Starting phenix.real_space_refine on Sat Jan 20 03:38:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4m_32308/01_2024/7w4m_32308_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4m_32308/01_2024/7w4m_32308.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4m_32308/01_2024/7w4m_32308_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4m_32308/01_2024/7w4m_32308_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4m_32308/01_2024/7w4m_32308_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4m_32308/01_2024/7w4m_32308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4m_32308/01_2024/7w4m_32308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4m_32308/01_2024/7w4m_32308_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4m_32308/01_2024/7w4m_32308_updated.pdb" } resolution = 3.3 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 31 5.49 5 Mg 1 5.21 5 S 473 5.16 5 C 42747 2.51 5 N 11065 2.21 5 O 11864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J GLU 346": "OE1" <-> "OE2" Residue "J GLU 351": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M GLU 396": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P GLU 167": "OE1" <-> "OE2" Residue "P PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 206": "OE1" <-> "OE2" Residue "Q GLU 208": "OE1" <-> "OE2" Residue "Q GLU 246": "OE1" <-> "OE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "U TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 130": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "d GLU 67": "OE1" <-> "OE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h GLU 89": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "j GLU 68": "OE1" <-> "OE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l GLU 268": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 445": "OE1" <-> "OE2" Residue "l GLU 503": "OE1" <-> "OE2" Residue "m GLU 138": "OE1" <-> "OE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "u GLU 6": "OE1" <-> "OE2" Residue "u GLU 17": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "u GLU 139": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "w GLU 47": "OE1" <-> "OE2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w GLU 115": "OE1" <-> "OE2" Residue "w GLU 185": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 264": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Residue "w GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66210 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3314 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 968 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 683 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 690 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 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: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2339 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 38} 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: "L" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 118} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 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: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1193 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 132} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 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: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3366 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'2MR:plan-2': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "S" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 563 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} 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: "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: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1017 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 133} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" 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: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 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: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} 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: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 875 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 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: "c" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1312 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 135} 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: "d" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1445 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 164} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 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: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 338 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 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: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 793 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 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: 4764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4764 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 12 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: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 460 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} 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: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2387 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1022 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "w" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2562 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 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: "I" 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: "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: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 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: "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: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "g" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {' UQ': 1} Classifications: {'undetermined': 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 2702 SG CYS A 382 48.649 49.959 172.358 1.00 19.81 S ATOM 3044 SG CYS A 425 48.006 45.845 177.600 1.00 20.87 S ATOM 2722 SG CYS A 385 45.430 45.400 171.909 1.00 24.20 S ATOM 2683 SG CYS A 379 43.336 49.986 176.207 1.00 13.32 S ATOM 3945 SG CYS B 113 37.359 68.406 138.779 1.00 22.19 S ATOM 3964 SG CYS B 116 42.639 65.666 142.318 1.00 18.66 S ATOM 3987 SG CYS B 119 43.466 68.817 137.237 1.00 22.56 S ATOM 4316 SG CYS B 162 40.721 62.983 137.413 1.00 11.16 S ATOM 4014 SG CYS B 123 49.508 71.821 132.860 1.00 38.35 S ATOM 4240 SG CYS B 152 47.748 70.617 126.751 1.00 29.82 S ATOM 4287 SG CYS B 158 45.743 66.566 131.253 1.00 10.97 S ATOM 4266 SG CYS B 155 51.876 66.893 129.825 1.00 22.49 S ATOM 5704 SG CYS C 166 53.890 70.894 122.543 1.00 7.64 S ATOM 4980 SG CYS C 72 55.082 72.776 116.438 1.00 0.00 S ATOM 4974 SG CYS C 71 59.378 70.923 118.728 1.00 7.21 S ATOM 5474 SG CYS C 136 56.651 75.468 121.574 1.00 7.93 S ATOM 14471 SG CYS M 131 41.877 64.838 154.522 1.00 7.01 S ATOM 14450 SG CYS M 128 45.341 60.499 151.027 1.00 23.14 S ATOM 14511 SG CYS M 137 47.453 63.572 156.548 1.00 13.27 S ATOM 14843 SG CYS M 179 45.878 62.843 167.637 1.00 6.09 S ATOM 15197 SG CYS M 226 42.817 65.845 163.533 1.00 19.10 S ATOM 14867 SG CYS M 182 40.521 65.395 169.609 1.00 16.69 S ATOM 14820 SG CYS M 176 40.234 60.188 165.705 1.00 19.66 S ATOM 14068 SG CYS M 78 57.596 57.867 170.728 1.00 19.76 S ATOM 14169 SG CYS M 92 55.804 59.485 173.441 1.00 15.61 S ATOM 13957 SG CYS M 64 51.503 59.758 171.043 1.00 22.00 S ATOM 14043 SG CYS M 75 52.407 58.094 167.920 1.00 8.03 S ATOM 20995 SG CYS O 135 32.383 31.849 179.284 1.00 65.91 S ATOM 21029 SG CYS O 140 32.156 28.340 179.893 1.00 70.34 S ATOM 21309 SG CYS O 176 36.778 33.450 181.875 1.00 74.58 S ATOM 21332 SG CYS O 180 36.961 29.879 181.615 1.00 65.25 S ATOM 27975 SG CYS T 86 30.020 54.699 145.832 1.00 15.48 S ATOM 28153 SG CYS T 111 31.017 57.836 146.911 1.00 23.15 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.65 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.65 Time building chain proxies: 26.92, per 1000 atoms: 0.41 Number of scatterers: 66210 At special positions: 0 Unit cell: (214.09, 230.559, 227.265, 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 473 16.00 P 31 15.00 Mg 1 11.99 O 11864 8.00 N 11065 7.00 C 42747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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=1.80 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.04 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: 20.05 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " 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="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " 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="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " 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="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " 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 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " 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: 335 helices and 28 sheets defined 52.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.22 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 82 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 163 through 178 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 303 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: 3.683A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.219A 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 78 removed outlier: 3.502A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 211 removed outlier: 5.785A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 removed outlier: 3.600A 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 111 through 123 Proline residue: C 115 - end of helix 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 189 through 194 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.306A 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: 4.354A 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: 4.896A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.774A 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 88 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.088A 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: 4.102A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.511A 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 119 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 213 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 322 Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 345 through 356 removed outlier: 4.636A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 80 removed outlier: 3.669A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 96 removed outlier: 3.745A pdb=" N GLU K 92 " --> pdb=" O ASP K 88 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 65 No H-bonds generated for 'chain 'L' and resid 62 through 65' 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 131 through 141 Processing helix chain 'L' and resid 161 through 163 No H-bonds generated for 'chain 'L' and resid 161 through 163' Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 128 through 130 No H-bonds generated for 'chain 'M' and resid 128 through 130' Processing helix chain 'M' and resid 138 through 146 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: 3.676A pdb=" N ILE M 222 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) 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 removed outlier: 3.572A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) 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 360 Processing helix chain 'M' and resid 382 through 384 No H-bonds generated for 'chain 'M' and resid 382 through 384' Processing helix chain 'M' and resid 390 through 395 removed outlier: 3.791A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 390 through 395' 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 522 through 528 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 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: 3.655A 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: 4.825A 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 146 through 156 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: 3.501A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.670A 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 163 through 173 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 46 removed outlier: 4.171A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.798A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.227A 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: 4.210A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.669A 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: 4.123A 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: 4.376A 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: 4.478A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 4.378A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA Q 449 " --> 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 30 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix removed outlier: 3.752A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) 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 55 Processing helix chain 'T' and resid 67 through 72 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 32 Processing helix chain 'U' and resid 38 through 47 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 removed outlier: 3.712A pdb=" N ALA V 116 " --> pdb=" O ALA V 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 99 Proline residue: W 73 - end of helix removed outlier: 3.610A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 125 Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.345A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 136 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 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 46 through 53 removed outlier: 3.671A pdb=" N GLU Z 49 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 58 No H-bonds generated for 'chain 'Z' and resid 56 through 58' 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: 3.913A 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 73 Processing helix chain 'b' and resid 76 through 88 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: 5.044A 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 124 removed outlier: 3.652A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 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: 4.111A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 131 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 removed outlier: 3.520A pdb=" N SER g 22 " --> pdb=" O GLU g 19 " (cutoff:3.500A) 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: 3.664A 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 112 through 121 Proline residue: i 116 - end of helix Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.790A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.965A 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 151 through 171 removed outlier: 4.009A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 191 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 4.041A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.513A 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: 4.328A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 340 through 345 Processing helix chain 'j' and resid 2 through 26 Proline residue: j 25 - end of helix Processing helix chain 'j' and resid 53 through 79 Proline residue: j 74 - end of helix removed outlier: 5.798A 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 50 Processing helix chain 'k' and resid 54 through 85 removed outlier: 4.117A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'l' and resid 3 through 23 removed outlier: 3.867A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.835A 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 56 removed outlier: 4.497A 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: 3.857A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 157 removed outlier: 3.904A pdb=" N TRP l 157 " --> pdb=" O LEU l 153 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 192 removed outlier: 3.975A 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: 4.273A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.572A 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 253 through 262 removed outlier: 3.767A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.030A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.175A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 3.628A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 387 through 400 removed outlier: 4.344A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 Processing helix chain 'l' and resid 448 through 471 removed outlier: 3.631A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.164A 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: 3.558A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.876A 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 526 through 547 Proline residue: l 530 - end of helix removed outlier: 4.211A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU l 536 " --> pdb=" O MET l 533 " (cutoff:3.500A) Proline residue: l 537 - end of helix removed outlier: 4.786A pdb=" N SER l 543 " --> 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: 3.979A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.155A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 8 through 34 removed outlier: 6.372A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.720A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' 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 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 94 through 96 No H-bonds generated for 'chain 'p' and resid 94 through 96' Processing helix chain 'p' and resid 102 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.680A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.918A 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: 4.148A 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: 4.214A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.880A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.494A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.671A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.520A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.481A 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 140 through 171 removed outlier: 4.142A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 4.120A pdb=" N THR r 171 " --> pdb=" O GLN r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 204 removed outlier: 4.117A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 221 removed outlier: 4.233A 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 237 through 249 removed outlier: 4.950A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.652A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 4.063A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER r 273 " --> pdb=" O MET r 269 " (cutoff:3.500A) removed outlier: 3.535A 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: 3.581A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 350 No H-bonds generated for 'chain 'r' and resid 348 through 350' 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: 3.877A 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: 3.884A 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 31 Proline residue: s 12 - end of helix removed outlier: 3.950A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.219A 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: 4.152A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 4.364A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 157 removed outlier: 3.986A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN s 157 " --> pdb=" O VAL s 153 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.583A 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 310 removed outlier: 5.222A 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 22 through 27 Processing helix chain 'u' and resid 29 through 35 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 97 through 114 removed outlier: 3.768A pdb=" N CYS u 100 " --> pdb=" O PHE u 97 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG u 101 " --> pdb=" O ARG u 98 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS u 102 " --> pdb=" O HIS u 99 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 9 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 81 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 197 removed outlier: 5.203A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 225 through 228 Processing helix chain 'w' and resid 231 through 244 Processing helix chain 'w' and resid 246 through 252 removed outlier: 3.981A pdb=" N LYS w 252 " --> pdb=" O GLU w 248 " (cutoff:3.500A) Processing helix chain 'w' and resid 262 through 264 No H-bonds generated for 'chain 'w' and resid 262 through 264' Processing helix chain 'w' and resid 266 through 275 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: 3.903A 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: 7.077A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.154A 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: 5.931A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.243A 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: 6.366A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.501A 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 57 removed outlier: 3.837A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.578A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.845A 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: 8.724A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.137A 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: 6.313A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.551A 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: 6.282A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.747A 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: 6.703A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.489A 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: 6.713A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (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: 3.700A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.537A 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 83 through 86 Processing sheet with id= Y, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= Z, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.372A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.505A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'w' and resid 84 through 86 2915 hydrogen bonds defined for protein. 8091 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: 20.03 Time building geometry restraints manager: 22.08 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: 27201 1.40 - 1.62: 39747 1.62 - 1.85: 830 1.85 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 67858 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.263 0.261 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.45e+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 1.297 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.300 0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 67853 not shown) Histogram of bond angle deviations from ideal: 73.55 - 85.94: 76 85.94 - 98.33: 1 98.33 - 110.72: 22854 110.72 - 123.11: 65698 123.11 - 135.50: 3259 Bond angle restraints: 91888 Sorted by residual: angle pdb=" C TYR c 75 " pdb=" N PRO c 76 " pdb=" CA PRO c 76 " ideal model delta sigma weight residual 119.85 129.25 -9.40 1.01e+00 9.80e-01 8.67e+01 angle pdb=" N LEU Q 240 " pdb=" CA LEU Q 240 " pdb=" C LEU Q 240 " ideal model delta sigma weight residual 111.28 120.69 -9.41 1.09e+00 8.42e-01 7.45e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.86 -16.12 1.95e+00 2.62e-01 6.80e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.53 -13.69 1.91e+00 2.73e-01 5.11e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.63 -9.30 1.32e+00 5.72e-01 4.95e+01 ... (remaining 91883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 39613 35.55 - 71.09: 1360 71.09 - 106.64: 108 106.64 - 142.19: 22 142.19 - 177.74: 14 Dihedral angle restraints: 41117 sinusoidal: 17417 harmonic: 23700 Sorted by residual: 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 43.39 -43.39 0 5.00e+00 4.00e-02 7.53e+01 dihedral pdb=" CB CYS u 88 " pdb=" SG CYS u 88 " pdb=" SG CYS u 100 " pdb=" CB CYS u 100 " ideal model delta sinusoidal sigma weight residual 93.00 165.11 -72.11 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CB CYS V 95 " pdb=" SG CYS V 95 " pdb=" SG CYS V 115 " pdb=" CB CYS V 115 " ideal model delta sinusoidal sigma weight residual -86.00 -15.66 -70.34 1 1.00e+01 1.00e-02 6.37e+01 ... (remaining 41114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 9243 0.081 - 0.161: 746 0.161 - 0.242: 26 0.242 - 0.323: 8 0.323 - 0.403: 4 Chirality restraints: 10027 Sorted by residual: 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 -2.34 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA THR l 251 " pdb=" N THR l 251 " pdb=" C THR l 251 " pdb=" CB THR l 251 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA ARG Y 45 " pdb=" N ARG Y 45 " pdb=" C ARG Y 45 " pdb=" CB ARG Y 45 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 10024 not shown) Planarity restraints: 11515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 401 " 0.369 2.00e-02 2.50e+03 4.79e-01 2.86e+03 pdb=" C11 UQ s 401 " 0.183 2.00e-02 2.50e+03 pdb=" C7 UQ s 401 " 0.563 2.00e-02 2.50e+03 pdb=" C8 UQ s 401 " -0.694 2.00e-02 2.50e+03 pdb=" C9 UQ s 401 " -0.421 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 401 " -0.325 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C18 UQ s 401 " 0.305 2.00e-02 2.50e+03 pdb=" C19 UQ s 401 " 0.379 2.00e-02 2.50e+03 pdb=" C20 UQ s 401 " -0.005 2.00e-02 2.50e+03 pdb=" C21 UQ s 401 " -0.353 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 401 " 0.274 2.00e-02 2.50e+03 2.67e-01 8.90e+02 pdb=" C13 UQ s 401 " -0.238 2.00e-02 2.50e+03 pdb=" C14 UQ s 401 " -0.357 2.00e-02 2.50e+03 pdb=" C15 UQ s 401 " 0.011 2.00e-02 2.50e+03 pdb=" C16 UQ s 401 " 0.311 2.00e-02 2.50e+03 ... (remaining 11512 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 692 2.62 - 3.19: 58678 3.19 - 3.76: 104060 3.76 - 4.33: 146121 4.33 - 4.90: 242349 Nonbonded interactions: 551900 Sorted by model distance: nonbonded pdb=" O4 PLX a 202 " pdb=" O7 PLX a 202 " model vdw 2.052 3.040 nonbonded pdb=" OD1 ASN A 185 " pdb=" N GLY A 190 " model vdw 2.202 2.520 nonbonded pdb=" O TRP A 413 " pdb=" OG SER A 416 " model vdw 2.205 2.440 nonbonded pdb=" OG1 THR E 15 " pdb=" O VAL L 55 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR w 118 " pdb=" O2' ADP w 401 " model vdw 2.205 2.440 ... (remaining 551895 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=0.65 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 8.450 Check model and map are aligned: 0.740 Set scattering table: 0.500 Process input model: 154.540 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 : 0.007 0.312 67858 Z= 0.450 Angle : 0.782 17.035 91888 Z= 0.405 Chirality : 0.045 0.403 10027 Planarity : 0.009 0.479 11515 Dihedral : 17.848 177.737 25810 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 0.43 % Allowed : 14.58 % Favored : 85.00 % Cbeta Deviations : 0.00 % 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: 1.06 (0.10), residues: 8027 helix: 1.64 (0.08), residues: 4238 sheet: 0.33 (0.25), residues: 424 loop : -0.42 (0.11), residues: 3365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP u 86 HIS 0.013 0.001 HIS T 122 PHE 0.038 0.002 PHE l 335 TYR 0.025 0.001 TYR l 422 ARG 0.005 0.000 ARG H 92 *********************** 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: 30 poor density : 1153 time to evaluate : 5.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6964 (t0) REVERT: B 76 TYR cc_start: 0.8220 (t80) cc_final: 0.7883 (t80) REVERT: O 130 TYR cc_start: 0.7229 (m-80) cc_final: 0.6902 (m-80) REVERT: P 68 ILE cc_start: 0.8897 (mt) cc_final: 0.8671 (mt) REVERT: Q 185 MET cc_start: 0.9456 (tpp) cc_final: 0.8886 (tpt) REVERT: b 70 PHE cc_start: 0.8710 (t80) cc_final: 0.8282 (t80) REVERT: b 108 ASP cc_start: 0.7757 (m-30) cc_final: 0.7460 (t0) REVERT: c 53 LYS cc_start: 0.8094 (tttp) cc_final: 0.7788 (ttpt) REVERT: c 70 MET cc_start: 0.8409 (mpp) cc_final: 0.8098 (mpp) REVERT: c 81 ARG cc_start: 0.7304 (mmt90) cc_final: 0.7045 (mmm-85) REVERT: d 7 LYS cc_start: 0.7842 (mmtp) cc_final: 0.7166 (mmmt) REVERT: f 67 LEU cc_start: 0.7928 (mm) cc_final: 0.7716 (mm) REVERT: i 14 MET cc_start: 0.8801 (mtt) cc_final: 0.8527 (mtt) REVERT: i 98 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8276 (ttm) REVERT: j 87 MET cc_start: 0.9183 (ppp) cc_final: 0.8908 (tmm) REVERT: l 331 MET cc_start: 0.8196 (mmt) cc_final: 0.7961 (mmp) REVERT: l 338 MET cc_start: 0.8840 (ttm) cc_final: 0.8573 (ttm) REVERT: l 359 MET cc_start: 0.7869 (ptp) cc_final: 0.7473 (ptp) REVERT: m 74 MET cc_start: 0.8490 (mtp) cc_final: 0.8203 (mtp) REVERT: v 16 GLU cc_start: 0.6112 (mt-10) cc_final: 0.3918 (tm-30) REVERT: v 54 GLN cc_start: 0.7510 (pm20) cc_final: 0.6948 (pm20) outliers start: 30 outliers final: 17 residues processed: 1164 average time/residue: 0.6314 time to fit residues: 1246.6076 Evaluate side-chains 1135 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1116 time to evaluate : 6.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain M residue 450 LYS Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain T residue 122 HIS Chi-restraints excluded: chain V residue 70 PHE Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain d residue 10 TYR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 98 MET Chi-restraints excluded: chain r residue 343 ILE 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: 7.9990 chunk 333 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 405 optimal weight: 10.0000 chunk 321 optimal weight: 0.7980 chunk 621 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 462 optimal weight: 2.9990 chunk 720 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN Q 234 GLN U 52 ASN Y 46 GLN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 70 GLN i 174 GLN i 232 HIS i 268 GLN j 82 ASN l 354 GLN ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 81 GLN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 82 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 67858 Z= 0.219 Angle : 0.552 11.644 91888 Z= 0.275 Chirality : 0.041 0.242 10027 Planarity : 0.005 0.063 11515 Dihedral : 13.291 172.494 9990 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.80 % Rotamer: Outliers : 2.07 % Allowed : 14.68 % Favored : 83.25 % 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: 1.12 (0.10), residues: 8027 helix: 1.68 (0.08), residues: 4253 sheet: 0.35 (0.25), residues: 423 loop : -0.39 (0.11), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS J 37 PHE 0.036 0.001 PHE l 335 TYR 0.028 0.001 TYR r 406 ARG 0.004 0.000 ARG H 92 *********************** 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 1316 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1171 time to evaluate : 6.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 MET cc_start: 0.8280 (tpt) cc_final: 0.7806 (tpt) REVERT: B 76 TYR cc_start: 0.8384 (t80) cc_final: 0.8103 (t80) REVERT: G 115 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: I 70 MET cc_start: 0.8794 (tmm) cc_final: 0.8496 (tmm) REVERT: J 324 MET cc_start: 0.7926 (tmm) cc_final: 0.7388 (tmm) REVERT: K 89 LEU cc_start: 0.8391 (mt) cc_final: 0.7983 (mp) REVERT: M 645 ARG cc_start: 0.8507 (tpt90) cc_final: 0.8306 (tpt90) REVERT: M 677 GLN cc_start: 0.6749 (tm-30) cc_final: 0.6369 (tm-30) REVERT: O 130 TYR cc_start: 0.7153 (m-80) cc_final: 0.6795 (m-80) REVERT: P 80 CYS cc_start: 0.7411 (t) cc_final: 0.7027 (t) REVERT: V 58 ARG cc_start: 0.5591 (ttp-110) cc_final: 0.4303 (ttt180) REVERT: W 9 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: a 100 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7691 (t0) REVERT: b 70 PHE cc_start: 0.8755 (t80) cc_final: 0.8345 (t80) REVERT: c 53 LYS cc_start: 0.8251 (tttp) cc_final: 0.7908 (ttpt) REVERT: c 70 MET cc_start: 0.8411 (mpp) cc_final: 0.8107 (mpp) REVERT: d 7 LYS cc_start: 0.7986 (mmtp) cc_final: 0.7333 (mmmt) REVERT: d 99 ASP cc_start: 0.8234 (m-30) cc_final: 0.7974 (m-30) REVERT: e 55 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6435 (pp) REVERT: e 56 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6976 (mm-40) REVERT: e 132 ASN cc_start: 0.8161 (m110) cc_final: 0.7932 (m110) REVERT: g 113 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7304 (pt0) REVERT: i 14 MET cc_start: 0.8799 (mtt) cc_final: 0.8546 (mtt) REVERT: k 1 MET cc_start: 0.5105 (tmm) cc_final: 0.4876 (tmm) REVERT: k 9 ILE cc_start: 0.9206 (mt) cc_final: 0.8898 (mp) REVERT: l 338 MET cc_start: 0.8849 (ttm) cc_final: 0.8600 (ttm) REVERT: l 411 MET cc_start: 0.8653 (mmp) cc_final: 0.8388 (mmm) REVERT: l 482 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6878 (mpp) REVERT: p 27 LEU cc_start: 0.8194 (tp) cc_final: 0.7971 (tt) REVERT: u 64 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.7591 (t0) REVERT: u 68 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8369 (mm) REVERT: v 16 GLU cc_start: 0.6083 (mt-10) cc_final: 0.3930 (tm-30) REVERT: v 54 GLN cc_start: 0.7538 (pm20) cc_final: 0.6964 (pm20) REVERT: v 83 GLU cc_start: 0.8255 (mp0) cc_final: 0.8048 (mp0) outliers start: 145 outliers final: 90 residues processed: 1250 average time/residue: 0.6874 time to fit residues: 1482.0318 Evaluate side-chains 1198 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1100 time to evaluate : 5.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 494 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 87 GLN Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 55 VAL Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 58 ASP Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain i residue 174 GLN Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 268 GLN Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 352 ASP Chi-restraints excluded: chain l residue 380 LEU Chi-restraints excluded: chain l residue 419 THR Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain o residue 128 SER Chi-restraints excluded: chain p residue 11 THR Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 148 GLU Chi-restraints excluded: chain w residue 296 MET Chi-restraints excluded: chain w residue 305 LEU Chi-restraints excluded: chain w residue 317 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 599 optimal weight: 0.6980 chunk 490 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 721 optimal weight: 0.9990 chunk 779 optimal weight: 10.0000 chunk 642 optimal weight: 9.9990 chunk 715 optimal weight: 7.9990 chunk 245 optimal weight: 9.9990 chunk 578 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 HIS H 71 GLN ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN O 144 ASN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 122 HIS U 52 ASN ** h 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 232 HIS i 235 ASN ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 GLN o 79 ASN ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 81 GLN r 220 HIS ** u 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 82 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 67858 Z= 0.304 Angle : 0.588 10.947 91888 Z= 0.295 Chirality : 0.043 0.197 10027 Planarity : 0.005 0.074 11515 Dihedral : 12.423 172.553 9959 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 3.02 % Allowed : 15.35 % Favored : 81.63 % 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: 0.93 (0.09), residues: 8027 helix: 1.56 (0.08), residues: 4266 sheet: 0.19 (0.25), residues: 419 loop : -0.52 (0.11), residues: 3342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP u 86 HIS 0.013 0.001 HIS T 122 PHE 0.034 0.002 PHE l 335 TYR 0.022 0.002 TYR r 406 ARG 0.005 0.000 ARG w 75 *********************** 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 1350 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1138 time to evaluate : 6.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASN cc_start: 0.7194 (OUTLIER) cc_final: 0.6871 (t0) REVERT: B 50 MET cc_start: 0.8571 (tpt) cc_final: 0.8002 (tpt) REVERT: E 114 ARG cc_start: 0.7100 (tpp-160) cc_final: 0.6898 (mtp85) REVERT: G 115 GLN cc_start: 0.8336 (tm-30) cc_final: 0.8129 (tm-30) REVERT: G 119 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7999 (tp) REVERT: H 63 PRO cc_start: 0.6663 (Cg_endo) cc_final: 0.6399 (Cg_exo) REVERT: I 70 MET cc_start: 0.8764 (tmm) cc_final: 0.8305 (tmm) REVERT: K 89 LEU cc_start: 0.8551 (mt) cc_final: 0.8184 (mp) REVERT: L 86 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8240 (m-40) REVERT: M 677 GLN cc_start: 0.6720 (tm-30) cc_final: 0.6401 (tm-30) REVERT: M 691 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.8981 (tp) REVERT: N 133 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8327 (mmtt) REVERT: O 130 TYR cc_start: 0.7205 (m-80) cc_final: 0.6879 (m-80) REVERT: P 80 CYS cc_start: 0.7407 (t) cc_final: 0.7085 (t) REVERT: Q 104 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: U 9 LEU cc_start: 0.9056 (mm) cc_final: 0.8777 (mm) REVERT: V 58 ARG cc_start: 0.5587 (ttp-110) cc_final: 0.4517 (ttt180) REVERT: W 9 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: X 108 LEU cc_start: 0.6962 (mm) cc_final: 0.6517 (mt) REVERT: Z 78 PHE cc_start: 0.8517 (t80) cc_final: 0.8211 (t80) REVERT: b 70 PHE cc_start: 0.8814 (t80) cc_final: 0.8387 (t80) REVERT: b 108 ASP cc_start: 0.7784 (m-30) cc_final: 0.7510 (t0) REVERT: b 121 LYS cc_start: 0.6501 (ttpp) cc_final: 0.5945 (tmtt) REVERT: c 53 LYS cc_start: 0.8380 (tttp) cc_final: 0.8030 (ttpt) REVERT: c 70 MET cc_start: 0.8566 (mpp) cc_final: 0.8290 (mpp) REVERT: d 7 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7385 (mmmt) REVERT: d 99 ASP cc_start: 0.8429 (m-30) cc_final: 0.8144 (m-30) REVERT: g 113 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7321 (pt0) REVERT: g 115 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8221 (tt) REVERT: i 14 MET cc_start: 0.8800 (mtt) cc_final: 0.8541 (mtt) REVERT: j 33 LYS cc_start: 0.3428 (tptp) cc_final: 0.2209 (ttpp) REVERT: j 97 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7538 (mp) REVERT: l 203 MET cc_start: 0.8781 (mmm) cc_final: 0.8417 (tpt) REVERT: l 244 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8790 (m) REVERT: l 584 ILE cc_start: 0.5861 (OUTLIER) cc_final: 0.5249 (tt) REVERT: p 176 GLU cc_start: 0.8015 (tp30) cc_final: 0.7679 (tp30) REVERT: r 166 TYR cc_start: 0.8865 (t80) cc_final: 0.8615 (t80) REVERT: r 294 MET cc_start: 0.9217 (mmm) cc_final: 0.8552 (mmm) REVERT: s 57 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8622 (p) REVERT: s 127 TYR cc_start: 0.6919 (t80) cc_final: 0.6289 (m-80) REVERT: s 287 HIS cc_start: 0.8136 (t-90) cc_final: 0.7585 (m-70) REVERT: u 68 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8360 (mm) REVERT: v 16 GLU cc_start: 0.6429 (mt-10) cc_final: 0.4263 (tm-30) REVERT: v 54 GLN cc_start: 0.7846 (pm20) cc_final: 0.7221 (pm20) outliers start: 212 outliers final: 139 residues processed: 1274 average time/residue: 0.6313 time to fit residues: 1372.3298 Evaluate side-chains 1236 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1084 time to evaluate : 5.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 317 THR Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 443 ASP Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 494 SER Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 691 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 50 ASP Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 55 VAL Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 152 SER Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain e residue 58 ASP Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 331 VAL Chi-restraints excluded: chain i residue 344 SER Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain l residue 244 SER Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 294 THR Chi-restraints excluded: chain l residue 352 ASP Chi-restraints excluded: chain l residue 419 THR Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 458 LEU Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 578 SER Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain o residue 128 SER Chi-restraints excluded: chain p residue 11 THR Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain p residue 137 VAL Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 85 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 220 HIS Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 299 VAL Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 169 GLN Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 296 MET Chi-restraints excluded: chain w residue 305 LEU Chi-restraints excluded: chain w residue 317 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 1.9990 chunk 542 optimal weight: 0.9990 chunk 374 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 344 optimal weight: 0.7980 chunk 484 optimal weight: 6.9990 chunk 724 optimal weight: 4.9990 chunk 766 optimal weight: 9.9990 chunk 378 optimal weight: 7.9990 chunk 686 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN O 87 GLN ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** h 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 235 ASN j 83 ASN m 175 ASN ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 220 HIS ** u 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 82 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 67858 Z= 0.172 Angle : 0.521 10.562 91888 Z= 0.261 Chirality : 0.040 0.176 10027 Planarity : 0.004 0.056 11515 Dihedral : 11.774 172.782 9959 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.16 % Favored : 95.83 % Rotamer: Outliers : 2.35 % Allowed : 16.50 % Favored : 81.14 % 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: 1.13 (0.10), residues: 8027 helix: 1.74 (0.08), residues: 4249 sheet: 0.22 (0.26), residues: 417 loop : -0.44 (0.11), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.010 0.001 HIS r 220 PHE 0.034 0.001 PHE l 335 TYR 0.023 0.001 TYR l 422 ARG 0.007 0.000 ARG u 98 *********************** 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 1339 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1174 time to evaluate : 6.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TRP cc_start: 0.7840 (p-90) cc_final: 0.7632 (p-90) REVERT: B 50 MET cc_start: 0.8510 (tpt) cc_final: 0.7977 (tpt) REVERT: G 115 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7747 (tm-30) REVERT: I 70 MET cc_start: 0.8592 (tmm) cc_final: 0.8251 (tmm) REVERT: J 324 MET cc_start: 0.7898 (tmm) cc_final: 0.7445 (tmm) REVERT: K 89 LEU cc_start: 0.8687 (mt) cc_final: 0.8337 (mp) REVERT: L 86 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8185 (m-40) REVERT: M 677 GLN cc_start: 0.6684 (tm-30) cc_final: 0.6409 (tm-30) REVERT: M 691 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.8980 (tp) REVERT: N 133 LYS cc_start: 0.8553 (mmtm) cc_final: 0.8352 (mmtt) REVERT: O 130 TYR cc_start: 0.7222 (m-80) cc_final: 0.6858 (m-80) REVERT: P 80 CYS cc_start: 0.7515 (t) cc_final: 0.7233 (t) REVERT: Q 104 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: Q 216 ARG cc_start: 0.8739 (mtp180) cc_final: 0.8476 (ttm170) REVERT: U 4 ARG cc_start: 0.4815 (tmt170) cc_final: 0.3979 (mtm180) REVERT: V 58 ARG cc_start: 0.5509 (ttp-110) cc_final: 0.4477 (ttt180) REVERT: X 108 LEU cc_start: 0.6866 (mm) cc_final: 0.6430 (mt) REVERT: b 70 PHE cc_start: 0.8759 (t80) cc_final: 0.8333 (t80) REVERT: c 53 LYS cc_start: 0.8449 (tttp) cc_final: 0.8109 (ttpt) REVERT: c 70 MET cc_start: 0.8570 (mpp) cc_final: 0.8273 (mpp) REVERT: d 7 LYS cc_start: 0.8020 (mmtp) cc_final: 0.7355 (mmmt) REVERT: d 99 ASP cc_start: 0.8424 (m-30) cc_final: 0.8081 (m-30) REVERT: f 56 ILE cc_start: 0.7448 (pt) cc_final: 0.7235 (mt) REVERT: f 67 LEU cc_start: 0.8101 (mm) cc_final: 0.7872 (mm) REVERT: f 68 GLU cc_start: 0.8582 (tm-30) cc_final: 0.7804 (tm-30) REVERT: i 14 MET cc_start: 0.8747 (mtt) cc_final: 0.8488 (mtt) REVERT: j 33 LYS cc_start: 0.3456 (tptp) cc_final: 0.2273 (ttpp) REVERT: k 9 ILE cc_start: 0.9251 (mt) cc_final: 0.8918 (mp) REVERT: l 20 MET cc_start: 0.8894 (mtm) cc_final: 0.8679 (mtm) REVERT: l 140 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8953 (tt) REVERT: l 203 MET cc_start: 0.8882 (mmm) cc_final: 0.8496 (tpt) REVERT: l 482 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6899 (mpp) REVERT: l 584 ILE cc_start: 0.5936 (OUTLIER) cc_final: 0.5363 (tt) REVERT: p 176 GLU cc_start: 0.8003 (tp30) cc_final: 0.7678 (tp30) REVERT: r 86 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8552 (mttm) REVERT: s 127 TYR cc_start: 0.6929 (t80) cc_final: 0.6233 (m-80) REVERT: s 287 HIS cc_start: 0.8082 (t-90) cc_final: 0.7517 (m-70) REVERT: u 68 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8351 (mm) REVERT: v 16 GLU cc_start: 0.6367 (mt-10) cc_final: 0.4309 (tm-30) REVERT: v 54 GLN cc_start: 0.7795 (pm20) cc_final: 0.7199 (pm20) REVERT: v 83 GLU cc_start: 0.8280 (mp0) cc_final: 0.7916 (mp0) REVERT: w 115 GLU cc_start: 0.6561 (pp20) cc_final: 0.6147 (pp20) REVERT: w 160 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: w 241 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.5874 (t80) outliers start: 165 outliers final: 117 residues processed: 1279 average time/residue: 0.6253 time to fit residues: 1365.6844 Evaluate side-chains 1240 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1114 time to evaluate : 6.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 21 PHE Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 691 ILE Chi-restraints excluded: chain M residue 693 ASP Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 87 GLN Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain e residue 58 ASP Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 344 SER Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 183 VAL Chi-restraints excluded: chain l residue 206 ASN Chi-restraints excluded: chain l residue 211 MET Chi-restraints excluded: chain l residue 352 ASP Chi-restraints excluded: chain l residue 380 LEU Chi-restraints excluded: chain l residue 419 THR Chi-restraints excluded: chain l residue 458 LEU Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 578 SER Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain r residue 85 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 220 HIS Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 299 VAL Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 9 THR Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 244 THR Chi-restraints excluded: chain w residue 296 MET Chi-restraints excluded: chain w residue 305 LEU Chi-restraints excluded: chain w residue 317 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 638 optimal weight: 6.9990 chunk 435 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 570 optimal weight: 7.9990 chunk 316 optimal weight: 8.9990 chunk 654 optimal weight: 0.7980 chunk 529 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 391 optimal weight: 9.9990 chunk 688 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN H 76 GLN J 37 HIS ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 GLN M 202 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 604 GLN N 54 GLN O 87 GLN O 123 ASN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 170 GLN ** b 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 27 HIS ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 579 ASN ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 55 ASN p 13 GLN ** p 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 82 HIS w 149 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 67858 Z= 0.542 Angle : 0.718 11.478 91888 Z= 0.362 Chirality : 0.049 0.203 10027 Planarity : 0.006 0.065 11515 Dihedral : 12.091 173.831 9959 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.81 % Rotamer: Outliers : 4.04 % Allowed : 16.16 % Favored : 79.80 % 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: 0.38 (0.09), residues: 8027 helix: 1.13 (0.08), residues: 4265 sheet: -0.19 (0.25), residues: 426 loop : -0.80 (0.11), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP u 86 HIS 0.027 0.002 HIS r 220 PHE 0.036 0.002 PHE k 53 TYR 0.028 0.002 TYR g 76 ARG 0.008 0.001 ARG r 245 *********************** 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 1394 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1111 time to evaluate : 6.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASN cc_start: 0.7099 (OUTLIER) cc_final: 0.6824 (t0) REVERT: B 76 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8248 (t80) REVERT: C 65 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8235 (tmm) REVERT: G 115 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7780 (tm-30) REVERT: K 89 LEU cc_start: 0.8664 (mt) cc_final: 0.8335 (mp) REVERT: L 86 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8395 (m-40) REVERT: M 74 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8291 (m110) REVERT: M 677 GLN cc_start: 0.6699 (tm-30) cc_final: 0.6463 (tm-30) REVERT: M 691 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9113 (tp) REVERT: O 187 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: Q 104 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: U 4 ARG cc_start: 0.5181 (tmt170) cc_final: 0.4473 (mtm180) REVERT: U 10 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8016 (mmmm) REVERT: V 58 ARG cc_start: 0.5542 (ttp-110) cc_final: 0.4632 (ttt180) REVERT: W 9 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: X 108 LEU cc_start: 0.7269 (mm) cc_final: 0.6934 (mt) REVERT: X 116 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8627 (t) REVERT: X 153 ASP cc_start: 0.7818 (m-30) cc_final: 0.7562 (m-30) REVERT: Z 52 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8421 (mtm-85) REVERT: b 70 PHE cc_start: 0.8934 (t80) cc_final: 0.8488 (t80) REVERT: c 53 LYS cc_start: 0.8363 (tttp) cc_final: 0.8055 (ttpt) REVERT: c 70 MET cc_start: 0.8743 (mpp) cc_final: 0.8434 (mpp) REVERT: d 7 LYS cc_start: 0.8132 (mmtp) cc_final: 0.7471 (mmmt) REVERT: e 125 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7985 (mt) REVERT: e 143 ASP cc_start: 0.7753 (p0) cc_final: 0.7308 (p0) REVERT: f 68 GLU cc_start: 0.8712 (tm-30) cc_final: 0.7837 (tm-30) REVERT: g 115 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8373 (tt) REVERT: h 91 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6599 (ttpt) REVERT: i 14 MET cc_start: 0.8858 (mtt) cc_final: 0.8622 (mtt) REVERT: i 174 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8634 (mm-40) REVERT: j 33 LYS cc_start: 0.4021 (tptp) cc_final: 0.2402 (ttpp) REVERT: j 97 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7713 (mp) REVERT: l 401 MET cc_start: 0.8017 (tpp) cc_final: 0.7810 (mmm) REVERT: o 59 VAL cc_start: 0.9133 (t) cc_final: 0.8918 (m) REVERT: o 98 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8882 (mp) REVERT: p 159 LYS cc_start: 0.8284 (mmtm) cc_final: 0.8013 (mmtm) REVERT: r 55 THR cc_start: 0.9067 (m) cc_final: 0.8823 (m) REVERT: s 34 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8800 (ptt180) REVERT: s 287 HIS cc_start: 0.8203 (t-90) cc_final: 0.7670 (m-70) REVERT: u 64 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.7733 (t0) REVERT: u 68 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8363 (mm) REVERT: u 104 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8307 (tt0) REVERT: v 16 GLU cc_start: 0.6740 (mt-10) cc_final: 0.4511 (tm-30) REVERT: v 54 GLN cc_start: 0.7938 (pm20) cc_final: 0.7545 (pm20) REVERT: w 37 GLN cc_start: 0.7656 (pm20) cc_final: 0.7121 (tt0) REVERT: w 160 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7700 (mp0) outliers start: 283 outliers final: 206 residues processed: 1315 average time/residue: 0.6451 time to fit residues: 1458.3196 Evaluate side-chains 1282 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1054 time to evaluate : 6.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 193 ASP Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 260 ASN Chi-restraints excluded: chain M residue 317 THR Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 443 ASP Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 494 SER Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 691 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 50 ASP Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 187 GLN Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 55 VAL Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 52 ARG Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 108 ASP Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain c residue 96 ASP Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 152 SER Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain e residue 58 ASP Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 77 LEU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain h residue 91 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain i residue 174 GLN Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 271 THR Chi-restraints excluded: chain i residue 319 HIS Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 331 VAL Chi-restraints excluded: chain i residue 344 SER Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain l residue 183 VAL Chi-restraints excluded: chain l residue 206 ASN Chi-restraints excluded: chain l residue 211 MET Chi-restraints excluded: chain l residue 277 THR Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 294 THR Chi-restraints excluded: chain l residue 352 ASP Chi-restraints excluded: chain l residue 419 THR Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 458 LEU Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 551 SER Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 566 THR Chi-restraints excluded: chain l residue 578 SER Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 98 LEU Chi-restraints excluded: chain o residue 124 THR Chi-restraints excluded: chain p residue 11 THR Chi-restraints excluded: chain p residue 17 LEU Chi-restraints excluded: chain p residue 103 CYS Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 85 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 299 VAL Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 34 ARG Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 69 SER Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 169 GLN Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 317 GLN Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain u residue 133 THR Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 158 VAL Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 244 THR Chi-restraints excluded: chain w residue 305 LEU Chi-restraints excluded: chain w residue 317 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 5.9990 chunk 690 optimal weight: 0.6980 chunk 151 optimal weight: 20.0000 chunk 450 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 767 optimal weight: 10.0000 chunk 636 optimal weight: 0.9990 chunk 355 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 253 optimal weight: 0.8980 chunk 402 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN H 71 GLN I 51 ASN ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 GLN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 359 ASN N 54 GLN O 144 ASN O 153 GLN P 107 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN U 62 ASN ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 50 HIS e 132 ASN ** h 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 268 GLN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 78 GLN ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 230 ASN ** u 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 82 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 67858 Z= 0.171 Angle : 0.536 10.625 91888 Z= 0.270 Chirality : 0.040 0.177 10027 Planarity : 0.005 0.057 11515 Dihedral : 11.340 174.092 9959 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.99 % Favored : 96.00 % Rotamer: Outliers : 2.48 % Allowed : 18.07 % Favored : 79.45 % 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: 0.85 (0.10), residues: 8027 helix: 1.56 (0.08), residues: 4269 sheet: 0.04 (0.25), residues: 422 loop : -0.65 (0.11), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 86 HIS 0.008 0.001 HIS r 20 PHE 0.033 0.001 PHE l 335 TYR 0.025 0.001 TYR F 41 ARG 0.005 0.000 ARG H 92 *********************** 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 1329 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1155 time to evaluate : 6.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7820 (mmtp) cc_final: 0.7470 (mttt) REVERT: G 115 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7588 (tm-30) REVERT: I 70 MET cc_start: 0.8788 (tmm) cc_final: 0.8504 (tmm) REVERT: J 87 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: K 80 GLU cc_start: 0.7473 (mp0) cc_final: 0.7224 (tp30) REVERT: K 89 LEU cc_start: 0.8716 (mt) cc_final: 0.8406 (mp) REVERT: M 215 MET cc_start: 0.8076 (mmt) cc_final: 0.7860 (mmt) REVERT: M 677 GLN cc_start: 0.6798 (tm-30) cc_final: 0.6393 (tm-30) REVERT: M 691 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9020 (tp) REVERT: O 187 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7112 (tt0) REVERT: Q 104 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: Q 216 ARG cc_start: 0.8803 (mtp180) cc_final: 0.8540 (mtp180) REVERT: Q 308 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8820 (p90) REVERT: Q 409 VAL cc_start: 0.9481 (OUTLIER) cc_final: 0.9194 (m) REVERT: T 52 ARG cc_start: 0.8579 (mtp180) cc_final: 0.8368 (mtp180) REVERT: U 4 ARG cc_start: 0.5194 (tmt170) cc_final: 0.4447 (mtm180) REVERT: V 58 ARG cc_start: 0.5559 (ttp-110) cc_final: 0.4706 (ttt180) REVERT: W 9 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: X 108 LEU cc_start: 0.7206 (mm) cc_final: 0.6947 (mt) REVERT: X 116 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8485 (t) REVERT: X 122 MET cc_start: 0.7295 (mmt) cc_final: 0.7012 (mmt) REVERT: X 129 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: X 153 ASP cc_start: 0.7609 (m-30) cc_final: 0.7368 (m-30) REVERT: Z 52 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.6605 (mtm-85) REVERT: a 50 HIS cc_start: 0.3988 (OUTLIER) cc_final: 0.3024 (t70) REVERT: b 70 PHE cc_start: 0.8768 (t80) cc_final: 0.8372 (t80) REVERT: c 53 LYS cc_start: 0.8302 (tttp) cc_final: 0.8043 (ttpt) REVERT: c 60 GLU cc_start: 0.7165 (mp0) cc_final: 0.6853 (mp0) REVERT: c 70 MET cc_start: 0.8719 (mpp) cc_final: 0.8436 (mpp) REVERT: d 7 LYS cc_start: 0.8010 (mmtp) cc_final: 0.7339 (mmmt) REVERT: d 99 ASP cc_start: 0.8495 (m-30) cc_final: 0.8197 (m-30) REVERT: f 68 GLU cc_start: 0.8672 (tm-30) cc_final: 0.7930 (tm-30) REVERT: h 91 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6530 (ttpt) REVERT: i 14 MET cc_start: 0.8761 (mtt) cc_final: 0.8504 (mtt) REVERT: i 174 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8617 (mm-40) REVERT: j 33 LYS cc_start: 0.4148 (tptp) cc_final: 0.2448 (ttpp) REVERT: j 97 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7743 (mp) REVERT: l 140 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8911 (tt) REVERT: l 374 ILE cc_start: 0.9105 (mt) cc_final: 0.8805 (mm) REVERT: l 584 ILE cc_start: 0.6158 (OUTLIER) cc_final: 0.5677 (tt) REVERT: o 59 VAL cc_start: 0.9061 (t) cc_final: 0.8837 (m) REVERT: p 10 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7636 (mp) REVERT: p 54 GLU cc_start: 0.6540 (tm-30) cc_final: 0.6325 (tm-30) REVERT: p 159 LYS cc_start: 0.8236 (mmtm) cc_final: 0.8011 (mmtm) REVERT: p 176 GLU cc_start: 0.7974 (tp30) cc_final: 0.7678 (tp30) REVERT: p 179 MET cc_start: 0.6144 (mtm) cc_final: 0.5814 (mtm) REVERT: r 55 THR cc_start: 0.9027 (m) cc_final: 0.8766 (m) REVERT: r 86 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8675 (mttm) REVERT: r 441 ILE cc_start: 0.9258 (tp) cc_final: 0.9036 (tp) REVERT: s 43 TYR cc_start: 0.8513 (m-80) cc_final: 0.8269 (m-80) REVERT: s 109 SER cc_start: 0.8795 (m) cc_final: 0.8455 (t) REVERT: s 154 LEU cc_start: 0.9158 (mt) cc_final: 0.8929 (mt) REVERT: s 230 ASN cc_start: 0.8676 (m-40) cc_final: 0.8458 (m-40) REVERT: s 251 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7918 (t) REVERT: s 287 HIS cc_start: 0.8178 (t-90) cc_final: 0.7590 (m-70) REVERT: u 64 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.7598 (t0) REVERT: u 104 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8339 (tt0) REVERT: v 16 GLU cc_start: 0.6709 (mt-10) cc_final: 0.4627 (tm-30) REVERT: v 54 GLN cc_start: 0.7818 (pm20) cc_final: 0.7297 (pm20) REVERT: v 105 GLU cc_start: 0.7133 (mp0) cc_final: 0.6853 (mp0) REVERT: w 37 GLN cc_start: 0.7526 (pm20) cc_final: 0.7047 (tt0) REVERT: w 160 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7526 (mp0) outliers start: 174 outliers final: 123 residues processed: 1266 average time/residue: 0.6688 time to fit residues: 1448.4967 Evaluate side-chains 1259 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1116 time to evaluate : 5.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 443 ASP Chi-restraints excluded: chain M residue 494 SER Chi-restraints excluded: chain M residue 500 ILE Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 691 ILE Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 187 GLN Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 236 ASN Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Z residue 52 ARG Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain a residue 50 HIS Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain h residue 91 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain i residue 174 GLN Chi-restraints excluded: chain i residue 209 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 268 GLN Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain l residue 102 GLU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 206 ASN Chi-restraints excluded: chain l residue 211 MET Chi-restraints excluded: chain l residue 352 ASP Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 566 THR Chi-restraints excluded: chain l residue 578 SER Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 342 MET Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 69 SER Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 43 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 244 THR Chi-restraints excluded: chain w residue 305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 739 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 437 optimal weight: 4.9990 chunk 560 optimal weight: 0.0970 chunk 434 optimal weight: 0.5980 chunk 645 optimal weight: 10.0000 chunk 428 optimal weight: 1.9990 chunk 764 optimal weight: 20.0000 chunk 478 optimal weight: 5.9990 chunk 465 optimal weight: 9.9990 chunk 352 optimal weight: 6.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 359 ASN N 54 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 122 HIS U 52 ASN ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN ** u 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 82 HIS w 149 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 67858 Z= 0.266 Angle : 0.566 10.926 91888 Z= 0.285 Chirality : 0.042 0.182 10027 Planarity : 0.005 0.058 11515 Dihedral : 11.200 173.696 9959 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.67 % Favored : 95.32 % Rotamer: Outliers : 3.02 % Allowed : 18.14 % Favored : 78.83 % 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: 0.82 (0.10), residues: 8027 helix: 1.54 (0.08), residues: 4266 sheet: -0.02 (0.25), residues: 422 loop : -0.66 (0.11), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 51 HIS 0.018 0.001 HIS a 50 PHE 0.031 0.001 PHE l 335 TYR 0.025 0.001 TYR b 88 ARG 0.005 0.000 ARG H 92 *********************** 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 1331 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1119 time to evaluate : 6.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7597 (tm-30) REVERT: I 70 MET cc_start: 0.8792 (tmm) cc_final: 0.8406 (tmm) REVERT: J 87 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7646 (mm-30) REVERT: K 89 LEU cc_start: 0.8720 (mt) cc_final: 0.8419 (mp) REVERT: L 86 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8297 (m-40) REVERT: M 691 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9045 (tp) REVERT: O 187 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7081 (tt0) REVERT: Q 84 PHE cc_start: 0.7866 (m-80) cc_final: 0.7448 (m-80) REVERT: Q 99 MET cc_start: 0.9048 (ptm) cc_final: 0.8808 (ptt) REVERT: Q 104 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: Q 216 ARG cc_start: 0.8825 (mtp180) cc_final: 0.8567 (mtp180) REVERT: T 52 ARG cc_start: 0.8620 (mtp180) cc_final: 0.8194 (mtm-85) REVERT: U 4 ARG cc_start: 0.5599 (tmt170) cc_final: 0.4801 (mtm180) REVERT: U 10 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7989 (mmmm) REVERT: V 58 ARG cc_start: 0.5523 (ttp-110) cc_final: 0.4670 (ttt180) REVERT: W 9 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: X 108 LEU cc_start: 0.7249 (mm) cc_final: 0.7019 (mt) REVERT: X 116 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8540 (t) REVERT: X 122 MET cc_start: 0.7459 (mmt) cc_final: 0.7057 (mmt) REVERT: X 129 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7748 (pp20) REVERT: X 151 LYS cc_start: 0.8023 (tptp) cc_final: 0.7818 (tptm) REVERT: X 153 ASP cc_start: 0.7591 (m-30) cc_final: 0.7346 (m-30) REVERT: Z 52 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.6599 (mtm-85) REVERT: b 70 PHE cc_start: 0.8871 (t80) cc_final: 0.8456 (t80) REVERT: c 53 LYS cc_start: 0.8325 (tttp) cc_final: 0.8063 (ttpt) REVERT: c 60 GLU cc_start: 0.7200 (mp0) cc_final: 0.6871 (mp0) REVERT: c 70 MET cc_start: 0.8737 (mpp) cc_final: 0.8445 (mpp) REVERT: c 140 MET cc_start: 0.8555 (mmt) cc_final: 0.8279 (mmt) REVERT: d 7 LYS cc_start: 0.8033 (mmtp) cc_final: 0.7358 (mmmt) REVERT: e 125 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8010 (mt) REVERT: f 68 GLU cc_start: 0.8690 (tm-30) cc_final: 0.7954 (tm-30) REVERT: g 84 MET cc_start: 0.8989 (mmt) cc_final: 0.8734 (mmm) REVERT: h 91 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6543 (ttpt) REVERT: i 14 MET cc_start: 0.8789 (mtt) cc_final: 0.8531 (mtt) REVERT: i 174 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8641 (mm-40) REVERT: j 33 LYS cc_start: 0.4287 (tptp) cc_final: 0.2499 (ttpp) REVERT: j 97 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7712 (mp) REVERT: l 374 ILE cc_start: 0.9133 (mt) cc_final: 0.8850 (mm) REVERT: l 584 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5670 (tt) REVERT: o 59 VAL cc_start: 0.9097 (t) cc_final: 0.8866 (m) REVERT: p 159 LYS cc_start: 0.8304 (mmtm) cc_final: 0.8076 (mmtm) REVERT: p 179 MET cc_start: 0.6136 (mtm) cc_final: 0.5791 (mtm) REVERT: r 55 THR cc_start: 0.9005 (m) cc_final: 0.8750 (m) REVERT: r 114 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: s 109 SER cc_start: 0.8836 (m) cc_final: 0.8474 (t) REVERT: s 251 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.7952 (t) REVERT: s 287 HIS cc_start: 0.8178 (t-90) cc_final: 0.7624 (m-70) REVERT: u 64 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.7673 (t0) REVERT: u 104 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8364 (tt0) REVERT: v 16 GLU cc_start: 0.6644 (mt-10) cc_final: 0.4674 (tm-30) REVERT: v 54 GLN cc_start: 0.7888 (pm20) cc_final: 0.7488 (pm20) REVERT: w 37 GLN cc_start: 0.7513 (pm20) cc_final: 0.7068 (tt0) REVERT: w 160 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7600 (mp0) outliers start: 212 outliers final: 159 residues processed: 1273 average time/residue: 0.6295 time to fit residues: 1366.7845 Evaluate side-chains 1269 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1091 time to evaluate : 5.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 193 ASP Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain M residue 443 ASP Chi-restraints excluded: chain M residue 494 SER Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 691 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 ASP Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 172 ILE Chi-restraints excluded: chain O residue 187 GLN Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 417 SER Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Z residue 52 ARG Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain e residue 58 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain h residue 91 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain i residue 174 GLN Chi-restraints excluded: chain i residue 209 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain l residue 183 VAL Chi-restraints excluded: chain l residue 206 ASN Chi-restraints excluded: chain l residue 211 MET Chi-restraints excluded: chain l residue 352 ASP Chi-restraints excluded: chain l residue 419 THR Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 551 SER Chi-restraints excluded: chain l residue 566 THR Chi-restraints excluded: chain l residue 578 SER Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 85 SER Chi-restraints excluded: chain r residue 88 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 299 VAL Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 342 MET Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 69 SER Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 141 SER Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain s residue 169 GLN Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 314 ILE Chi-restraints excluded: chain s residue 317 GLN Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 244 THR Chi-restraints excluded: chain w residue 305 LEU Chi-restraints excluded: chain w residue 317 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 472 optimal weight: 0.8980 chunk 305 optimal weight: 0.7980 chunk 456 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 485 optimal weight: 8.9990 chunk 520 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 600 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: