Starting phenix.real_space_refine on Fri Feb 16 01:14:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4j_32305/02_2024/7w4j_32305_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4j_32305/02_2024/7w4j_32305.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4j_32305/02_2024/7w4j_32305_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4j_32305/02_2024/7w4j_32305_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4j_32305/02_2024/7w4j_32305_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4j_32305/02_2024/7w4j_32305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4j_32305/02_2024/7w4j_32305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4j_32305/02_2024/7w4j_32305_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4j_32305/02_2024/7w4j_32305_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 36 5.49 5 Mg 1 5.21 5 S 474 5.16 5 C 43027 2.51 5 N 11095 2.21 5 O 11945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "G TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "I GLU 30": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "K PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M GLU 118": "OE1" <-> "OE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M GLU 244": "OE1" <-> "OE2" Residue "M GLU 269": "OE1" <-> "OE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 284": "OE1" <-> "OE2" Residue "M GLU 320": "OE1" <-> "OE2" Residue "M TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "M PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 647": "OE1" <-> "OE2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "N PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "Q GLU 370": "OE1" <-> "OE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 49": "OE1" <-> "OE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 130": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "a GLU 153": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "b GLU 112": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "d TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "d GLU 67": "OE1" <-> "OE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d GLU 117": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "e GLU 130": "OE1" <-> "OE2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 105": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "j GLU 68": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "l GLU 102": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 445": "OE1" <-> "OE2" Residue "l TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 559": "OE1" <-> "OE2" Residue "m GLU 138": "OE1" <-> "OE2" Residue "m GLU 139": "OE1" <-> "OE2" Residue "o GLU 28": "OE1" <-> "OE2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p GLU 131": "OE1" <-> "OE2" Residue "p GLU 136": "OE1" <-> "OE2" Residue "p GLU 142": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 253": "OE1" <-> "OE2" Residue "u GLU 42": "OE1" <-> "OE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "u GLU 149": "OE1" <-> "OE2" Residue "u GLU 153": "OE1" <-> "OE2" Residue "u GLU 155": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "w TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 197": "OE1" <-> "OE2" Residue "w GLU 213": "OE1" <-> "OE2" Residue "w GLU 267": "OE1" <-> "OE2" Residue "w GLU 271": "OE1" <-> "OE2" Residue "w GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 66607 Number of models: 1 Model: "" Number of chains: 65 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1244 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2359 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3377 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 27, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1009 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 133} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1173 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "X" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 597 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 671 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 80} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 868 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4780 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "m" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 948 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1058 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 71 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "i" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 165 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "j" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 244 Unusual residues: {'CDL': 1, 'PEE': 2, 'PLX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "m" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "r" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 203 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {' UQ': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 35 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2706 SG CYS A 382 48.047 49.426 173.330 1.00 37.56 S ATOM 3048 SG CYS A 425 47.515 45.409 178.663 1.00 29.51 S ATOM 2726 SG CYS A 385 45.033 44.765 173.015 1.00 23.70 S ATOM 2687 SG CYS A 379 42.825 49.568 177.232 1.00 28.61 S ATOM 3949 SG CYS B 113 36.799 67.794 139.331 1.00 25.52 S ATOM 3968 SG CYS B 116 41.880 64.922 142.983 1.00 19.73 S ATOM 3991 SG CYS B 119 42.950 68.034 137.632 1.00 17.93 S ATOM 4320 SG CYS B 162 40.156 62.317 138.030 1.00 14.62 S ATOM 4018 SG CYS B 123 49.111 70.844 133.083 1.00 15.08 S ATOM 4244 SG CYS B 152 47.141 69.547 127.160 1.00 19.87 S ATOM 4291 SG CYS B 158 44.987 65.730 131.895 1.00 23.12 S ATOM 4270 SG CYS B 155 51.294 65.866 130.272 1.00 19.74 S ATOM 5708 SG CYS C 166 53.323 69.738 122.962 1.00 16.95 S ATOM 4978 SG CYS C 71 58.304 69.662 118.733 1.00 18.70 S ATOM 4984 SG CYS C 72 54.718 71.578 116.716 1.00 12.72 S ATOM 4978 SG CYS C 71 58.304 69.662 118.733 1.00 18.70 S ATOM 5478 SG CYS C 136 56.040 74.370 121.782 1.00 25.35 S ATOM 14534 SG CYS M 131 41.353 64.166 155.170 1.00 0.51 S ATOM 14513 SG CYS M 128 44.786 59.719 151.702 1.00 18.15 S ATOM 14574 SG CYS M 137 46.906 62.879 157.104 1.00 13.62 S ATOM 14906 SG CYS M 179 45.376 62.276 168.396 1.00 20.61 S ATOM 15260 SG CYS M 226 42.297 65.214 164.347 1.00 17.76 S ATOM 14930 SG CYS M 182 39.969 64.887 170.454 1.00 11.42 S ATOM 14883 SG CYS M 176 39.723 59.603 166.554 1.00 18.10 S ATOM 14131 SG CYS M 78 56.826 57.149 171.544 1.00 19.64 S ATOM 14232 SG CYS M 92 55.002 58.793 174.358 1.00 32.79 S ATOM 14020 SG CYS M 64 50.737 59.235 171.862 1.00 26.42 S ATOM 14106 SG CYS M 75 51.838 57.571 168.722 1.00 17.79 S ATOM 21069 SG CYS O 135 31.686 31.798 180.282 1.00 59.46 S ATOM 21103 SG CYS O 140 31.549 28.307 180.945 1.00 73.80 S ATOM 21383 SG CYS O 176 36.244 33.233 182.758 1.00 67.54 S ATOM 21406 SG CYS O 180 36.545 29.767 183.230 1.00 69.50 S ATOM 28064 SG CYS T 86 29.419 53.971 146.536 1.00 30.81 S ATOM 28242 SG CYS T 111 30.392 57.329 147.566 1.00 32.44 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.70 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.70 Time building chain proxies: 26.40, per 1000 atoms: 0.40 Number of scatterers: 66607 At special positions: 0 Unit cell: (211.895, 228.363, 229.461, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 474 16.00 P 36 15.00 Mg 1 11.99 O 11945 8.00 N 11095 7.00 C 43027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.10 Conformation dependent library (CDL) restraints added in 9.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15286 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 339 helices and 29 sheets defined 52.9% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.59 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.529A pdb=" N ASN A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.761A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.069A pdb=" N ASP A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 77 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 180 through 183 Processing helix chain 'B' and resid 187 through 211 removed outlier: 6.072A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.555A pdb=" N VAL C 47 " --> pdb=" O GLY C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 123 Proline residue: C 115 - end of helix removed outlier: 3.554A pdb=" N GLN C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.226A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.365A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.601A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 137 removed outlier: 4.960A pdb=" N LYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.990A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 76 removed outlier: 4.172A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 97 removed outlier: 3.845A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 120 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 219 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 317 through 323 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 345 through 356 removed outlier: 4.567A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 removed outlier: 3.834A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 80' Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.324A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 120 through 123 removed outlier: 4.392A pdb=" N ASN L 123 " --> pdb=" O PRO L 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 120 through 123' Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 160 through 164 Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 145 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.844A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 359 Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 390 through 396 removed outlier: 3.732A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 390 through 396' Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 480 No H-bonds generated for 'chain 'M' and resid 478 through 480' Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 521 through 527 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 575 through 578 No H-bonds generated for 'chain 'M' and resid 575 through 578' Processing helix chain 'M' and resid 619 through 629 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 671 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.702A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.284A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.710A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 173 removed outlier: 3.729A pdb=" N ASN P 164 " --> pdb=" O LYS P 161 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 48 removed outlier: 4.133A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY Q 48 " --> pdb=" O ALA Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 60 removed outlier: 4.205A pdb=" N HIS Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 57 through 60' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.779A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 139 Proline residue: Q 134 - end of helix removed outlier: 4.228A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 4.403A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 251 through 262 Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.395A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 438 removed outlier: 4.385A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 3.777A pdb=" N VAL Q 448 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 29 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 44 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 54 Processing helix chain 'T' and resid 67 through 73 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 3 through 13 Processing helix chain 'U' and resid 17 through 34 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 4 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 32 through 99 Proline residue: W 73 - end of helix removed outlier: 3.692A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 124 No H-bonds generated for 'chain 'W' and resid 121 through 124' Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.369A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.134A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 78 through 81 No H-bonds generated for 'chain 'Y' and resid 78 through 81' Processing helix chain 'Z' and resid 28 through 37 Processing helix chain 'Z' and resid 50 through 53 Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.811A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 65 through 74 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 126 through 149 Processing helix chain 'd' and resid 29 through 57 removed outlier: 4.686A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 143 removed outlier: 6.461A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA d 126 " --> pdb=" O ARG d 122 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LYS d 127 " --> pdb=" O GLN d 123 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU d 128 " --> pdb=" O ASN d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 removed outlier: 4.139A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 115 through 132 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 4 through 6 No H-bonds generated for 'chain 'g' and resid 4 through 6' Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 55 Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 removed outlier: 3.627A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.320A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.819A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.930A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 193 removed outlier: 4.098A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.591A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 273 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.455A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 removed outlier: 3.575A pdb=" N MET i 313 " --> pdb=" O ASN i 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 345 Proline residue: i 341 - end of helix removed outlier: 3.502A pdb=" N SER i 344 " --> pdb=" O PRO i 341 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 27 Proline residue: j 25 - end of helix Processing helix chain 'j' and resid 53 through 78 Proline residue: j 74 - end of helix removed outlier: 5.716A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 54 through 85 removed outlier: 3.922A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 23 removed outlier: 3.743A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.707A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 28 Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.553A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 84 through 107 Proline residue: l 91 - end of helix removed outlier: 3.927A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 133 Processing helix chain 'l' and resid 137 through 155 removed outlier: 3.625A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.955A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 4.333A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.226A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 272 through 294 removed outlier: 4.778A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 319 Processing helix chain 'l' and resid 322 through 349 removed outlier: 3.721A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 387 through 400 removed outlier: 4.014A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 430 Processing helix chain 'l' and resid 448 through 470 removed outlier: 3.743A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 487 No H-bonds generated for 'chain 'l' and resid 484 through 487' Processing helix chain 'l' and resid 489 through 509 removed outlier: 3.817A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 529 through 547 Proline residue: l 537 - end of helix removed outlier: 3.836A pdb=" N MET l 544 " --> pdb=" O HIS l 540 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.881A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 148 removed outlier: 4.169A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER m 148 " --> pdb=" O ALA m 144 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 8 through 35 removed outlier: 6.511A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.645A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU n 35 " --> pdb=" O SER n 31 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 23 No H-bonds generated for 'chain 'o' and resid 20 through 23' Processing helix chain 'o' and resid 27 through 51 Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 48 Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 66 through 73 Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.828A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS p 138 " --> pdb=" O GLU p 134 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 16 Proline residue: r 7 - end of helix removed outlier: 4.133A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.308A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.908A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.421A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.732A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.633A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 142 through 170 removed outlier: 4.066A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.649A pdb=" N VAL r 162 " --> pdb=" O LEU r 158 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 204 removed outlier: 4.052A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.239A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 235 through 249 removed outlier: 4.514A pdb=" N GLY r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.843A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.513A pdb=" N MET r 263 " --> pdb=" O TYR r 259 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER r 273 " --> pdb=" O MET r 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.698A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 392 through 415 removed outlier: 3.624A pdb=" N THR r 414 " --> pdb=" O MET r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.176A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.821A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.390A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 4.394A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.920A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.593A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 177 No H-bonds generated for 'chain 's' and resid 174 through 177' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 311 removed outlier: 5.167A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 12 No H-bonds generated for 'chain 'u' and resid 10 through 12' Processing helix chain 'u' and resid 22 through 35 removed outlier: 5.020A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 101 through 114 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 27 through 29 No H-bonds generated for 'chain 'v' and resid 27 through 29' Processing helix chain 'v' and resid 43 through 48 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 96 No H-bonds generated for 'chain 'w' and resid 94 through 96' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 195 Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 244 Processing helix chain 'w' and resid 246 through 249 No H-bonds generated for 'chain 'w' and resid 246 through 249' Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 306 through 309 removed outlier: 4.034A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 309' Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.578A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.035A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.444A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 removed outlier: 6.978A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.467A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= I, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= J, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= K, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= L, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= M, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= N, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= O, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.712A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'M' and resid 513 through 516 removed outlier: 6.284A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= R, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.646A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.939A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.880A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= V, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.773A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= X, first strand: chain 'T' and resid 77 through 79 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Z, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AA, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.346A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.585A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'w' and resid 84 through 86 2922 hydrogen bonds defined for protein. 8238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.85 Time building geometry restraints manager: 23.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27268 1.40 - 1.62: 40065 1.62 - 1.84: 844 1.84 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 68257 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.265 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.289 0.239 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.632 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.299 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.301 0.223 2.00e-02 2.50e+03 1.25e+02 ... (remaining 68252 not shown) Histogram of bond angle deviations from ideal: 73.65 - 86.03: 76 86.03 - 98.41: 3 98.41 - 110.79: 23623 110.79 - 123.17: 65714 123.17 - 135.55: 2944 Bond angle restraints: 92360 Sorted by residual: angle pdb=" N HIS Q 233 " pdb=" CA HIS Q 233 " pdb=" C HIS Q 233 " ideal model delta sigma weight residual 111.28 122.29 -11.01 1.09e+00 8.42e-01 1.02e+02 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.64 -15.90 1.95e+00 2.62e-01 6.62e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.72 -14.88 1.91e+00 2.73e-01 6.04e+01 angle pdb=" N ASP Q 140 " pdb=" CA ASP Q 140 " pdb=" C ASP Q 140 " ideal model delta sigma weight residual 108.34 95.70 12.64 1.64e+00 3.72e-01 5.94e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.53 -9.20 1.32e+00 5.72e-01 4.85e+01 ... (remaining 92355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 39775 35.04 - 70.07: 1511 70.07 - 105.11: 125 105.11 - 140.14: 29 140.14 - 175.18: 15 Dihedral angle restraints: 41455 sinusoidal: 17753 harmonic: 23702 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual 257.59 82.41 175.18 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 100.27 -160.27 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" CA GLU C 126 " pdb=" C GLU C 126 " pdb=" N PRO C 127 " pdb=" CA PRO C 127 " ideal model delta harmonic sigma weight residual 0.00 33.84 -33.84 0 5.00e+00 4.00e-02 4.58e+01 ... (remaining 41452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 9305 0.081 - 0.162: 679 0.162 - 0.243: 39 0.243 - 0.323: 9 0.323 - 0.404: 3 Chirality restraints: 10035 Sorted by residual: chirality pdb=" CA PHE l 429 " pdb=" N PHE l 429 " pdb=" C PHE l 429 " pdb=" CB PHE l 429 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.35 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA ILE r 246 " pdb=" N ILE r 246 " pdb=" C ILE r 246 " pdb=" CB ILE r 246 " both_signs ideal model delta sigma weight residual False 2.43 2.08 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 10032 not shown) Planarity restraints: 11551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " -0.209 2.00e-02 2.50e+03 4.81e-01 2.89e+03 pdb=" C11 UQ s 402 " -0.345 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " -0.568 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " 0.706 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " 0.416 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " -0.281 2.00e-02 2.50e+03 2.76e-01 9.50e+02 pdb=" C18 UQ s 402 " 0.246 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " 0.370 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " -0.012 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " -0.322 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.129 2.00e-02 2.50e+03 2.54e-01 8.04e+02 pdb=" C3N NDP J 401 " 0.420 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.056 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.288 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.205 2.00e-02 2.50e+03 ... (remaining 11548 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5025 2.74 - 3.28: 66390 3.28 - 3.82: 112529 3.82 - 4.36: 137256 4.36 - 4.90: 234621 Nonbonded interactions: 555821 Sorted by model distance: nonbonded pdb=" OG1 THR l 387 " pdb=" O SER l 461 " model vdw 2.198 2.440 nonbonded pdb=" O TRP A 413 " pdb=" OG SER A 416 " model vdw 2.201 2.440 nonbonded pdb=" OE1 GLU s 24 " pdb=" OH TYR s 228 " model vdw 2.203 2.440 nonbonded pdb=" OG SER r 82 " pdb=" OE1 GLU r 335 " model vdw 2.205 2.440 nonbonded pdb=" N MET G 139 " pdb=" OE2 GLU G 143 " model vdw 2.205 2.520 ... (remaining 555816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 69 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 or (resid 96 through 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 156 or resid 201)) selection = (chain 'X' and (resid 69 through 149 or (resid 150 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.70 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 8.490 Check model and map are aligned: 0.760 Set scattering table: 0.490 Process input model: 155.920 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 0.312 68257 Z= 0.413 Angle : 0.770 17.529 92360 Z= 0.402 Chirality : 0.044 0.404 10035 Planarity : 0.008 0.481 11551 Dihedral : 18.146 175.179 26151 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 0.21 % Allowed : 15.15 % Favored : 84.64 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.85 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: 1.04 (0.10), residues: 8027 helix: 1.67 (0.08), residues: 4237 sheet: 0.44 (0.25), residues: 438 loop : -0.52 (0.11), residues: 3352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP l 144 HIS 0.008 0.001 HIS A 457 PHE 0.031 0.001 PHE i 292 TYR 0.025 0.001 TYR P 64 ARG 0.005 0.000 ARG K 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1168 time to evaluate : 5.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: M 145 MET cc_start: 0.9229 (mmt) cc_final: 0.8962 (mmt) REVERT: P 79 SER cc_start: 0.9246 (p) cc_final: 0.9039 (m) REVERT: T 47 ASP cc_start: 0.6842 (t0) cc_final: 0.6630 (t0) REVERT: l 230 HIS cc_start: 0.8676 (p-80) cc_final: 0.7931 (p-80) REVERT: l 599 MET cc_start: 0.7919 (mmm) cc_final: 0.7649 (mmt) REVERT: m 57 PHE cc_start: 0.8587 (m-80) cc_final: 0.8382 (m-80) REVERT: n 30 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7219 (ttp80) REVERT: o 19 ASP cc_start: 0.8441 (t0) cc_final: 0.8178 (t0) REVERT: s 54 LYS cc_start: 0.8970 (tmtt) cc_final: 0.8638 (tmmt) REVERT: s 194 ASN cc_start: 0.8329 (m-40) cc_final: 0.8101 (m-40) REVERT: u 87 THR cc_start: 0.9178 (m) cc_final: 0.8867 (m) REVERT: u 172 MET cc_start: 0.8899 (mtp) cc_final: 0.8695 (mtm) REVERT: v 103 GLU cc_start: 0.8030 (tp30) cc_final: 0.7556 (tp30) outliers start: 15 outliers final: 6 residues processed: 1175 average time/residue: 0.6732 time to fit residues: 1336.6870 Evaluate side-chains 1122 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1115 time to evaluate : 5.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain i residue 119 THR Chi-restraints excluded: chain l residue 488 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 0.8980 chunk 601 optimal weight: 1.9990 chunk 333 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 405 optimal weight: 8.9990 chunk 321 optimal weight: 5.9990 chunk 621 optimal weight: 0.7980 chunk 240 optimal weight: 0.8980 chunk 377 optimal weight: 0.0770 chunk 462 optimal weight: 7.9990 chunk 720 optimal weight: 2.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN N 116 ASN O 106 GLN Q 190 HIS Q 234 GLN Z 33 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 73 ASN k 7 ASN l 2 ASN l 170 GLN v 54 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.0485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 68257 Z= 0.161 Angle : 0.524 12.121 92360 Z= 0.260 Chirality : 0.040 0.195 10035 Planarity : 0.004 0.066 11551 Dihedral : 13.933 179.044 10184 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 1.89 % Allowed : 14.54 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 1.20 (0.10), residues: 8027 helix: 1.83 (0.08), residues: 4242 sheet: 0.45 (0.25), residues: 440 loop : -0.49 (0.11), residues: 3345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP u 86 HIS 0.005 0.001 HIS p 33 PHE 0.030 0.001 PHE i 292 TYR 0.025 0.001 TYR r 406 ARG 0.005 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1156 time to evaluate : 5.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: C 119 LYS cc_start: 0.8884 (tttt) cc_final: 0.8622 (tttm) REVERT: F 40 ARG cc_start: 0.7804 (ptp-170) cc_final: 0.7234 (mtm180) REVERT: H 54 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6993 (mt-10) REVERT: H 85 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: M 145 MET cc_start: 0.9198 (mmt) cc_final: 0.8928 (mmt) REVERT: M 539 LYS cc_start: 0.7831 (mmmt) cc_final: 0.7547 (mmtt) REVERT: P 79 SER cc_start: 0.9253 (p) cc_final: 0.9036 (m) REVERT: T 47 ASP cc_start: 0.6826 (t0) cc_final: 0.6617 (t0) REVERT: a 78 THR cc_start: 0.8392 (m) cc_final: 0.8086 (m) REVERT: a 134 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8785 (mm-30) REVERT: c 111 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8528 (ttm) REVERT: d 59 ASN cc_start: 0.7047 (t0) cc_final: 0.6734 (t0) REVERT: l 1 MET cc_start: 0.6027 (tmm) cc_final: 0.5811 (tmm) REVERT: l 511 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8783 (mp) REVERT: l 584 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.8001 (pt) REVERT: l 599 MET cc_start: 0.7894 (mmm) cc_final: 0.7692 (mmt) REVERT: n 30 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7222 (ttp80) REVERT: o 19 ASP cc_start: 0.8381 (t0) cc_final: 0.8063 (t0) REVERT: o 28 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7669 (tp30) REVERT: s 54 LYS cc_start: 0.9003 (tmtt) cc_final: 0.8754 (tmmt) REVERT: s 56 PHE cc_start: 0.8314 (m-10) cc_final: 0.7963 (m-80) REVERT: s 270 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8466 (t80) REVERT: u 87 THR cc_start: 0.9096 (m) cc_final: 0.8712 (m) REVERT: u 172 MET cc_start: 0.8900 (mtp) cc_final: 0.8692 (mtm) REVERT: v 84 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7885 (tp-100) REVERT: v 105 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7487 (tm-30) outliers start: 133 outliers final: 68 residues processed: 1231 average time/residue: 0.6392 time to fit residues: 1332.3047 Evaluate side-chains 1185 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1109 time to evaluate : 5.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 608 VAL Chi-restraints excluded: chain O residue 200 ASP Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 151 LYS Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 170 GLN Chi-restraints excluded: chain l residue 305 SER Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain l residue 589 LEU Chi-restraints excluded: chain m residue 18 VAL Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 184 MET Chi-restraints excluded: chain s residue 246 SER Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 134 ASP Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 0.0370 chunk 223 optimal weight: 6.9990 chunk 599 optimal weight: 7.9990 chunk 490 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 721 optimal weight: 0.6980 chunk 779 optimal weight: 6.9990 chunk 642 optimal weight: 9.9990 chunk 715 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 578 optimal weight: 1.9990 overall best weight: 2.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN N 116 ASN O 106 GLN P 75 GLN P 77 GLN Z 33 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 GLN l 2 ASN r 338 HIS v 54 GLN w 215 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 68257 Z= 0.306 Angle : 0.586 11.174 92360 Z= 0.293 Chirality : 0.043 0.222 10035 Planarity : 0.005 0.060 11551 Dihedral : 13.334 176.398 10176 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.85 % Rotamer: Outliers : 2.78 % Allowed : 15.04 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 0.99 (0.09), residues: 8027 helix: 1.66 (0.08), residues: 4247 sheet: 0.31 (0.25), residues: 424 loop : -0.57 (0.11), residues: 3356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS Q 233 PHE 0.034 0.002 PHE i 292 TYR 0.021 0.002 TYR r 406 ARG 0.006 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1317 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1121 time to evaluate : 5.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 HIS cc_start: 0.6460 (m90) cc_final: 0.6185 (m-70) REVERT: B 76 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7249 (t80) REVERT: F 68 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7486 (ttp80) REVERT: H 70 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7082 (mt-10) REVERT: K 93 LEU cc_start: 0.8821 (mt) cc_final: 0.8617 (mt) REVERT: M 133 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8846 (tp40) REVERT: M 145 MET cc_start: 0.9195 (mmt) cc_final: 0.8915 (mmt) REVERT: M 387 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8658 (tp) REVERT: M 539 LYS cc_start: 0.7819 (mmmt) cc_final: 0.7530 (mmtt) REVERT: Q 308 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.7346 (p90) REVERT: S 64 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8468 (mmtt) REVERT: T 47 ASP cc_start: 0.6877 (t0) cc_final: 0.6660 (t0) REVERT: Z 72 LYS cc_start: 0.7672 (mtpt) cc_final: 0.6696 (mmtt) REVERT: c 111 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8653 (ttm) REVERT: d 59 ASN cc_start: 0.7191 (t0) cc_final: 0.6906 (t0) REVERT: f 68 GLU cc_start: 0.8635 (tp30) cc_final: 0.8399 (tp30) REVERT: j 8 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8215 (mp) REVERT: l 1 MET cc_start: 0.6098 (tmm) cc_final: 0.5832 (tmm) REVERT: l 511 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8852 (mp) REVERT: l 584 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8155 (pt) REVERT: n 30 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7184 (ttp80) REVERT: o 19 ASP cc_start: 0.8424 (t0) cc_final: 0.8122 (t0) REVERT: p 62 GLN cc_start: 0.8169 (tp40) cc_final: 0.7780 (tp40) REVERT: r 14 MET cc_start: 0.9109 (tmm) cc_final: 0.8746 (ttp) REVERT: s 54 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8633 (tmmt) REVERT: s 56 PHE cc_start: 0.8558 (m-10) cc_final: 0.8253 (m-80) REVERT: s 150 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9052 (tp) REVERT: s 270 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8756 (t80) REVERT: u 87 THR cc_start: 0.9122 (m) cc_final: 0.8756 (m) REVERT: u 172 MET cc_start: 0.8928 (mtp) cc_final: 0.8683 (mtm) REVERT: v 105 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: w 75 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6961 (mtt180) REVERT: w 261 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6602 (ttt90) outliers start: 196 outliers final: 123 residues processed: 1240 average time/residue: 0.7021 time to fit residues: 1491.6658 Evaluate side-chains 1209 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1071 time to evaluate : 5.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 133 GLN Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 608 VAL Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 178 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 151 LYS Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 171 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 119 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 305 SER Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain l residue 589 LEU Chi-restraints excluded: chain m residue 18 VAL Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain r residue 9 THR Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 272 THR Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 246 SER Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain u residue 121 ASP Chi-restraints excluded: chain u residue 134 ASP Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 75 ARG Chi-restraints excluded: chain w residue 215 GLN Chi-restraints excluded: chain w residue 261 ARG Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 4.9990 chunk 542 optimal weight: 0.0980 chunk 374 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 344 optimal weight: 10.0000 chunk 484 optimal weight: 7.9990 chunk 724 optimal weight: 0.9980 chunk 766 optimal weight: 10.0000 chunk 378 optimal weight: 7.9990 chunk 686 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN H 71 GLN I 51 ASN J 79 GLN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 569 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN N 116 ASN O 106 GLN P 75 GLN P 77 GLN Z 33 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 GLN l 2 ASN l 170 GLN v 54 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 68257 Z= 0.230 Angle : 0.542 10.847 92360 Z= 0.271 Chirality : 0.042 0.216 10035 Planarity : 0.004 0.054 11551 Dihedral : 12.651 176.019 10173 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 2.83 % Allowed : 15.93 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 1.03 (0.09), residues: 8027 helix: 1.72 (0.08), residues: 4240 sheet: 0.31 (0.25), residues: 422 loop : -0.58 (0.11), residues: 3365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.005 0.001 HIS p 33 PHE 0.033 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.003 0.000 ARG N 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1123 time to evaluate : 5.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: B 76 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.7538 (t80) REVERT: F 68 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7452 (ttp80) REVERT: H 70 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7069 (mt-10) REVERT: H 85 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: K 100 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8179 (mt0) REVERT: M 145 MET cc_start: 0.9158 (mmt) cc_final: 0.8854 (mmt) REVERT: Q 270 ASN cc_start: 0.8737 (m110) cc_final: 0.8303 (m110) REVERT: Q 308 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.7329 (p90) REVERT: S 64 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8475 (mmtt) REVERT: T 47 ASP cc_start: 0.6827 (t0) cc_final: 0.6622 (t0) REVERT: Z 72 LYS cc_start: 0.7647 (mtpt) cc_final: 0.6724 (mmtt) REVERT: c 111 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8602 (ttm) REVERT: c 113 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8897 (pt) REVERT: c 142 PHE cc_start: 0.8561 (t80) cc_final: 0.8273 (t80) REVERT: d 59 ASN cc_start: 0.7108 (t0) cc_final: 0.6847 (t0) REVERT: f 72 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7739 (mtt180) REVERT: k 22 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6685 (m-80) REVERT: l 1 MET cc_start: 0.6071 (tmm) cc_final: 0.5800 (tmm) REVERT: l 90 ILE cc_start: 0.8618 (mm) cc_final: 0.8058 (mm) REVERT: l 129 MET cc_start: 0.8677 (mmp) cc_final: 0.8473 (mmp) REVERT: l 184 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9080 (tp) REVERT: l 340 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.7676 (t80) REVERT: l 511 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8886 (mp) REVERT: l 584 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7990 (pt) REVERT: n 30 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7144 (ttp80) REVERT: o 19 ASP cc_start: 0.8468 (t0) cc_final: 0.8163 (t0) REVERT: p 62 GLN cc_start: 0.8195 (tp40) cc_final: 0.7861 (tp40) REVERT: r 14 MET cc_start: 0.9051 (tmm) cc_final: 0.8719 (ttp) REVERT: s 54 LYS cc_start: 0.9019 (tmtt) cc_final: 0.8688 (tmmt) REVERT: s 56 PHE cc_start: 0.8537 (m-10) cc_final: 0.8212 (m-80) REVERT: s 108 MET cc_start: 0.8827 (mmm) cc_final: 0.8265 (mtt) REVERT: s 150 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9077 (tp) REVERT: s 270 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8743 (t80) REVERT: u 76 ARG cc_start: 0.8020 (ttp-110) cc_final: 0.7776 (ttp-110) REVERT: u 87 THR cc_start: 0.9083 (m) cc_final: 0.8719 (m) REVERT: u 172 MET cc_start: 0.8936 (mtp) cc_final: 0.8706 (mtm) REVERT: v 105 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: w 75 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6911 (mtt180) outliers start: 200 outliers final: 118 residues processed: 1252 average time/residue: 0.6644 time to fit residues: 1413.7297 Evaluate side-chains 1226 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1090 time to evaluate : 5.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain M residue 608 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 200 ASP Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 178 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 151 LYS Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 119 THR Chi-restraints excluded: chain i residue 160 LEU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 184 LEU Chi-restraints excluded: chain l residue 305 SER Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain l residue 589 LEU Chi-restraints excluded: chain m residue 18 VAL Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 44 VAL Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 129 ASP Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 272 THR Chi-restraints excluded: chain r residue 440 HIS Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 193 THR Chi-restraints excluded: chain s residue 246 SER Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 121 ASP Chi-restraints excluded: chain u residue 134 ASP Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 75 ARG Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 244 THR Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 638 optimal weight: 8.9990 chunk 435 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 570 optimal weight: 7.9990 chunk 316 optimal weight: 7.9990 chunk 654 optimal weight: 5.9990 chunk 529 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 391 optimal weight: 2.9990 chunk 688 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN E 95 ASN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN J 79 GLN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS M 202 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN P 75 GLN ** P 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 454 GLN S 44 GLN Z 33 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 2 ASN s 235 ASN v 54 GLN ** v 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 215 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 68257 Z= 0.452 Angle : 0.680 11.660 92360 Z= 0.342 Chirality : 0.047 0.225 10035 Planarity : 0.006 0.057 11551 Dihedral : 12.765 177.381 10173 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 3.57 % Allowed : 16.10 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 0.51 (0.09), residues: 8027 helix: 1.28 (0.08), residues: 4242 sheet: 0.06 (0.25), residues: 418 loop : -0.82 (0.10), residues: 3367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP u 86 HIS 0.010 0.002 HIS p 76 PHE 0.037 0.002 PHE i 292 TYR 0.024 0.002 TYR c 112 ARG 0.006 0.001 ARG M 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1351 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1099 time to evaluate : 6.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.7888 (t80) REVERT: B 98 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.7731 (mtm110) REVERT: C 119 LYS cc_start: 0.9016 (tttt) cc_final: 0.8686 (tttm) REVERT: F 50 ASP cc_start: 0.8128 (t0) cc_final: 0.7816 (t0) REVERT: F 68 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7546 (ttp80) REVERT: H 70 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7155 (mt-10) REVERT: J 87 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: J 143 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: K 106 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8619 (tm-30) REVERT: M 42 MET cc_start: 0.8854 (mmp) cc_final: 0.8643 (mmp) REVERT: M 145 MET cc_start: 0.9143 (mmt) cc_final: 0.8868 (mmt) REVERT: M 539 LYS cc_start: 0.8012 (mmmt) cc_final: 0.7663 (mmtt) REVERT: Q 308 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.7414 (p90) REVERT: S 44 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8904 (pt0) REVERT: S 64 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8470 (mmtt) REVERT: U 47 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8160 (ttm-80) REVERT: Y 85 PRO cc_start: 0.8583 (Cg_endo) cc_final: 0.8329 (Cg_exo) REVERT: Z 23 LYS cc_start: 0.7186 (mtmm) cc_final: 0.6936 (ttmm) REVERT: Z 72 LYS cc_start: 0.7891 (mtpt) cc_final: 0.6995 (mmtt) REVERT: c 111 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8746 (ttm) REVERT: d 59 ASN cc_start: 0.7298 (t0) cc_final: 0.7005 (t0) REVERT: j 8 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8470 (mp) REVERT: l 1 MET cc_start: 0.6116 (tmm) cc_final: 0.5890 (tmm) REVERT: l 511 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8920 (mp) REVERT: l 584 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8247 (pt) REVERT: m 23 LYS cc_start: 0.7624 (mtmm) cc_final: 0.6596 (mtpt) REVERT: n 30 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7124 (ttp80) REVERT: o 19 ASP cc_start: 0.8535 (t0) cc_final: 0.8223 (t0) REVERT: p 62 GLN cc_start: 0.8191 (tp40) cc_final: 0.7903 (tp40) REVERT: r 14 MET cc_start: 0.9160 (tmm) cc_final: 0.8854 (ttp) REVERT: r 103 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8721 (tt0) REVERT: s 54 LYS cc_start: 0.9092 (tmtt) cc_final: 0.8772 (tmmt) REVERT: s 56 PHE cc_start: 0.8680 (m-10) cc_final: 0.8334 (m-80) REVERT: s 150 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9118 (tp) REVERT: s 270 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.8718 (t80) REVERT: u 87 THR cc_start: 0.9131 (m) cc_final: 0.8794 (m) REVERT: u 172 MET cc_start: 0.8941 (mtp) cc_final: 0.8690 (mtm) REVERT: v 101 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7958 (mm-30) REVERT: v 105 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: w 75 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7019 (mtt180) REVERT: w 241 TYR cc_start: 0.9269 (OUTLIER) cc_final: 0.7999 (m-80) outliers start: 252 outliers final: 167 residues processed: 1270 average time/residue: 0.6471 time to fit residues: 1384.9746 Evaluate side-chains 1251 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1065 time to evaluate : 5.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 608 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 178 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 59 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 151 LYS Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 171 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 119 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 160 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 24 LEU Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 305 SER Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain l residue 589 LEU Chi-restraints excluded: chain m residue 18 VAL Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 163 ILE Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 143 GLU Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 9 THR Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 343 ILE Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 458 LEU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 115 SER Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 193 THR Chi-restraints excluded: chain s residue 194 ASN Chi-restraints excluded: chain s residue 246 SER Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 16 GLN Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain u residue 121 ASP Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 134 ASP Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 59 CYS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 101 GLU Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 75 ARG Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 0.3980 chunk 690 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 450 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 767 optimal weight: 2.9990 chunk 636 optimal weight: 4.9990 chunk 355 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 253 optimal weight: 0.0170 chunk 402 optimal weight: 9.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 51 ASN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS J 376 ASN M 202 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN Z 33 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 2 ASN ** r 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN w 215 GLN w 223 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 68257 Z= 0.154 Angle : 0.523 10.843 92360 Z= 0.264 Chirality : 0.040 0.216 10035 Planarity : 0.004 0.053 11551 Dihedral : 11.936 175.290 10173 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.45 % Favored : 96.50 % Rotamer: Outliers : 2.41 % Allowed : 17.62 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 0.97 (0.10), residues: 8027 helix: 1.68 (0.08), residues: 4254 sheet: 0.25 (0.25), residues: 426 loop : -0.66 (0.11), residues: 3347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP u 86 HIS 0.005 0.001 HIS J 37 PHE 0.028 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.004 0.000 ARG n 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1169 time to evaluate : 6.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8310 (tpt-90) REVERT: A 278 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8478 (pt) REVERT: B 76 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.7628 (t80) REVERT: F 40 ARG cc_start: 0.7839 (ptp-170) cc_final: 0.7521 (ptp-170) REVERT: F 68 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7267 (ttp80) REVERT: G 105 MET cc_start: 0.6428 (mmm) cc_final: 0.6190 (mmm) REVERT: G 122 MET cc_start: 0.8291 (mmt) cc_final: 0.8014 (mmm) REVERT: H 70 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7192 (mt-10) REVERT: H 85 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: J 121 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7507 (tm-30) REVERT: K 100 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8048 (mt0) REVERT: K 106 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8558 (tm-30) REVERT: M 145 MET cc_start: 0.9071 (mmt) cc_final: 0.8744 (mmt) REVERT: M 539 LYS cc_start: 0.7953 (mmmt) cc_final: 0.7603 (mmtt) REVERT: Q 249 LYS cc_start: 0.8680 (ptmt) cc_final: 0.8446 (ptmm) REVERT: Q 270 ASN cc_start: 0.8709 (m110) cc_final: 0.8401 (m-40) REVERT: Q 308 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.7274 (p90) REVERT: S 64 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8450 (mmtt) REVERT: T 47 ASP cc_start: 0.6757 (t0) cc_final: 0.6508 (t0) REVERT: U 47 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8162 (ttm-80) REVERT: Z 23 LYS cc_start: 0.7104 (mtmm) cc_final: 0.6858 (ttmm) REVERT: Z 35 LYS cc_start: 0.7147 (tptp) cc_final: 0.6705 (tptp) REVERT: Z 39 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7739 (mtp180) REVERT: Z 72 LYS cc_start: 0.7901 (mtpt) cc_final: 0.6991 (mmtt) REVERT: Z 87 TYR cc_start: 0.4691 (OUTLIER) cc_final: 0.3947 (m-10) REVERT: c 113 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8905 (pt) REVERT: d 47 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7934 (mp) REVERT: d 59 ASN cc_start: 0.7043 (t0) cc_final: 0.6790 (t0) REVERT: d 129 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8443 (tt) REVERT: h 93 THR cc_start: 0.7922 (m) cc_final: 0.7704 (m) REVERT: j 68 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7841 (mm-30) REVERT: k 43 MET cc_start: 0.9175 (ttt) cc_final: 0.8733 (ttt) REVERT: l 184 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9104 (tp) REVERT: l 340 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.7692 (t80) REVERT: l 411 MET cc_start: 0.8189 (mmp) cc_final: 0.7948 (mmp) REVERT: l 511 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8905 (mp) REVERT: n 30 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.6999 (ttt90) REVERT: o 19 ASP cc_start: 0.8469 (t0) cc_final: 0.8189 (t0) REVERT: p 62 GLN cc_start: 0.8106 (tp40) cc_final: 0.7843 (tp40) REVERT: r 14 MET cc_start: 0.9016 (tmm) cc_final: 0.8606 (ttp) REVERT: r 103 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8564 (tt0) REVERT: r 387 SER cc_start: 0.9044 (t) cc_final: 0.8585 (p) REVERT: s 54 LYS cc_start: 0.9029 (tmtt) cc_final: 0.8738 (tmmt) REVERT: s 56 PHE cc_start: 0.8556 (m-10) cc_final: 0.8265 (m-80) REVERT: s 70 MET cc_start: 0.7969 (mmm) cc_final: 0.7630 (mmt) REVERT: s 150 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9158 (tp) REVERT: u 172 MET cc_start: 0.8941 (mtp) cc_final: 0.8724 (mtm) REVERT: v 101 GLU cc_start: 0.8154 (tp30) cc_final: 0.7826 (mm-30) REVERT: v 105 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: w 75 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6979 (mtt180) REVERT: w 160 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: w 241 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.7884 (m-80) outliers start: 170 outliers final: 114 residues processed: 1269 average time/residue: 0.6409 time to fit residues: 1375.8063 Evaluate side-chains 1239 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1105 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 178 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain T residue 119 ARG Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 151 LYS Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 87 TYR Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 160 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 24 LEU Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 184 LEU Chi-restraints excluded: chain l residue 305 SER Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 589 LEU Chi-restraints excluded: chain m residue 18 VAL Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 44 VAL Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 129 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 440 HIS Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 170 GLU Chi-restraints excluded: chain s residue 193 THR Chi-restraints excluded: chain s residue 246 SER Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 134 ASP Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 75 ARG Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 739 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 437 optimal weight: 7.9990 chunk 560 optimal weight: 0.8980 chunk 434 optimal weight: 0.0050 chunk 645 optimal weight: 6.9990 chunk 428 optimal weight: 2.9990 chunk 764 optimal weight: 8.9990 chunk 478 optimal weight: 0.0470 chunk 465 optimal weight: 6.9990 chunk 352 optimal weight: 4.9990 overall best weight: 1.7896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN I 51 ASN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN ** Z 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 HIS l 570 GLN ** r 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN w 223 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 68257 Z= 0.223 Angle : 0.548 14.428 92360 Z= 0.274 Chirality : 0.041 0.228 10035 Planarity : 0.004 0.053 11551 Dihedral : 11.765 175.322 10173 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 2.65 % Allowed : 17.92 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 0.98 (0.10), residues: 8027 helix: 1.69 (0.08), residues: 4260 sheet: 0.25 (0.25), residues: 428 loop : -0.63 (0.11), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP u 86 HIS 0.005 0.001 HIS G 103 PHE 0.032 0.001 PHE i 292 TYR 0.021 0.001 TYR A 63 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1124 time to evaluate : 5.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 TYR cc_start: 0.6754 (t80) cc_final: 0.6536 (t80) REVERT: A 147 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8421 (tpt-90) REVERT: A 278 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8492 (pt) REVERT: A 457 HIS cc_start: 0.6300 (m90) cc_final: 0.5888 (m90) REVERT: B 76 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.7622 (t80) REVERT: B 98 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.7864 (mtm110) REVERT: F 40 ARG cc_start: 0.7840 (ptp-170) cc_final: 0.7521 (ptp-170) REVERT: F 68 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7395 (ttp80) REVERT: G 122 MET cc_start: 0.8308 (mmt) cc_final: 0.8021 (mmm) REVERT: H 70 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7236 (mt-10) REVERT: H 85 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: J 336 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7412 (mp0) REVERT: K 100 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8053 (mt0) REVERT: K 106 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8579 (tm-30) REVERT: M 145 MET cc_start: 0.9105 (mmt) cc_final: 0.8797 (mmt) REVERT: M 539 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7651 (mmtt) REVERT: O 185 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7254 (ptm) REVERT: O 226 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: Q 270 ASN cc_start: 0.8699 (m110) cc_final: 0.8398 (m-40) REVERT: Q 308 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.7248 (p90) REVERT: S 64 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8460 (mmtt) REVERT: U 47 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.8245 (ttm-80) REVERT: W 22 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8361 (mmtp) REVERT: Z 35 LYS cc_start: 0.7243 (tptp) cc_final: 0.6816 (tptp) REVERT: Z 39 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7847 (mtp180) REVERT: Z 72 LYS cc_start: 0.7869 (mtpt) cc_final: 0.6991 (mmtt) REVERT: Z 87 TYR cc_start: 0.4695 (OUTLIER) cc_final: 0.3921 (m-10) REVERT: a 78 THR cc_start: 0.8404 (m) cc_final: 0.8157 (m) REVERT: c 113 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8916 (pt) REVERT: d 47 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7927 (mp) REVERT: d 59 ASN cc_start: 0.7075 (t0) cc_final: 0.6816 (t0) REVERT: d 129 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8465 (tt) REVERT: e 134 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7317 (mp) REVERT: g 36 MET cc_start: 0.8842 (mmm) cc_final: 0.8608 (mmm) REVERT: h 93 THR cc_start: 0.7842 (m) cc_final: 0.7627 (m) REVERT: j 105 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8416 (tp30) REVERT: k 43 MET cc_start: 0.9177 (ttt) cc_final: 0.8725 (ttt) REVERT: k 97 GLN cc_start: 0.6769 (OUTLIER) cc_final: 0.6517 (mt0) REVERT: l 184 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9081 (tp) REVERT: l 411 MET cc_start: 0.8246 (mmp) cc_final: 0.7976 (mmp) REVERT: l 511 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8907 (mp) REVERT: n 30 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7008 (ttt90) REVERT: o 19 ASP cc_start: 0.8487 (t0) cc_final: 0.8163 (t0) REVERT: o 28 GLU cc_start: 0.7950 (mp0) cc_final: 0.7708 (tp30) REVERT: p 62 GLN cc_start: 0.8107 (tp40) cc_final: 0.7851 (tp40) REVERT: r 14 MET cc_start: 0.9055 (tmm) cc_final: 0.8688 (ttp) REVERT: r 103 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: s 56 PHE cc_start: 0.8589 (m-10) cc_final: 0.8268 (m-80) REVERT: s 150 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9090 (tp) REVERT: u 87 THR cc_start: 0.8858 (m) cc_final: 0.8478 (m) REVERT: u 172 MET cc_start: 0.8934 (mtp) cc_final: 0.8718 (mtm) REVERT: v 101 GLU cc_start: 0.8224 (tp30) cc_final: 0.7925 (mm-30) REVERT: v 105 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: w 75 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7014 (mtt180) REVERT: w 160 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: w 241 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.7942 (m-80) outliers start: 187 outliers final: 141 residues processed: 1241 average time/residue: 0.6494 time to fit residues: 1363.1560 Evaluate side-chains 1258 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1091 time to evaluate : 5.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain M residue 608 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 185 MET Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 178 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain T residue 119 ARG Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 22 LYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 151 LYS Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 87 TYR Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 134 LEU Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 119 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 160 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 24 LEU Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 114 ILE Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 166 THR Chi-restraints excluded: chain l residue 184 LEU Chi-restraints excluded: chain l residue 305 SER Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 589 LEU Chi-restraints excluded: chain m residue 18 VAL Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 129 ASP Chi-restraints excluded: chain m residue 132 ASP Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 9 THR Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 285 LEU Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 170 GLU Chi-restraints excluded: chain s residue 193 THR Chi-restraints excluded: chain s residue 246 SER Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 134 ASP Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 75 ARG Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 298 VAL Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 472 optimal weight: 0.0370 chunk 305 optimal weight: 2.9990 chunk 456 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 485 optimal weight: 6.9990 chunk 520 optimal weight: 4.9990 chunk 377 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 600 optimal weight: 0.8980 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN I 51 ASN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 540 ASN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN Z 33 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 2 ASN ** r 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN w 223 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 68257 Z= 0.187 Angle : 0.532 11.580 92360 Z= 0.266 Chirality : 0.041 0.209 10035 Planarity : 0.004 0.052 11551 Dihedral : 11.408 175.085 10173 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.10 % Rotamer: Outliers : 2.71 % Allowed : 18.02 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 1.06 (0.10), residues: 8027 helix: 1.75 (0.08), residues: 4260 sheet: 0.31 (0.25), residues: 430 loop : -0.60 (0.11), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.005 0.001 HIS r 83 PHE 0.031 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1131 time to evaluate : 5.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8473 (pt) REVERT: A 349 LEU cc_start: 0.7815 (tt) cc_final: 0.7604 (tt) REVERT: A 457 HIS cc_start: 0.6226 (m90) cc_final: 0.5746 (m90) REVERT: B 76 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.7657 (t80) REVERT: B 98 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.7920 (mtm110) REVERT: B 211 TYR cc_start: 0.9470 (m-80) cc_final: 0.9189 (m-80) REVERT: F 40 ARG cc_start: 0.7809 (ptp-170) cc_final: 0.7481 (ptp-170) REVERT: F 68 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7320 (ttp80) REVERT: F 86 GLN cc_start: 0.7192 (mt0) cc_final: 0.6890 (mt0) REVERT: G 90 TYR cc_start: 0.7224 (t80) cc_final: 0.6768 (t80) REVERT: G 122 MET cc_start: 0.8293 (mmt) cc_final: 0.8022 (mmm) REVERT: H 70 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7226 (mt-10) REVERT: H 85 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: J 87 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: J 154 GLN cc_start: 0.8062 (tt0) cc_final: 0.7763 (tm-30) REVERT: J 336 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7397 (mp0) REVERT: K 100 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8054 (mt0) REVERT: K 106 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8578 (tm-30) REVERT: M 145 MET cc_start: 0.9080 (mmt) cc_final: 0.8784 (mmt) REVERT: O 185 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.7192 (ptm) REVERT: Q 270 ASN cc_start: 0.8697 (m110) cc_final: 0.8395 (m-40) REVERT: Q 308 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.7296 (p90) REVERT: S 64 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8450 (mmtt) REVERT: U 47 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.8234 (ttm-80) REVERT: W 22 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8220 (mmtp) REVERT: W 66 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8259 (mt-10) REVERT: Z 23 LYS cc_start: 0.7640 (ttmm) cc_final: 0.6786 (mttm) REVERT: Z 35 LYS cc_start: 0.7233 (tptp) cc_final: 0.6776 (tptp) REVERT: Z 39 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7776 (mtp180) REVERT: Z 72 LYS cc_start: 0.7857 (mtpt) cc_final: 0.6972 (mmtt) REVERT: Z 87 TYR cc_start: 0.4706 (OUTLIER) cc_final: 0.4157 (m-80) REVERT: a 78 THR cc_start: 0.8268 (m) cc_final: 0.7979 (m) REVERT: c 113 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8894 (pt) REVERT: d 47 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7952 (mp) REVERT: d 59 ASN cc_start: 0.7025 (t0) cc_final: 0.6753 (t0) REVERT: d 129 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8465 (tt) REVERT: e 134 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7395 (mp) REVERT: j 105 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8400 (tp30) REVERT: k 97 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6522 (mt0) REVERT: l 184 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9062 (tp) REVERT: l 340 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.7688 (t80) REVERT: l 411 MET cc_start: 0.8233 (mmp) cc_final: 0.7956 (mmp) REVERT: l 511 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8884 (mp) REVERT: n 30 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7003 (ttt90) REVERT: o 19 ASP cc_start: 0.8466 (t0) cc_final: 0.8141 (t0) REVERT: o 28 GLU cc_start: 0.7949 (mp0) cc_final: 0.7700 (tp30) REVERT: p 62 GLN cc_start: 0.8047 (tp40) cc_final: 0.7807 (tp40) REVERT: r 14 MET cc_start: 0.9020 (tmm) cc_final: 0.8646 (ttp) REVERT: r 103 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8586 (tt0) REVERT: r 387 SER cc_start: 0.9058 (t) cc_final: 0.8600 (p) REVERT: s 56 PHE cc_start: 0.8563 (m-10) cc_final: 0.8218 (m-80) REVERT: s 150 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9073 (tp) REVERT: s 270 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8748 (t80) REVERT: u 87 THR cc_start: 0.9025 (m) cc_final: 0.8754 (m) REVERT: u 172 MET cc_start: 0.8997 (mtp) cc_final: 0.8789 (mtm) REVERT: v 83 GLU cc_start: 0.8388 (mp0) cc_final: 0.8149 (mp0) REVERT: v 101 GLU cc_start: 0.8291 (tp30) cc_final: 0.8000 (mm-30) REVERT: v 105 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: w 75 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7001 (mtt180) REVERT: w 160 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.6645 (mp0) REVERT: w 241 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.7869 (m-80) outliers start: 191 outliers final: 140 residues processed: 1255 average time/residue: 0.6672 time to fit residues: 1418.8415 Evaluate side-chains 1286 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1119 time to evaluate : 5.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 535 GLU Chi-restraints excluded: chain M residue 608 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 185 MET Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 178 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain T residue 119 ARG Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 22 LYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 151 LYS Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain Z residue 87 TYR Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 134 LEU Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 119 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 160 LEU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 24 LEU Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 166 THR Chi-restraints excluded: chain l residue 184 LEU Chi-restraints excluded: chain l residue 305 SER Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 589 LEU Chi-restraints excluded: chain m residue 18 VAL Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 129 ASP Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 9 THR Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 170 GLU Chi-restraints excluded: chain s residue 193 THR Chi-restraints excluded: chain s residue 246 SER Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 134 ASP Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 75 ARG Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 298 VAL Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 695 optimal weight: 0.7980 chunk 732 optimal weight: 7.9990 chunk 668 optimal weight: 7.9990 chunk 712 optimal weight: 5.9990 chunk 428 optimal weight: 1.9990 chunk 310 optimal weight: 6.9990 chunk 559 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 643 optimal weight: 1.9990 chunk 673 optimal weight: 4.9990 chunk 709 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 51 ASN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN S 44 GLN Z 33 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 2 ASN ** r 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN w 223 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 68257 Z= 0.227 Angle : 0.549 12.192 92360 Z= 0.274 Chirality : 0.042 0.214 10035 Planarity : 0.004 0.052 11551 Dihedral : 11.329 175.377 10173 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.78 % Rotamer: Outliers : 2.83 % Allowed : 17.90 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 1.02 (0.10), residues: 8027 helix: 1.71 (0.08), residues: 4260 sheet: 0.29 (0.25), residues: 426 loop : -0.61 (0.11), residues: 3341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.005 0.001 HIS G 103 PHE 0.032 0.001 PHE i 292 TYR 0.020 0.001 TYR r 406 ARG 0.004 0.000 ARG F 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1125 time to evaluate : 5.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8478 (pt) REVERT: A 457 HIS cc_start: 0.6238 (m90) cc_final: 0.5809 (m90) REVERT: B 76 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.7690 (t80) REVERT: B 98 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.7892 (mtm110) REVERT: F 40 ARG cc_start: 0.7829 (ptp-170) cc_final: 0.7498 (ptp-170) REVERT: F 68 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7322 (ttp80) REVERT: F 86 GLN cc_start: 0.7063 (mt0) cc_final: 0.6591 (mt0) REVERT: G 90 TYR cc_start: 0.7231 (t80) cc_final: 0.6753 (t80) REVERT: G 122 MET cc_start: 0.8302 (mmt) cc_final: 0.8026 (mmm) REVERT: H 70 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7228 (mt-10) REVERT: H 85 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: J 87 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: J 154 GLN cc_start: 0.8065 (tt0) cc_final: 0.7764 (tm-30) REVERT: J 336 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7398 (mp0) REVERT: K 100 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8059 (mt0) REVERT: K 106 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8546 (tm-30) REVERT: M 145 MET cc_start: 0.9091 (mmt) cc_final: 0.8801 (mmt) REVERT: O 185 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7180 (ptm) REVERT: Q 270 ASN cc_start: 0.8717 (m110) cc_final: 0.8416 (m-40) REVERT: Q 308 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7230 (p90) REVERT: S 64 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8456 (mmtt) REVERT: U 47 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8255 (ttm-80) REVERT: W 22 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8357 (mmtp) REVERT: W 66 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8261 (mt-10) REVERT: Z 23 LYS cc_start: 0.7743 (ttmm) cc_final: 0.6934 (mttm) REVERT: Z 35 LYS cc_start: 0.7229 (tptp) cc_final: 0.6760 (tptp) REVERT: Z 39 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7755 (mtp180) REVERT: Z 72 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7057 (mmtt) REVERT: Z 87 TYR cc_start: 0.4520 (OUTLIER) cc_final: 0.3789 (m-10) REVERT: a 78 THR cc_start: 0.8237 (m) cc_final: 0.7965 (m) REVERT: c 113 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8887 (pt) REVERT: d 47 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7962 (mp) REVERT: d 59 ASN cc_start: 0.7029 (t0) cc_final: 0.6767 (t0) REVERT: d 129 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8487 (tt) REVERT: e 134 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7328 (mp) REVERT: j 105 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8404 (tp30) REVERT: k 97 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6517 (mt0) REVERT: l 184 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9061 (tp) REVERT: l 340 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.7705 (t80) REVERT: l 411 MET cc_start: 0.8262 (mmp) cc_final: 0.7975 (mmp) REVERT: l 511 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8874 (mp) REVERT: n 30 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.7003 (ttt90) REVERT: o 19 ASP cc_start: 0.8493 (t0) cc_final: 0.8173 (t0) REVERT: o 28 GLU cc_start: 0.7953 (mp0) cc_final: 0.7705 (tp30) REVERT: p 62 GLN cc_start: 0.8055 (tp40) cc_final: 0.7814 (tp40) REVERT: r 14 MET cc_start: 0.9045 (tmm) cc_final: 0.8698 (ttp) REVERT: r 103 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8581 (tt0) REVERT: s 56 PHE cc_start: 0.8579 (m-10) cc_final: 0.8221 (m-80) REVERT: s 150 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9084 (tp) REVERT: u 87 THR cc_start: 0.9041 (m) cc_final: 0.8780 (m) REVERT: u 172 MET cc_start: 0.8997 (mtp) cc_final: 0.8788 (mtm) REVERT: v 101 GLU cc_start: 0.8309 (tp30) cc_final: 0.8024 (mm-30) REVERT: v 105 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: w 75 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7008 (mtt180) REVERT: w 160 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: w 241 TYR cc_start: 0.9234 (OUTLIER) cc_final: 0.7881 (m-80) outliers start: 200 outliers final: 156 residues processed: 1251 average time/residue: 0.6731 time to fit residues: 1428.6976 Evaluate side-chains 1294 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1112 time to evaluate : 6.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 608 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 185 MET Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 178 THR Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 119 ARG Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 22 LYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 151 LYS Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain Z residue 87 TYR Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 171 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 134 LEU Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 119 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 160 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 24 LEU Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 114 ILE Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 166 THR Chi-restraints excluded: chain l residue 184 LEU Chi-restraints excluded: chain l residue 272 LEU Chi-restraints excluded: chain l residue 305 SER Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 589 LEU Chi-restraints excluded: chain m residue 18 VAL Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 129 ASP Chi-restraints excluded: chain m residue 132 ASP Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 9 THR Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 440 HIS Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 170 GLU Chi-restraints excluded: chain s residue 193 THR Chi-restraints excluded: chain s residue 246 SER Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 134 ASP Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 75 ARG Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 298 VAL Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 467 optimal weight: 0.6980 chunk 753 optimal weight: 8.9990 chunk 459 optimal weight: 5.9990 chunk 357 optimal weight: 0.8980 chunk 523 optimal weight: 0.6980 chunk 790 optimal weight: 0.9990 chunk 727 optimal weight: 0.8980 chunk 629 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 485 optimal weight: 6.9990 chunk 385 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN P 75 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 2 ASN r 169 ASN r 304 GLN v 54 GLN w 223 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 68257 Z= 0.155 Angle : 0.521 11.624 92360 Z= 0.260 Chirality : 0.040 0.210 10035 Planarity : 0.004 0.052 11551 Dihedral : 10.959 174.494 10173 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 2.30 % Allowed : 18.48 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 1.17 (0.10), residues: 8027 helix: 1.84 (0.08), residues: 4252 sheet: 0.35 (0.25), residues: 418 loop : -0.55 (0.11), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP u 86 HIS 0.005 0.001 HIS p 26 PHE 0.030 0.001 PHE i 292 TYR 0.022 0.001 TYR r 406 ARG 0.004 0.000 ARG g 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1320 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1158 time to evaluate : 5.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 TYR cc_start: 0.6969 (t80) cc_final: 0.6702 (t80) REVERT: A 278 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8470 (pt) REVERT: A 457 HIS cc_start: 0.6163 (m90) cc_final: 0.5709 (m90) REVERT: B 76 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.7441 (t80) REVERT: B 98 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.7947 (mtm110) REVERT: B 211 TYR cc_start: 0.9449 (m-80) cc_final: 0.9124 (m-80) REVERT: F 40 ARG cc_start: 0.7769 (ptp-170) cc_final: 0.7480 (ptp-170) REVERT: G 90 TYR cc_start: 0.7190 (t80) cc_final: 0.6767 (t80) REVERT: G 122 MET cc_start: 0.8266 (mmt) cc_final: 0.8034 (mmm) REVERT: H 70 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7217 (mt-10) REVERT: H 85 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: J 87 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: J 154 GLN cc_start: 0.8061 (tt0) cc_final: 0.7785 (tm-30) REVERT: J 336 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7387 (mp0) REVERT: K 100 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8095 (mt0) REVERT: K 106 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8513 (tm-30) REVERT: M 145 MET cc_start: 0.9046 (mmt) cc_final: 0.8746 (mmt) REVERT: O 185 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7163 (ptm) REVERT: Q 270 ASN cc_start: 0.8709 (m110) cc_final: 0.8398 (m-40) REVERT: Q 308 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.7208 (p90) REVERT: S 64 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8431 (mmtt) REVERT: W 66 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8223 (mt-10) REVERT: W 94 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8474 (tt0) REVERT: X 146 ASP cc_start: 0.8325 (m-30) cc_final: 0.7681 (m-30) REVERT: Z 23 LYS cc_start: 0.7542 (ttmm) cc_final: 0.6858 (mttm) REVERT: Z 35 LYS cc_start: 0.7312 (tptp) cc_final: 0.6888 (tptp) REVERT: Z 39 ARG cc_start: 0.7986 (ttm170) cc_final: 0.7677 (mtp180) REVERT: Z 72 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7058 (mmtt) REVERT: Z 87 TYR cc_start: 0.4429 (OUTLIER) cc_final: 0.3836 (m-10) REVERT: a 78 THR cc_start: 0.8086 (m) cc_final: 0.7785 (m) REVERT: c 113 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8882 (pt) REVERT: d 35 LYS cc_start: 0.7600 (tttt) cc_final: 0.7080 (tptp) REVERT: d 47 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7909 (mp) REVERT: d 59 ASN cc_start: 0.6943 (t0) cc_final: 0.6686 (t0) REVERT: d 129 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8423 (tt) REVERT: e 134 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7349 (mt) REVERT: j 68 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7803 (mm-30) REVERT: l 184 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9042 (tp) REVERT: l 340 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.7682 (t80) REVERT: l 411 MET cc_start: 0.8194 (mmp) cc_final: 0.7925 (mmp) REVERT: l 511 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8859 (mp) REVERT: l 550 SER cc_start: 0.8999 (t) cc_final: 0.8775 (m) REVERT: m 57 PHE cc_start: 0.8753 (m-80) cc_final: 0.8544 (m-80) REVERT: m 141 MET cc_start: 0.8524 (mmt) cc_final: 0.8282 (mmt) REVERT: n 30 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.6993 (ttt90) REVERT: n 48 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7916 (mm-30) REVERT: o 19 ASP cc_start: 0.8469 (t0) cc_final: 0.8183 (t0) REVERT: o 28 GLU cc_start: 0.7966 (mp0) cc_final: 0.7622 (tp30) REVERT: p 62 GLN cc_start: 0.8017 (tp40) cc_final: 0.7799 (tp40) REVERT: r 14 MET cc_start: 0.8964 (tmm) cc_final: 0.8565 (ttp) REVERT: r 103 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8561 (tt0) REVERT: r 387 SER cc_start: 0.9000 (t) cc_final: 0.8553 (p) REVERT: s 56 PHE cc_start: 0.8536 (m-10) cc_final: 0.8206 (m-80) REVERT: s 150 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9066 (tp) REVERT: u 137 LEU cc_start: 0.8706 (tp) cc_final: 0.8484 (tp) REVERT: v 101 GLU cc_start: 0.8330 (tp30) cc_final: 0.8039 (mm-30) REVERT: v 105 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: w 160 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: w 241 TYR cc_start: 0.9207 (OUTLIER) cc_final: 0.7793 (m-80) outliers start: 162 outliers final: 116 residues processed: 1250 average time/residue: 0.6643 time to fit residues: 1406.3266 Evaluate side-chains 1271 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1134 time to evaluate : 5.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 185 MET Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 178 THR Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain T residue 119 ARG Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 151 LYS Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 87 TYR Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 134 LEU Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 160 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain j residue 24 LEU Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 166 THR Chi-restraints excluded: chain l residue 184 LEU Chi-restraints excluded: chain l residue 272 LEU Chi-restraints excluded: chain l residue 305 SER Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 511 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 589 LEU Chi-restraints excluded: chain m residue 18 VAL Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain r residue 9 THR Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 440 HIS Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 170 GLU Chi-restraints excluded: chain s residue 193 THR Chi-restraints excluded: chain s residue 246 SER Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 21 SER Chi-restraints excluded: chain u residue 134 ASP Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 298 VAL Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 499 optimal weight: 0.9980 chunk 670 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 580 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 630 optimal weight: 0.0010 chunk 263 optimal weight: 20.0000 chunk 647 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 454 GLN Z 33 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 2 ASN r 139 GLN v 54 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100550 restraints weight = 95926.534| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.35 r_work: 0.2912 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 68257 Z= 0.224 Angle : 0.551 15.460 92360 Z= 0.274 Chirality : 0.042 0.248 10035 Planarity : 0.004 0.052 11551 Dihedral : 10.948 175.041 10173 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.05 % Favored : 95.91 % Rotamer: Outliers : 2.38 % Allowed : 18.53 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: 1.11 (0.10), residues: 8027 helix: 1.78 (0.08), residues: 4261 sheet: 0.34 (0.25), residues: 419 loop : -0.55 (0.11), residues: 3347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP u 86 HIS 0.006 0.001 HIS G 103 PHE 0.032 0.001 PHE i 292 TYR 0.025 0.001 TYR E 40 ARG 0.009 0.000 ARG E 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20566.33 seconds wall clock time: 359 minutes 2.54 seconds (21542.54 seconds total)