP X 66 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 143 through 146 Processing sheet with id=AE5, first strand: chain 'X' and resid 123 through 124 removed outlier: 4.502A pdb=" N VAL X 179 " --> pdb=" O VAL X 156 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 22 through 23 removed outlier: 6.622A pdb=" N ILE Y 59 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 30 through 31 Processing sheet with id=AE8, first strand: chain 'Z' and resid 13 through 17 Processing sheet with id=AE9, first strand: chain 'Z' and resid 20 through 23 Processing sheet with id=AF1, first strand: chain 'Z' and resid 46 through 53 Processing sheet with id=AF2, first strand: chain 'b' and resid 75 through 79 Processing sheet with id=AF3, first strand: chain 'c' and resid 22 through 27 removed outlier: 7.541A pdb=" N LEU c 11 " --> pdb=" O GLU c 42 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU c 33 " --> pdb=" O LEU c 45 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'd' and resid 28 through 30 Processing sheet with id=AF5, first strand: chain 'e' and resid 25 through 30 removed outlier: 3.743A pdb=" N LYS e 49 " --> pdb=" O CYS e 44 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 16 through 17 Processing sheet with id=AF7, first strand: chain 'h' and resid 2 through 4 removed outlier: 3.895A pdb=" N ARG h 35 " --> pdb=" O LYS h 2 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU h 23 " --> pdb=" O GLN h 36 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'i' and resid 24 through 31 1140 hydrogen bonds defined for protein. 3129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1703 hydrogen bonds 2676 hydrogen bond angles 0 basepair planarities 732 basepair parallelities 1647 stacking parallelities Total time for adding SS restraints: 143.06 Time building geometry restraints manager: 43.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10317 1.32 - 1.45: 42169 1.45 - 1.58: 39142 1.58 - 1.70: 5742 1.70 - 1.83: 165 Bond restraints: 97535 Sorted by residual: bond pdb=" CB PHE i 30 " pdb=" CG PHE i 30 " ideal model delta sigma weight residual 1.502 1.412 0.090 2.30e-02 1.89e+03 1.53e+01 bond pdb=" CB GLU R 33 " pdb=" CG GLU R 33 " ideal model delta sigma weight residual 1.520 1.419 0.101 3.00e-02 1.11e+03 1.13e+01 bond pdb=" C ASN L 142 " pdb=" O ASN L 142 " ideal model delta sigma weight residual 1.235 1.220 0.015 4.70e-03 4.53e+04 1.07e+01 bond pdb=" CA GLN e 35 " pdb=" C GLN e 35 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.34e-02 5.57e+03 9.20e+00 bond pdb=" CA LYS O 12 " pdb=" C LYS O 12 " ideal model delta sigma weight residual 1.522 1.486 0.036 1.24e-02 6.50e+03 8.46e+00 ... (remaining 97530 not shown) Histogram of bond angle deviations from ideal: 71.09 - 84.74: 80 84.74 - 98.38: 26 98.38 - 112.03: 67443 112.03 - 125.67: 66292 125.67 - 139.32: 11747 Bond angle restraints: 145588 Sorted by residual: angle pdb=" OP1 G A1559 " pdb=" P G A1559 " pdb=" OP2 G A1559 " ideal model delta sigma weight residual 119.60 78.99 40.61 3.00e+00 1.11e-01 1.83e+02 angle pdb=" O3' C A1558 " pdb=" P G A1559 " pdb=" OP2 G A1559 " ideal model delta sigma weight residual 108.00 71.09 36.91 3.00e+00 1.11e-01 1.51e+02 angle pdb=" CA ARG i 52 " pdb=" CB ARG i 52 " pdb=" CG ARG i 52 " ideal model delta sigma weight residual 114.10 136.79 -22.69 2.00e+00 2.50e-01 1.29e+02 angle pdb=" OP1 G A1559 " pdb=" P G A1559 " pdb=" O5' G A1559 " ideal model delta sigma weight residual 108.00 78.71 29.29 3.00e+00 1.11e-01 9.53e+01 angle pdb=" O3' C A1558 " pdb=" P G A1559 " pdb=" OP1 G A1559 " ideal model delta sigma weight residual 108.00 136.97 -28.97 3.00e+00 1.11e-01 9.33e+01 ... (remaining 145583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 54889 35.91 - 71.82: 5877 71.82 - 107.72: 610 107.72 - 143.63: 13 143.63 - 179.54: 34 Dihedral angle restraints: 61423 sinusoidal: 51435 harmonic: 9988 Sorted by residual: dihedral pdb=" O4' C B 41 " pdb=" C1' C B 41 " pdb=" N1 C B 41 " pdb=" C2 C B 41 " ideal model delta sinusoidal sigma weight residual 200.00 43.31 156.69 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" O4' U A1833 " pdb=" C1' U A1833 " pdb=" N1 U A1833 " pdb=" C2 U A1833 " ideal model delta sinusoidal sigma weight residual 200.00 57.28 142.72 1 1.50e+01 4.44e-03 7.66e+01 dihedral pdb=" O4' U A1862 " pdb=" C1' U A1862 " pdb=" N1 U A1862 " pdb=" C2 U A1862 " ideal model delta sinusoidal sigma weight residual 200.00 58.23 141.77 1 1.50e+01 4.44e-03 7.62e+01 ... (remaining 61420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.413: 18409 0.413 - 0.826: 0 0.826 - 1.239: 1 1.239 - 1.652: 0 1.652 - 2.065: 44 Chirality restraints: 18454 Sorted by residual: chirality pdb=" P G A 532 " pdb=" OP1 G A 532 " pdb=" OP2 G A 532 " pdb=" O5' G A 532 " both_signs ideal model delta sigma weight residual True 2.41 0.35 2.06 2.00e-01 2.50e+01 1.07e+02 chirality pdb=" P U A1620 " pdb=" OP1 U A1620 " pdb=" OP2 U A1620 " pdb=" O5' U A1620 " both_signs ideal model delta sigma weight residual True 2.41 0.35 2.06 2.00e-01 2.50e+01 1.06e+02 chirality pdb=" P A A1520 " pdb=" OP1 A A1520 " pdb=" OP2 A A1520 " pdb=" O5' A A1520 " both_signs ideal model delta sigma weight residual True 2.41 0.35 2.06 2.00e-01 2.50e+01 1.06e+02 ... (remaining 18451 not shown) Planarity restraints: 7709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 163 " -0.047 2.00e-02 2.50e+03 9.09e-02 8.26e+01 pdb=" C MET E 163 " 0.157 2.00e-02 2.50e+03 pdb=" O MET E 163 " -0.059 2.00e-02 2.50e+03 pdb=" N ALA E 164 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE i 30 " -0.072 2.00e-02 2.50e+03 4.73e-02 3.92e+01 pdb=" CG PHE i 30 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 PHE i 30 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE i 30 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE i 30 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE i 30 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE i 30 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU O 80 " 0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" CD GLU O 80 " -0.085 2.00e-02 2.50e+03 pdb=" OE1 GLU O 80 " 0.030 2.00e-02 2.50e+03 pdb=" OE2 GLU O 80 " 0.030 2.00e-02 2.50e+03 ... (remaining 7706 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1795 2.63 - 3.20: 72965 3.20 - 3.77: 175316 3.77 - 4.33: 240098 4.33 - 4.90: 320368 Nonbonded interactions: 810542 Sorted by model distance: nonbonded pdb=" NE2 GLN G 66 " pdb=" O THR G 93 " model vdw 2.063 2.520 nonbonded pdb=" OD2 ASP c 16 " pdb=" OG1 THR c 51 " model vdw 2.093 2.440 nonbonded pdb=" OD1 ASP N 81 " pdb=" NZ LYS N 118 " model vdw 2.096 2.520 nonbonded pdb=" O ARG N 44 " pdb=" NH1 ARG N 44 " model vdw 2.125 2.520 nonbonded pdb=" OG SER X 114 " pdb=" O VAL X 150 " model vdw 2.134 2.440 ... (remaining 810537 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 21.540 Check model and map are aligned: 0.990 Set scattering table: 0.670 Process input model: 333.530 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.210 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:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 367.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.006 0.101 97535 Z= 0.368 Angle : 0.885 40.614 145588 Z= 0.376 Chirality : 0.103 2.065 18454 Planarity : 0.005 0.099 7709 Dihedral : 21.936 179.538 55142 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 3569 helix: 0.53 (0.16), residues: 1012 sheet: -0.58 (0.18), residues: 775 loop : -1.40 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP D 251 HIS 0.021 0.002 HIS E 140 PHE 0.090 0.003 PHE i 30 TYR 0.042 0.002 TYR T 93 ARG 0.032 0.002 ARG i 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1001 time to evaluate : 4.063 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 121 MET cc_start: 0.7917 (ttm) cc_final: 0.7632 (ttt) REVERT: F 6 PHE cc_start: 0.8235 (m-80) cc_final: 0.7895 (m-80) REVERT: G 99 MET cc_start: 0.6135 (ttp) cc_final: 0.5387 (ttp) REVERT: G 109 LEU cc_start: 0.8569 (mt) cc_final: 0.8291 (tp) REVERT: G 113 ARG cc_start: 0.5727 (mtp-110) cc_final: 0.5466 (mmm160) REVERT: H 80 THR cc_start: 0.8835 (t) cc_final: 0.8561 (t) REVERT: I 6 LYS cc_start: 0.7733 (ttmt) cc_final: 0.7517 (tmtt) REVERT: O 112 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6828 (mm-30) REVERT: Q 33 THR cc_start: 0.8221 (p) cc_final: 0.7703 (p) REVERT: Q 41 PHE cc_start: 0.7822 (t80) cc_final: 0.7392 (t80) REVERT: Q 79 VAL cc_start: 0.7654 (t) cc_final: 0.6852 (t) REVERT: Q 108 PHE cc_start: 0.8535 (t80) cc_final: 0.8319 (t80) REVERT: T 40 LEU cc_start: 0.8496 (tt) cc_final: 0.8171 (tt) REVERT: W 41 ASN cc_start: 0.7364 (t0) cc_final: 0.7062 (t0) REVERT: Y 14 ARG cc_start: 0.7484 (mtm110) cc_final: 0.6902 (mtm-85) REVERT: Y 56 ASP cc_start: 0.8584 (p0) cc_final: 0.8317 (p0) REVERT: a 12 MET cc_start: 0.7507 (mtm) cc_final: 0.7211 (mtt) REVERT: b 100 VAL cc_start: 0.8131 (t) cc_final: 0.7794 (t) REVERT: c 45 LEU cc_start: 0.7644 (tp) cc_final: 0.7217 (pp) REVERT: e 54 LYS cc_start: 0.7825 (ttmm) cc_final: 0.7261 (mttt) outliers start: 0 outliers final: 0 residues processed: 1001 average time/residue: 0.9162 time to fit residues: 1523.7695 Evaluate side-chains 491 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 4.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 537 optimal weight: 1.9990 chunk 482 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 325 optimal weight: 0.9990 chunk 257 optimal weight: 10.0000 chunk 498 optimal weight: 5.9990 chunk 192 optimal weight: 30.0000 chunk 303 optimal weight: 20.0000 chunk 371 optimal weight: 7.9990 chunk 577 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 HIS E 67 GLN G 2 ASN G 30 GLN G 182 ASN H 112 GLN N 98 ASN N 143 GLN O 92 HIS O 94 ASN P 8 ASN P 31 HIS P 89 GLN R 101 ASN ** V 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 41 ASN W 69 ASN W 88 ASN X 10 GLN b 46 GLN i 32 ASN i 46 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 97535 Z= 0.291 Angle : 0.960 39.931 145588 Z= 0.406 Chirality : 0.102 2.063 18454 Planarity : 0.005 0.102 7709 Dihedral : 22.564 179.506 47946 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer: Outliers : 3.26 % Allowed : 16.73 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3569 helix: 1.03 (0.17), residues: 1010 sheet: -0.49 (0.18), residues: 800 loop : -1.11 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP i 20 HIS 0.010 0.001 HIS U 65 PHE 0.027 0.002 PHE T 19 TYR 0.042 0.003 TYR g 15 ARG 0.011 0.001 ARG O 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 560 time to evaluate : 4.163 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.1676 (mmt) cc_final: 0.1294 (mtp) REVERT: E 121 MET cc_start: 0.8069 (ttm) cc_final: 0.7608 (ttt) REVERT: F 33 TYR cc_start: 0.8777 (t80) cc_final: 0.8381 (t80) REVERT: G 99 MET cc_start: 0.5760 (ttp) cc_final: 0.5281 (ttp) REVERT: G 109 LEU cc_start: 0.8606 (mt) cc_final: 0.8162 (tp) REVERT: G 113 ARG cc_start: 0.5697 (mtp-110) cc_final: 0.5081 (mmt90) REVERT: H 81 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7995 (tm-30) REVERT: M 112 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7662 (mmm) REVERT: O 138 ARG cc_start: 0.6700 (pmt170) cc_final: 0.6450 (pmt170) REVERT: P 11 SER cc_start: 0.8853 (m) cc_final: 0.8591 (p) REVERT: P 32 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7543 (tm-30) REVERT: Q 6 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7362 (tm-30) REVERT: Q 40 TYR cc_start: 0.7850 (m-80) cc_final: 0.7600 (m-10) REVERT: R 70 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6164 (mt-10) REVERT: W 41 ASN cc_start: 0.7568 (t0) cc_final: 0.7360 (t0) REVERT: W 42 MET cc_start: 0.7773 (tpp) cc_final: 0.7487 (tpp) REVERT: Y 14 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7413 (ttm110) REVERT: Z 48 ASN cc_start: 0.7319 (p0) cc_final: 0.7019 (p0) REVERT: a 44 ILE cc_start: 0.9102 (mm) cc_final: 0.8874 (mm) REVERT: c 45 LEU cc_start: 0.7567 (tp) cc_final: 0.7224 (pp) REVERT: e 29 LYS cc_start: 0.7867 (tmmt) cc_final: 0.7548 (tptt) outliers start: 97 outliers final: 64 residues processed: 621 average time/residue: 0.8510 time to fit residues: 914.4041 Evaluate side-chains 536 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 471 time to evaluate : 4.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain R residue 2 ASP Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain U residue 41 CYS Chi-restraints excluded: chain V residue 43 ILE Chi-restraints excluded: chain W residue 18 ASP Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 89 TYR Chi-restraints excluded: chain X residue 162 VAL Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 56 CYS Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain d residue 13 SER Chi-restraints excluded: chain d residue 30 GLU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain e residue 28 THR Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain g residue 52 SER Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 5 VAL Chi-restraints excluded: chain h residue 12 GLU Chi-restraints excluded: chain h residue 22 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 320 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 480 optimal weight: 0.8980 chunk 393 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 578 optimal weight: 0.8980 chunk 625 optimal weight: 5.9990 chunk 515 optimal weight: 6.9990 chunk 573 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 464 optimal weight: 20.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN N 51 GLN ** N 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN Q 44 GLN ** h 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 97535 Z= 0.236 Angle : 0.916 39.776 145588 Z= 0.386 Chirality : 0.102 2.064 18454 Planarity : 0.004 0.045 7709 Dihedral : 22.771 179.554 47946 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.90 % Rotamer: Outliers : 4.27 % Allowed : 18.82 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3569 helix: 1.18 (0.17), residues: 1017 sheet: -0.44 (0.18), residues: 804 loop : -0.99 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP i 20 HIS 0.007 0.001 HIS X 90 PHE 0.020 0.002 PHE Y 69 TYR 0.019 0.002 TYR E 79 ARG 0.010 0.001 ARG Q 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 543 time to evaluate : 4.177 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.1441 (mmt) cc_final: -0.0506 (ttm) REVERT: D 227 MET cc_start: 0.6756 (mtp) cc_final: 0.6330 (mtp) REVERT: E 121 MET cc_start: 0.8156 (ttm) cc_final: 0.7630 (ttt) REVERT: F 33 TYR cc_start: 0.8749 (t80) cc_final: 0.8511 (t80) REVERT: G 99 MET cc_start: 0.5709 (ttp) cc_final: 0.5448 (ttp) REVERT: G 109 LEU cc_start: 0.8506 (mt) cc_final: 0.8141 (tp) REVERT: G 113 ARG cc_start: 0.5555 (mtp-110) cc_final: 0.4782 (mmt90) REVERT: G 141 PHE cc_start: 0.5732 (m-80) cc_final: 0.5193 (t80) REVERT: H 47 ASN cc_start: 0.6622 (p0) cc_final: 0.6307 (p0) REVERT: H 81 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7626 (tm-30) REVERT: L 108 GLU cc_start: 0.8151 (tt0) cc_final: 0.7914 (tt0) REVERT: M 112 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7616 (mmm) REVERT: O 112 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7103 (tp30) REVERT: O 138 ARG cc_start: 0.6883 (pmt170) cc_final: 0.6606 (pmt170) REVERT: P 32 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7329 (tm-30) REVERT: R 70 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6423 (mt-10) REVERT: V 57 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8237 (mp) REVERT: W 41 ASN cc_start: 0.7589 (t0) cc_final: 0.7290 (t0) REVERT: W 42 MET cc_start: 0.7841 (tpp) cc_final: 0.7596 (tpp) REVERT: X 142 PHE cc_start: 0.7057 (p90) cc_final: 0.6841 (p90) REVERT: Y 14 ARG cc_start: 0.7773 (mtm110) cc_final: 0.7391 (ttm110) REVERT: b 51 ARG cc_start: 0.8576 (mtp85) cc_final: 0.8253 (mtp85) REVERT: c 45 LEU cc_start: 0.7621 (tp) cc_final: 0.7262 (pp) outliers start: 127 outliers final: 78 residues processed: 621 average time/residue: 0.8308 time to fit residues: 901.1532 Evaluate side-chains 566 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 486 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 180 PHE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 59 ASN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 76 TYR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain T residue 6 GLU Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain U residue 41 CYS Chi-restraints excluded: chain V residue 43 ILE Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 72 ILE Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 89 TYR Chi-restraints excluded: chain X residue 162 VAL Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain a residue 6 ASN Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 2 ARG Chi-restraints excluded: chain d residue 13 SER Chi-restraints excluded: chain d residue 19 ILE Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain e residue 28 THR Chi-restraints excluded: chain g residue 52 SER Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain h residue 5 VAL Chi-restraints excluded: chain h residue 22 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 571 optimal weight: 5.9990 chunk 435 optimal weight: 3.9990 chunk 300 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 276 optimal weight: 20.0000 chunk 388 optimal weight: 8.9990 chunk 580 optimal weight: 0.6980 chunk 614 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 550 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 HIS F 162 GLN G 2 ASN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN L 54 GLN ** Q 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 ASN R 101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 97535 Z= 0.244 Angle : 0.920 40.061 145588 Z= 0.387 Chirality : 0.102 2.092 18454 Planarity : 0.004 0.045 7709 Dihedral : 22.896 179.347 47946 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 4.27 % Allowed : 20.26 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3569 helix: 1.21 (0.17), residues: 1016 sheet: -0.33 (0.19), residues: 735 loop : -0.93 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP i 20 HIS 0.008 0.001 HIS X 90 PHE 0.016 0.002 PHE Q 41 TYR 0.025 0.002 TYR f 5 ARG 0.007 0.001 ARG G 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 518 time to evaluate : 4.173 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 REVERT: D 1 MET cc_start: 0.1212 (mmt) cc_final: -0.0851 (ttm) REVERT: D 227 MET cc_start: 0.6778 (mtp) cc_final: 0.6558 (mtp) REVERT: E 118 GLN cc_start: 0.8432 (tp40) cc_final: 0.8188 (tp40) REVERT: E 121 MET cc_start: 0.8309 (ttm) cc_final: 0.7751 (ttm) REVERT: F 33 TYR cc_start: 0.8762 (t80) cc_final: 0.8536 (t80) REVERT: F 205 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8413 (pm20) REVERT: G 99 MET cc_start: 0.6343 (ttp) cc_final: 0.5872 (ttp) REVERT: G 109 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8203 (tt) REVERT: H 47 ASN cc_start: 0.6777 (p0) cc_final: 0.6479 (p0) REVERT: H 81 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7711 (tm-30) REVERT: I 1 MET cc_start: 0.7710 (ttp) cc_final: 0.7116 (ttp) REVERT: M 112 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7536 (mmm) REVERT: N 1 MET cc_start: 0.8098 (mmt) cc_final: 0.7614 (mmt) REVERT: O 111 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7572 (tm-30) REVERT: O 138 ARG cc_start: 0.7179 (pmt170) cc_final: 0.6486 (pmt170) REVERT: P 32 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7393 (tm-30) REVERT: R 31 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8718 (mm) REVERT: V 5 ASP cc_start: 0.7236 (p0) cc_final: 0.6565 (p0) REVERT: W 86 GLU cc_start: 0.7569 (pp20) cc_final: 0.7268 (pp20) REVERT: W 100 ARG cc_start: 0.7793 (tpp80) cc_final: 0.6996 (mmt90) REVERT: Y 14 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7392 (ttm110) REVERT: Z 20 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8537 (mtp85) REVERT: b 51 ARG cc_start: 0.8497 (mtp85) cc_final: 0.8142 (mtp85) REVERT: b 74 ASP cc_start: 0.7643 (m-30) cc_final: 0.7410 (m-30) REVERT: c 45 LEU cc_start: 0.7453 (tp) cc_final: 0.7134 (pp) REVERT: g 51 LEU cc_start: 0.8946 (mp) cc_final: 0.8745 (mp) outliers start: 127 outliers final: 78 residues processed: 598 average time/residue: 0.8268 time to fit residues: 866.5003 Evaluate side-chains 555 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 473 time to evaluate : 4.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 180 PHE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 59 ASN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 123 GLU Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 76 TYR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain U residue 41 CYS Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 73 CYS Chi-restraints excluded: chain X residue 89 TYR Chi-restraints excluded: chain X residue 162 VAL Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain a residue 6 ASN Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain g residue 52 SER Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain h residue 5 VAL Chi-restraints excluded: chain h residue 12 GLU Chi-restraints excluded: chain h residue 22 VAL Chi-restraints excluded: chain i residue 47 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 511 optimal weight: 9.9990 chunk 348 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 457 optimal weight: 7.9990 chunk 253 optimal weight: 10.0000 chunk 524 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 313 optimal weight: 2.9990 chunk 551 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN F 162 GLN G 2 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 HIS ** Q 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN ** Z 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 ASN d 27 GLN g 32 HIS h 34 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 97535 Z= 0.354 Angle : 0.985 39.784 145588 Z= 0.425 Chirality : 0.104 2.100 18454 Planarity : 0.005 0.068 7709 Dihedral : 23.150 179.465 47946 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.12 % Rotamer: Outliers : 5.15 % Allowed : 21.54 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3569 helix: 1.01 (0.16), residues: 1005 sheet: -0.50 (0.19), residues: 709 loop : -1.09 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP i 20 HIS 0.013 0.002 HIS Q 52 PHE 0.021 0.002 PHE S 24 TYR 0.026 0.002 TYR f 5 ARG 0.011 0.001 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 484 time to evaluate : 5.369 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 revert: symmetry clash revert: symmetry clash REVERT: E 121 MET cc_start: 0.8287 (ttm) cc_final: 0.7715 (ttm) REVERT: F 33 TYR cc_start: 0.8852 (t80) cc_final: 0.8615 (t80) REVERT: G 81 LYS cc_start: 0.8396 (mmtm) cc_final: 0.7913 (ptpt) REVERT: G 99 MET cc_start: 0.6286 (ttp) cc_final: 0.5937 (ttp) REVERT: G 109 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8152 (tt) REVERT: G 113 ARG cc_start: 0.5616 (mtp-110) cc_final: 0.4972 (mmt90) REVERT: H 47 ASN cc_start: 0.6901 (p0) cc_final: 0.6697 (p0) REVERT: H 75 MET cc_start: 0.7699 (ttm) cc_final: 0.7442 (mtt) REVERT: H 81 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7788 (tm-30) REVERT: L 85 ARG cc_start: 0.8675 (mmm-85) cc_final: 0.8314 (mtp-110) REVERT: M 112 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7432 (mmm) REVERT: N 134 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8206 (mp) REVERT: O 111 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7841 (tm-30) REVERT: P 32 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7495 (tm-30) REVERT: Q 52 HIS cc_start: 0.7129 (OUTLIER) cc_final: 0.6347 (t-90) REVERT: R 31 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8811 (mm) REVERT: V 57 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8124 (mp) REVERT: W 100 ARG cc_start: 0.7898 (tpp80) cc_final: 0.7283 (mmt90) REVERT: a 1 MET cc_start: 0.6808 (tmm) cc_final: 0.6299 (tpp) REVERT: b 51 ARG cc_start: 0.8574 (mtp85) cc_final: 0.8075 (mtp85) outliers start: 153 outliers final: 103 residues processed: 586 average time/residue: 0.8607 time to fit residues: 879.1818 Evaluate side-chains 553 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 444 time to evaluate : 4.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 130 ASN Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 180 PHE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 59 ASN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 52 HIS Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 76 TYR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain U residue 41 CYS Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 72 ILE Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 73 CYS Chi-restraints excluded: chain X residue 89 TYR Chi-restraints excluded: chain X residue 162 VAL Chi-restraints excluded: chain Y residue 12 ASN Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 56 CYS Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain c residue 2 ARG Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain e residue 28 THR Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain g residue 52 SER Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain h residue 5 VAL Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 12 GLU Chi-restraints excluded: chain h residue 22 VAL Chi-restraints excluded: chain i residue 47 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 206 optimal weight: 30.0000 chunk 553 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 360 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 615 optimal weight: 10.0000 chunk 510 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN G 97 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 30 ASN h 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 97535 Z= 0.426 Angle : 1.030 40.444 145588 Z= 0.450 Chirality : 0.104 2.118 18454 Planarity : 0.005 0.070 7709 Dihedral : 23.339 179.752 47946 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.79 % Allowed : 21.88 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3569 helix: 0.75 (0.16), residues: 1011 sheet: -0.66 (0.19), residues: 682 loop : -1.24 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP i 20 HIS 0.012 0.002 HIS Q 52 PHE 0.032 0.002 PHE G 102 TYR 0.030 0.003 TYR f 5 ARG 0.009 0.001 ARG O 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 457 time to evaluate : 4.198 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: D 1 MET cc_start: 0.1674 (mmt) cc_final: 0.0442 (mtp) REVERT: D 49 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7404 (mpt90) REVERT: E 79 TYR cc_start: 0.7818 (m-80) cc_final: 0.7407 (m-80) REVERT: E 121 MET cc_start: 0.8400 (ttm) cc_final: 0.7777 (ttm) REVERT: F 33 TYR cc_start: 0.8727 (t80) cc_final: 0.8482 (t80) REVERT: G 63 ILE cc_start: 0.4062 (OUTLIER) cc_final: 0.3336 (mt) REVERT: G 84 GLN cc_start: 0.6679 (tp-100) cc_final: 0.6388 (tp40) REVERT: G 99 MET cc_start: 0.6343 (ttp) cc_final: 0.5992 (ttp) REVERT: G 105 LYS cc_start: 0.6672 (ttpt) cc_final: 0.6423 (tmtt) REVERT: G 128 ASN cc_start: 0.7691 (m-40) cc_final: 0.7428 (m110) REVERT: H 36 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7685 (p0) REVERT: H 81 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7925 (tm-30) REVERT: I 1 MET cc_start: 0.7958 (ttp) cc_final: 0.7670 (ttp) REVERT: I 22 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7279 (mmt180) REVERT: L 144 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8056 (mt) REVERT: M 112 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7459 (mmm) REVERT: N 1 MET cc_start: 0.7977 (mmt) cc_final: 0.7581 (mmt) REVERT: N 134 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8200 (mp) REVERT: P 32 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7473 (tm-30) REVERT: Q 52 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.6816 (t-90) REVERT: R 31 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8928 (mm) REVERT: S 76 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.6510 (p90) REVERT: S 107 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8468 (mmtm) REVERT: T 65 GLU cc_start: 0.7936 (pp20) cc_final: 0.7507 (pp20) REVERT: V 57 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8230 (mp) REVERT: W 85 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6698 (m-80) REVERT: a 1 MET cc_start: 0.6721 (tmm) cc_final: 0.6093 (tpp) REVERT: b 51 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8150 (mtp85) REVERT: d 45 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8921 (pp) outliers start: 172 outliers final: 116 residues processed: 579 average time/residue: 0.8263 time to fit residues: 833.9188 Evaluate side-chains 554 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 424 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 136 LYS Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 130 ASN Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 180 PHE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 59 ASN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 94 TYR Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 52 HIS Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 76 TYR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 107 LYS Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 41 CYS Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 72 ILE Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 85 PHE Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 73 CYS Chi-restraints excluded: chain X residue 89 TYR Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 142 PHE Chi-restraints excluded: chain X residue 162 VAL Chi-restraints excluded: chain Y residue 12 ASN Chi-restraints excluded: chain Y residue 16 SER Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain a residue 6 ASN Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain c residue 2 ARG Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 19 ILE Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain e residue 20 THR Chi-restraints excluded: chain g residue 17 PHE Chi-restraints excluded: chain g residue 52 SER Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain h residue 5 VAL Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 12 GLU Chi-restraints excluded: chain h residue 22 VAL Chi-restraints excluded: chain i residue 47 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 593 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 350 optimal weight: 0.9990 chunk 449 optimal weight: 7.9990 chunk 348 optimal weight: 0.9990 chunk 518 optimal weight: 9.9990 chunk 343 optimal weight: 7.9990 chunk 613 optimal weight: 9.9990 chunk 383 optimal weight: 0.0870 chunk 373 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN H 35 GLN Q 52 HIS R 11 ASN ** W 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 97535 Z= 0.212 Angle : 0.918 40.346 145588 Z= 0.387 Chirality : 0.103 2.133 18454 Planarity : 0.004 0.069 7709 Dihedral : 23.233 179.895 47946 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.87 % Allowed : 24.74 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3569 helix: 1.14 (0.17), residues: 1006 sheet: -0.50 (0.19), residues: 680 loop : -1.11 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 65 HIS 0.008 0.001 HIS X 90 PHE 0.030 0.001 PHE S 24 TYR 0.021 0.002 TYR e 43 ARG 0.014 0.000 ARG i 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 487 time to evaluate : 5.222 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: D 1 MET cc_start: 0.1475 (mmt) cc_final: 0.0521 (mtp) REVERT: D 49 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7152 (mpt90) REVERT: D 227 MET cc_start: 0.7377 (mtp) cc_final: 0.7047 (mtt) REVERT: E 79 TYR cc_start: 0.7548 (m-80) cc_final: 0.7085 (m-80) REVERT: E 121 MET cc_start: 0.8368 (ttm) cc_final: 0.7650 (ttm) REVERT: F 16 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8499 (tt) REVERT: G 84 GLN cc_start: 0.6677 (tp-100) cc_final: 0.6357 (tp40) REVERT: G 99 MET cc_start: 0.6076 (ttp) cc_final: 0.5757 (ttp) REVERT: G 109 LEU cc_start: 0.8645 (mp) cc_final: 0.8172 (tt) REVERT: G 113 ARG cc_start: 0.5398 (mtp-110) cc_final: 0.4935 (mmt180) REVERT: G 141 PHE cc_start: 0.5952 (OUTLIER) cc_final: 0.5396 (t80) REVERT: H 81 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7648 (tm-30) REVERT: I 1 MET cc_start: 0.7990 (ttp) cc_final: 0.7502 (ttp) REVERT: I 7 GLU cc_start: 0.7138 (tt0) cc_final: 0.6854 (tt0) REVERT: I 22 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7184 (mmt180) REVERT: M 112 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7291 (mmm) REVERT: N 99 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7700 (ptmt) REVERT: P 32 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7473 (tm-30) REVERT: S 76 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.6448 (p90) REVERT: T 65 GLU cc_start: 0.7889 (pp20) cc_final: 0.7628 (pp20) REVERT: V 57 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8101 (mp) REVERT: a 40 LYS cc_start: 0.8526 (tppt) cc_final: 0.8306 (tppt) REVERT: b 51 ARG cc_start: 0.8512 (mtp85) cc_final: 0.7751 (mtp85) REVERT: d 45 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8937 (pp) REVERT: e 37 LYS cc_start: 0.8639 (mmtp) cc_final: 0.8190 (mmtm) outliers start: 115 outliers final: 82 residues processed: 562 average time/residue: 0.8649 time to fit residues: 850.3903 Evaluate side-chains 549 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 459 time to evaluate : 4.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 180 PHE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 76 TYR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain U residue 41 CYS Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 89 TYR Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 162 VAL Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 56 CYS Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 2 ARG Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain e residue 20 THR Chi-restraints excluded: chain g residue 17 PHE Chi-restraints excluded: chain g residue 52 SER Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain i residue 47 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 379 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 chunk 389 optimal weight: 4.9990 chunk 417 optimal weight: 7.9990 chunk 303 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 481 optimal weight: 6.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 HIS G 2 ASN G 128 ASN Q 52 HIS ** S 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 13 ASN ** Z 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 97535 Z= 0.354 Angle : 0.984 40.677 145588 Z= 0.423 Chirality : 0.103 2.130 18454 Planarity : 0.005 0.064 7709 Dihedral : 23.283 179.817 47946 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.48 % Allowed : 24.77 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3569 helix: 0.92 (0.17), residues: 1013 sheet: -0.53 (0.19), residues: 682 loop : -1.23 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP i 20 HIS 0.009 0.002 HIS Q 52 PHE 0.058 0.002 PHE S 24 TYR 0.019 0.002 TYR T 12 ARG 0.012 0.001 ARG S 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 461 time to evaluate : 4.150 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: D 1 MET cc_start: 0.1770 (mmt) cc_final: 0.0822 (mtt) REVERT: D 49 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7169 (mpt90) REVERT: E 121 MET cc_start: 0.8425 (ttm) cc_final: 0.7738 (ttm) REVERT: F 66 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8710 (tm-30) REVERT: G 99 MET cc_start: 0.6078 (ttp) cc_final: 0.5834 (ttp) REVERT: G 113 ARG cc_start: 0.5251 (mtp-110) cc_final: 0.4874 (mmt180) REVERT: G 128 ASN cc_start: 0.7700 (m-40) cc_final: 0.7425 (m110) REVERT: G 141 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.5641 (t80) REVERT: H 81 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7849 (tm-30) REVERT: I 1 MET cc_start: 0.7994 (ttp) cc_final: 0.7587 (ttp) REVERT: I 22 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7358 (mmt180) REVERT: M 112 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7351 (mmm) REVERT: N 99 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7564 (mtmt) REVERT: O 66 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9026 (mp) REVERT: P 32 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7518 (tm-30) REVERT: Q 69 ASN cc_start: 0.7774 (t0) cc_final: 0.7483 (m-40) REVERT: R 64 SER cc_start: 0.8703 (t) cc_final: 0.8413 (p) REVERT: S 76 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.6560 (p90) REVERT: S 107 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8450 (mmtm) REVERT: U 100 ARG cc_start: 0.7194 (mtp180) cc_final: 0.6948 (mtp180) REVERT: V 57 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8169 (mp) REVERT: W 85 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: b 51 ARG cc_start: 0.8499 (mtp85) cc_final: 0.7934 (mtp85) REVERT: d 45 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8954 (pp) outliers start: 133 outliers final: 105 residues processed: 544 average time/residue: 0.8569 time to fit residues: 811.2812 Evaluate side-chains 563 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 448 time to evaluate : 4.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 136 LYS Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 97 ASN Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 180 PHE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 76 TYR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 107 LYS Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 41 CYS Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 94 LYS Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 85 PHE Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 89 TYR Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 142 PHE Chi-restraints excluded: chain X residue 162 VAL Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain a residue 6 ASN Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 60 LEU Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain c residue 2 ARG Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain e residue 23 ARG Chi-restraints excluded: chain g residue 17 PHE Chi-restraints excluded: chain g residue 50 ASN Chi-restraints excluded: chain g residue 52 SER Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain h residue 5 VAL Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 12 GLU Chi-restraints excluded: chain i residue 16 LEU Chi-restraints excluded: chain i residue 47 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 557 optimal weight: 0.0870 chunk 587 optimal weight: 10.0000 chunk 535 optimal weight: 0.5980 chunk 571 optimal weight: 20.0000 chunk 343 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 448 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 516 optimal weight: 0.7980 chunk 540 optimal weight: 6.9990 chunk 569 optimal weight: 3.9990 overall best weight: 2.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 30 ASN h 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 97535 Z= 0.155 Angle : 0.902 40.268 145588 Z= 0.376 Chirality : 0.102 2.132 18454 Planarity : 0.004 0.073 7709 Dihedral : 23.195 179.718 47946 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.30 % Allowed : 25.95 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3569 helix: 1.24 (0.17), residues: 1006 sheet: -0.40 (0.20), residues: 691 loop : -1.08 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 65 HIS 0.008 0.001 HIS X 90 PHE 0.028 0.001 PHE S 24 TYR 0.022 0.001 TYR T 12 ARG 0.008 0.000 ARG S 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 509 time to evaluate : 4.143 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: D 1 MET cc_start: 0.1103 (mmt) cc_final: -0.0946 (ttm) REVERT: D 49 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7150 (mpt90) REVERT: E 121 MET cc_start: 0.8368 (ttm) cc_final: 0.7603 (ttm) REVERT: G 109 LEU cc_start: 0.8642 (mp) cc_final: 0.8175 (tt) REVERT: G 113 ARG cc_start: 0.5261 (mtp-110) cc_final: 0.4959 (mmt180) REVERT: H 81 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7652 (tm-30) REVERT: I 1 MET cc_start: 0.7991 (ttp) cc_final: 0.7607 (ttp) REVERT: I 22 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7229 (mmt180) REVERT: M 112 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7193 (mmm) REVERT: N 99 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7693 (ptmt) REVERT: O 66 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9053 (mp) REVERT: P 32 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7510 (tm-30) REVERT: Q 69 ASN cc_start: 0.7695 (t0) cc_final: 0.7410 (m-40) REVERT: R 64 SER cc_start: 0.8615 (t) cc_final: 0.8385 (p) REVERT: S 37 ASP cc_start: 0.7157 (m-30) cc_final: 0.6924 (m-30) REVERT: W 85 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6631 (m-80) REVERT: W 86 GLU cc_start: 0.7702 (pp20) cc_final: 0.7303 (pp20) REVERT: X 89 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.6706 (p90) REVERT: X 107 PRO cc_start: 0.6525 (Cg_exo) cc_final: 0.6314 (Cg_endo) REVERT: b 51 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8162 (mtp85) REVERT: c 15 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7718 (tptp) REVERT: d 45 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8894 (pt) REVERT: g 33 ILE cc_start: 0.8711 (pt) cc_final: 0.8328 (pt) outliers start: 98 outliers final: 75 residues processed: 571 average time/residue: 0.8259 time to fit residues: 823.2959 Evaluate side-chains 556 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 474 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 136 LYS Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 97 ASN Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain G residue 180 PHE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 76 TYR Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain U residue 41 CYS Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 85 PHE Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 89 TYR Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 162 VAL Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 46 LEU Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 56 CYS Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 2 ARG Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain e residue 23 ARG Chi-restraints excluded: chain g residue 17 PHE Chi-restraints excluded: chain g residue 50 ASN Chi-restraints excluded: chain h residue 12 GLU Chi-restraints excluded: chain i residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 375 optimal weight: 20.0000 chunk 604 optimal weight: 2.9990 chunk 368 optimal weight: 0.0980 chunk 286 optimal weight: 20.0000 chunk 419 optimal weight: 1.9990 chunk 633 optimal weight: 9.9990 chunk 583 optimal weight: 8.9990 chunk 504 optimal weight: 0.4980 chunk 52 optimal weight: 9.9990 chunk 389 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN G 2 ASN G 128 ASN L 53 HIS ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 13 ASN X 60 ASN ** Z 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.129 97535 Z= 0.145 Angle : 0.888 40.536 145588 Z= 0.366 Chirality : 0.102 2.146 18454 Planarity : 0.004 0.073 7709 Dihedral : 23.060 179.812 47946 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.73 % Allowed : 26.62 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3569 helix: 1.38 (0.17), residues: 1001 sheet: -0.34 (0.19), residues: 722 loop : -0.94 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 251 HIS 0.007 0.001 HIS X 90 PHE 0.063 0.001 PHE E 117 TYR 0.021 0.001 TYR T 12 ARG 0.019 0.000 ARG U 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7138 Ramachandran restraints generated. 3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 526 time to evaluate : 4.590 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: D 1 MET cc_start: 0.1246 (mmt) cc_final: -0.0071 (mtt) REVERT: D 49 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7173 (mpt90) REVERT: E 121 MET cc_start: 0.8430 (ttm) cc_final: 0.7746 (ttm) REVERT: F 66 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8607 (tm-30) REVERT: G 113 ARG cc_start: 0.5180 (mtp-110) cc_final: 0.4703 (mmt180) REVERT: G 128 ASN cc_start: 0.7421 (m-40) cc_final: 0.7189 (m110) REVERT: H 81 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7872 (tm-30) REVERT: I 1 MET cc_start: 0.7848 (ttp) cc_final: 0.7320 (ttp) REVERT: I 22 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.7116 (mmt180) REVERT: M 112 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7252 (mmm) REVERT: N 136 ILE cc_start: 0.9050 (tp) cc_final: 0.8759 (mt) REVERT: P 32 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7499 (tm-30) REVERT: R 64 SER cc_start: 0.8602 (t) cc_final: 0.8384 (p) REVERT: W 85 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6642 (m-80) REVERT: W 86 GLU cc_start: 0.7510 (pp20) cc_final: 0.7211 (pp20) REVERT: Y 14 ARG cc_start: 0.7806 (mtm110) cc_final: 0.7581 (mtm-85) REVERT: b 51 ARG cc_start: 0.8543 (mtp85) cc_final: 0.7733 (mtp85) REVERT: c 11 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5518 (mt) REVERT: c 41 LYS cc_start: 0.6793 (pttt) cc_final: 0.5941 (mptt) REVERT: d 45 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8907 (pt) outliers start: 81 outliers final: 67 residues processed: 577 average time/residue: 0.8720 time to fit residues: 887.7299 Evaluate side-chains 553 residues out of total 3165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 480 time to evaluate : 4.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 136 LYS Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain G residue 180 PHE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 54 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 76 TYR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 85 PHE Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 89 TYR Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 162 VAL Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 46 LEU Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 56 CYS Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 2 ARG Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain e residue 23 ARG Chi-restraints excluded: chain g residue 17 PHE Chi-restraints excluded: chain g residue 50 ASN Chi-restraints excluded: chain g residue 52 SER Chi-restraints excluded: chain h residue 12 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 400 optimal weight: 50.0000 chunk 537 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 465 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 505 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 518 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 overall best weight: 5.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN R 101 ASN ** S 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 13 ASN ** V 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 30 ASN h 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.067486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.052258 restraints weight = 411199.761| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.97 r_work: 0.2935 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 97535 Z= 0.316 Angle : 0.967 40.667 145588 Z= 0.413 Chirality : 0.103 2.147 18454 Planarity : 0.005 0.048 7709 Dihedral : 23.180 179.656 47946 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.33 % Allowed : 26.69 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3569 helix: 1.07 (0.17), residues: 1007 sheet: -0.46 (0.19), residues: 698 loop : -1.12 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP i 20 HIS 0.018 0.002 HIS L 53 PHE 0.073 0.002 PHE E 117 TYR 0.026 0.002 TYR G 3 ARG 0.012 0.001 ARG U 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16925.60 seconds wall clock time: 302 minutes 59.82 seconds (18179.82 seconds total)