Starting phenix.real_space_refine on Fri Feb 16 23:01:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1z_32259/02_2024/7w1z_32259_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1z_32259/02_2024/7w1z_32259.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1z_32259/02_2024/7w1z_32259_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1z_32259/02_2024/7w1z_32259_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1z_32259/02_2024/7w1z_32259_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1z_32259/02_2024/7w1z_32259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1z_32259/02_2024/7w1z_32259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1z_32259/02_2024/7w1z_32259_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1z_32259/02_2024/7w1z_32259_updated.pdb" } resolution = 2.6 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= 0.007 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 46 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44116 2.51 5 N 11236 2.21 5 O 12217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 320": "OE1" <-> "OE2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "J GLU 365": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 395": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M ASP 563": "OD1" <-> "OD2" Residue "M GLU 628": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 57": "OE1" <-> "OE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "T GLU 36": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V GLU 51": "OE1" <-> "OE2" Residue "V GLU 82": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "X PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 143": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Z GLU 49": "OE1" <-> "OE2" Residue "a GLU 95": "OE1" <-> "OE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 179": "OE1" <-> "OE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 130": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h GLU 37": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "i GLU 274": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l GLU 268": "OE1" <-> "OE2" Residue "l GLU 445": "OE1" <-> "OE2" Residue "l GLU 503": "OE1" <-> "OE2" Residue "l PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 100": "OE1" <-> "OE2" Residue "m GLU 138": "OE1" <-> "OE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s GLU 143": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s GLU 192": "OE1" <-> "OE2" Residue "s GLU 202": "OE1" <-> "OE2" Residue "s GLU 206": "OE1" <-> "OE2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "s GLU 253": "OE1" <-> "OE2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "u GLU 155": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 38": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w GLU 160": "OE1" <-> "OE2" Residue "w GLU 274": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Residue "w GLU 333": "OE1" <-> "OE2" Residue "w GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68127 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} 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: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 684 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5293 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 657} 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: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 734 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 91} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 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: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1161 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1311 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 135} 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: "d" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1457 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 164} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1005 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4797 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "m" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1276 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 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: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3624 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} 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: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} 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: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1036 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PEE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 145 Unusual residues: {' UQ': 1, 'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 133 Unusual residues: {' UQ': 1, 'NDP': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' 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: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'970': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "V" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 94 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" 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: "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: 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: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'PEE': 2, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "k" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "l" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 196 Unusual residues: {'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "o" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 254 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 89 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "u" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 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 2718 SG CYS A 382 48.339 49.202 170.462 1.00 21.25 S ATOM 3060 SG CYS A 425 47.482 45.598 176.181 1.00 28.63 S ATOM 2738 SG CYS A 385 45.165 44.702 170.285 1.00 20.14 S ATOM 2699 SG CYS A 379 42.905 49.578 174.019 1.00 21.61 S ATOM 3961 SG CYS B 113 38.161 64.216 135.117 1.00 5.81 S ATOM 3980 SG CYS B 116 43.227 62.246 139.082 1.00 14.15 S ATOM 4003 SG CYS B 119 44.404 64.801 133.556 1.00 8.70 S ATOM 4332 SG CYS B 162 41.946 58.930 134.178 1.00 5.41 S ATOM 4030 SG CYS B 123 50.490 67.771 129.250 1.00 0.11 S ATOM 4256 SG CYS B 152 49.142 65.915 123.272 1.00 7.84 S ATOM 4303 SG CYS B 158 47.198 62.206 128.303 1.00 14.25 S ATOM 4282 SG CYS B 155 53.191 62.483 126.920 1.00 7.54 S ATOM 5724 SG CYS C 166 55.893 66.122 119.393 1.00 16.48 S ATOM 4996 SG CYS C 72 56.574 67.670 112.993 1.00 3.83 S ATOM 4990 SG CYS C 71 61.763 66.001 116.308 1.00 12.83 S ATOM 5494 SG CYS C 136 58.158 71.130 118.289 1.00 5.56 S ATOM 14946 SG CYS M 131 41.891 62.319 151.061 1.00 17.41 S ATOM 14925 SG CYS M 128 45.795 57.891 148.120 1.00 12.53 S ATOM 14986 SG CYS M 137 47.537 61.292 153.433 1.00 10.74 S ATOM 15318 SG CYS M 179 45.443 61.506 164.380 1.00 11.30 S ATOM 15672 SG CYS M 226 42.261 64.168 160.013 1.00 13.79 S ATOM 15342 SG CYS M 182 39.745 63.966 165.926 1.00 22.56 S ATOM 15295 SG CYS M 176 39.815 58.582 162.521 1.00 10.78 S ATOM 14543 SG CYS M 78 56.878 57.158 168.650 1.00 15.95 S ATOM 14644 SG CYS M 92 54.912 59.306 170.838 1.00 18.18 S ATOM 14432 SG CYS M 64 50.679 59.079 168.527 1.00 10.66 S ATOM 14518 SG CYS M 75 51.889 57.231 165.459 1.00 11.43 S ATOM 21478 SG CYS O 135 32.452 31.348 177.680 1.00 37.64 S ATOM 21512 SG CYS O 140 32.365 28.076 179.124 1.00 51.89 S ATOM 21792 SG CYS O 176 36.751 33.055 180.709 1.00 44.22 S ATOM 21815 SG CYS O 180 37.286 29.929 181.726 1.00 52.52 S ATOM 28547 SG CYS T 86 30.847 50.992 142.667 1.00 25.45 S ATOM 28725 SG CYS T 111 31.943 54.404 143.581 1.00 17.73 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.60 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.60 Time building chain proxies: 26.28, per 1000 atoms: 0.39 Number of scatterers: 68127 At special positions: 0 Unit cell: (216.988, 222.359, 227.73, 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 482 16.00 P 46 15.00 Mg 1 11.99 O 12217 8.00 N 11236 7.00 C 44116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.04 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " 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: 20.02 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb=" SF4 A 501 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " 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=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " 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="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " 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="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " 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=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 364 helices and 29 sheets defined 52.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.52 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.451A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 204 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 removed outlier: 3.766A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) 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 334 removed outlier: 5.278A pdb=" N THR A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) 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: 4.234A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.013A pdb=" N ASP A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 441 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.558A 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 206 removed outlier: 5.656A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 135 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 195 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: 4.147A 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: 4.253A 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 39 removed outlier: 5.003A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 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 95 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.937A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 61 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 78 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 20 through 22 No H-bonds generated for 'chain 'I' and resid 20 through 22' 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 75 removed outlier: 4.121A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 5.238A 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 222 removed outlier: 3.859A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.951A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 345 through 348 No H-bonds generated for 'chain 'J' and resid 345 through 348' Processing helix chain 'J' and resid 350 through 356 removed outlier: 5.759A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'K' and resid 77 through 80 Processing helix chain 'K' and resid 85 through 95 removed outlier: 4.362A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (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 73 removed outlier: 4.041A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.735A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) 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 134 through 136 No H-bonds generated for 'chain 'M' and resid 134 through 136' 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: 3.733A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' Processing helix chain 'M' and resid 288 through 298 removed outlier: 5.178A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 378 through 380 No H-bonds generated for 'chain 'M' and resid 378 through 380' 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 392 through 396 Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 removed outlier: 3.737A pdb=" N SER M 457 " --> pdb=" O ASP M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 478 through 481 No H-bonds generated for 'chain 'M' and resid 478 through 481' Processing helix chain 'M' and resid 484 through 504 removed outlier: 4.644A pdb=" N THR M 487 " --> pdb=" O SER M 484 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER M 504 " --> pdb=" O ARG M 501 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' 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 654 Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 695 removed outlier: 4.056A pdb=" N TYR M 695 " --> pdb=" O LYS M 692 " (cutoff:3.500A) 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: 3.516A 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 removed outlier: 3.761A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.090A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix removed outlier: 3.893A pdb=" N ASN O 90 " --> pdb=" O GLN O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 209 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.591A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.517A pdb=" N ASN P 164 " --> pdb=" O LYS P 161 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET P 173 " --> pdb=" O ILE P 170 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.231A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 60 No H-bonds generated for 'chain 'Q' and resid 58 through 60' Processing helix chain 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'Q' and resid 120 through 126 Processing helix chain 'Q' and resid 133 through 139 removed outlier: 3.789A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.573A 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: 3.857A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.970A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) 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: 4.694A 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 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 350 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: 4.418A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 4 No H-bonds generated for 'chain 'S' and resid 2 through 4' Processing helix chain 'S' and resid 6 through 31 removed outlier: 3.553A pdb=" N ILE S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 54 Processing helix chain 'T' and resid 67 through 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 4 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 80 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 32 through 97 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.470A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.609A 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 137 removed outlier: 4.296A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.901A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) 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 removed outlier: 3.532A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 53 removed outlier: 4.773A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 90 removed outlier: 3.546A pdb=" N TYR Z 87 " --> pdb=" O GLY Z 83 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER Z 90 " --> pdb=" O TYR Z 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 92 removed outlier: 4.113A pdb=" N THR a 78 " --> pdb=" O TYR a 74 " (cutoff:3.500A) Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.804A 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 70 through 73 No H-bonds generated for 'chain 'b' and resid 70 through 73' Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 83 through 85 No H-bonds generated for 'chain 'c' and resid 83 through 85' 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 129 through 149 Processing helix chain 'd' and resid 29 through 40 Processing helix chain 'd' and resid 42 through 58 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: 3.721A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.374A 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 175 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 95 Processing helix chain 'e' and resid 100 through 107 Processing helix chain 'e' and resid 115 through 132 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 72 Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.747A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' 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 removed outlier: 3.910A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 88 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 51 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.183A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 4.029A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.727A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 192 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.817A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.584A 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 272 Proline residue: i 262 - end of helix removed outlier: 3.731A pdb=" N ILE i 267 " --> pdb=" O TRP i 264 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN i 268 " --> pdb=" O MET i 265 " (cutoff:3.500A) Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.002A pdb=" N LEU i 287 " --> pdb=" O ALA i 283 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU i 296 " --> pdb=" O PHE i 292 " (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 337 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 31 through 34 No H-bonds generated for 'chain 'j' and resid 31 through 34' Processing helix chain 'j' and resid 56 through 80 removed outlier: 3.780A pdb=" N LEU j 63 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU j 64 " --> pdb=" O ILE j 60 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.660A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 20 Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 55 through 85 Proline residue: k 60 - end of helix removed outlier: 3.789A pdb=" N PHE k 66 " --> pdb=" O LEU k 63 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS k 69 " --> pdb=" O PHE k 66 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA k 72 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU k 73 " --> pdb=" O GLU k 70 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU k 75 " --> pdb=" O ALA k 72 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL k 81 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 23 removed outlier: 3.763A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 5.049A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.166A 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: 3.907A 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 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.661A pdb=" N GLY l 178 " --> pdb=" O TYR l 174 " (cutoff:3.500A) removed outlier: 4.024A 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: 4.067A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.220A 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 252 through 262 removed outlier: 4.318A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.314A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 3.683A pdb=" N ALA l 289 " --> pdb=" O THR l 285 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 319 Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.049A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 387 through 401 removed outlier: 4.111A pdb=" N LYS l 392 " --> pdb=" O PHE l 389 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASP l 393 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.644A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 469 removed outlier: 3.584A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.457A 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: 3.774A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.334A 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 533 Proline residue: l 530 - end of helix removed outlier: 4.069A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 removed outlier: 3.715A pdb=" N GLN l 546 " --> pdb=" O LEU l 542 " (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 removed outlier: 3.663A pdb=" N LEU l 589 " --> pdb=" O LYS l 585 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 removed outlier: 3.554A pdb=" N PHE m 47 " --> pdb=" O ILE m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.567A pdb=" N ALA m 73 " --> pdb=" O GLY m 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 87 through 108 Processing helix chain 'm' and resid 124 through 127 removed outlier: 3.687A pdb=" N ILE m 127 " --> pdb=" O ASP m 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 124 through 127' Processing helix chain 'm' and resid 138 through 147 removed outlier: 4.152A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 171 Processing helix chain 'n' and resid 4 through 8 Processing helix chain 'n' and resid 12 through 34 removed outlier: 3.614A pdb=" N LEU n 16 " --> pdb=" O VAL n 13 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL n 17 " --> pdb=" O HIS n 14 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.925A pdb=" N PHE n 23 " --> pdb=" O GLY n 20 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG n 30 " --> pdb=" O LEU n 27 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 23 Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.686A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 117 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.701A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 95 through 97 No H-bonds generated for 'chain 'p' and resid 95 through 97' Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.678A pdb=" N TRP p 133 " --> pdb=" O ARG p 129 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (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: 4.092A 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: 4.331A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 80 removed outlier: 3.723A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.557A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.705A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.371A 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: 3.601A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA r 145 " --> pdb=" O ARG r 142 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE r 151 " --> pdb=" O TYR r 148 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR r 153 " --> pdb=" O LEU r 150 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU r 154 " --> pdb=" O PHE r 151 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.927A pdb=" N VAL r 165 " --> pdb=" O VAL r 162 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN r 168 " --> pdb=" O VAL r 165 " (cutoff:3.500A) removed outlier: 4.135A 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 198 Processing helix chain 'r' and resid 201 through 206 removed outlier: 3.589A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 3.992A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL r 221 " --> pdb=" O PRO r 217 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 237 through 249 removed outlier: 4.936A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.575A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 4.139A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 4.076A pdb=" N LEU r 296 " --> pdb=" O SER r 292 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL r 297 " --> pdb=" O HIS r 293 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.646A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 3.905A pdb=" N MET r 396 " --> pdb=" O ILE r 393 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY r 397 " --> pdb=" O ILE r 394 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA r 404 " --> pdb=" O MET r 401 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR r 406 " --> pdb=" O THR r 403 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER r 407 " --> pdb=" O ALA r 404 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU r 408 " --> pdb=" O LEU r 405 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR r 409 " --> pdb=" O TYR r 406 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 448 Proline residue: r 443 - end of helix removed outlier: 4.035A pdb=" N THR r 448 " --> pdb=" O LEU r 444 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.735A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 47 through 56 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.454A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 3.958A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.231A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 Processing helix chain 's' and resid 174 through 176 No H-bonds generated for 'chain 's' and resid 174 through 176' Processing helix chain 's' and resid 179 through 192 removed outlier: 3.551A pdb=" N MET s 184 " --> pdb=" O PRO s 180 " (cutoff:3.500A) Processing helix chain 's' and resid 204 through 207 No H-bonds generated for 'chain 's' and resid 204 through 207' Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 217 through 242 Processing helix chain 's' and resid 252 through 274 Processing helix chain 's' and resid 282 through 291 Processing helix chain 's' and resid 293 through 310 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 80 through 91 Processing helix chain 'u' and resid 97 through 99 No H-bonds generated for 'chain 'u' and resid 97 through 99' Processing helix chain 'u' and resid 102 through 114 removed outlier: 3.668A pdb=" N ASP u 113 " --> pdb=" O GLU u 109 " (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 123 removed outlier: 3.511A pdb=" N LYS v 113 " --> pdb=" O LEU v 109 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG v 114 " --> pdb=" O GLN v 110 " (cutoff:3.500A) Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 95 through 97 No H-bonds generated for 'chain 'w' and resid 95 through 97' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 175 removed outlier: 3.935A pdb=" N GLU w 171 " --> pdb=" O VAL w 168 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA w 172 " --> pdb=" O PHE w 169 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 192 Processing helix chain 'w' and resid 195 through 197 No H-bonds generated for 'chain 'w' and resid 195 through 197' Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 243 Processing helix chain 'w' and resid 245 through 250 Processing helix chain 'w' and resid 260 through 263 No H-bonds generated for 'chain 'w' and resid 260 through 263' Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 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: 6.974A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.324A 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: 5.896A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.672A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.386A 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: 3.695A pdb=" N GLN F 73 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.500A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.578A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.224A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.555A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.671A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.743A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.157A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Z, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AA, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.632A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.485A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'w' and resid 84 through 86 2898 hydrogen bonds defined for protein. 8010 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: 20.55 Time building geometry restraints manager: 22.15 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: 27708 1.40 - 1.62: 41149 1.62 - 1.84: 879 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 69816 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 1.70e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.289 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.633 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.300 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 ... (remaining 69811 not shown) Histogram of bond angle deviations from ideal: 73.54 - 85.94: 76 85.94 - 98.34: 3 98.34 - 110.74: 23317 110.74 - 123.15: 67907 123.15 - 135.55: 3092 Bond angle restraints: 94395 Sorted by residual: angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 124.49 -16.75 1.95e+00 2.62e-01 7.35e+01 angle pdb=" N GLU T 64 " pdb=" CA GLU T 64 " pdb=" C GLU T 64 " ideal model delta sigma weight residual 111.36 120.48 -9.12 1.09e+00 8.42e-01 7.01e+01 angle pdb=" N MET b 120 " pdb=" CA MET b 120 " pdb=" C MET b 120 " ideal model delta sigma weight residual 109.62 121.31 -11.69 1.50e+00 4.44e-01 6.07e+01 angle pdb=" C51 CDL a 201 " pdb=" CB5 CDL a 201 " pdb=" OB6 CDL a 201 " ideal model delta sigma weight residual 111.33 121.15 -9.82 1.32e+00 5.72e-01 5.51e+01 angle pdb=" C11 CDL i 401 " pdb=" CA5 CDL i 401 " pdb=" OA6 CDL i 401 " ideal model delta sigma weight residual 111.33 120.33 -9.00 1.32e+00 5.72e-01 4.63e+01 ... (remaining 94390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 40577 35.95 - 71.90: 1813 71.90 - 107.84: 126 107.84 - 143.79: 23 143.79 - 179.74: 13 Dihedral angle restraints: 42552 sinusoidal: 18461 harmonic: 24091 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual 257.59 77.85 179.74 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 80.65 -140.65 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -138.01 52.01 1 1.00e+01 1.00e-02 3.69e+01 ... (remaining 42549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 9335 0.078 - 0.156: 821 0.156 - 0.235: 26 0.235 - 0.313: 5 0.313 - 0.391: 8 Chirality restraints: 10195 Sorted by residual: chirality pdb=" CA VAL T 62 " pdb=" N VAL T 62 " pdb=" C VAL T 62 " pdb=" CB VAL T 62 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA TYR m 60 " pdb=" N TYR m 60 " pdb=" C TYR m 60 " pdb=" CB TYR m 60 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA PHE T 55 " pdb=" N PHE T 55 " pdb=" C PHE T 55 " pdb=" CB PHE T 55 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 10192 not shown) Planarity restraints: 11762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.435 2.00e-02 2.50e+03 3.84e-01 1.84e+03 pdb=" C18 UQ J 402 " 0.471 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " 0.397 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " -0.022 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.410 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ C 304 " 0.350 2.00e-02 2.50e+03 3.23e-01 1.30e+03 pdb=" C18 UQ C 304 " -0.331 2.00e-02 2.50e+03 pdb=" C19 UQ C 304 " -0.389 2.00e-02 2.50e+03 pdb=" C20 UQ C 304 " -0.001 2.00e-02 2.50e+03 pdb=" C21 UQ C 304 " 0.371 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " 0.325 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C13 UQ J 402 " -0.297 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " -0.380 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " -0.000 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " 0.352 2.00e-02 2.50e+03 ... (remaining 11759 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 6658 2.74 - 3.28: 66217 3.28 - 3.82: 119568 3.82 - 4.36: 148863 4.36 - 4.90: 244483 Nonbonded interactions: 585789 Sorted by model distance: nonbonded pdb=" OH TYR c 62 " pdb=" O ASP c 74 " model vdw 2.204 2.440 nonbonded pdb=" NZ LYS C 119 " pdb=" OE1 GLU j 32 " model vdw 2.205 2.520 nonbonded pdb=" O LEU m 61 " pdb=" OH TYR s 114 " model vdw 2.212 2.440 nonbonded pdb=" ND2 ASN L 109 " pdb=" O LEU L 111 " model vdw 2.213 2.520 nonbonded pdb=" OG SER C 61 " pdb=" OD1 ASP s 51 " model vdw 2.215 2.440 ... (remaining 585784 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=0.60 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: 1.980 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: 0.070 Extract box with map and model: 8.690 Check model and map are aligned: 0.840 Set scattering table: 0.480 Process input model: 151.740 Find NCS groups from input model: 2.200 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:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.318 69816 Z= 0.528 Angle : 0.815 17.763 94395 Z= 0.411 Chirality : 0.045 0.391 10195 Planarity : 0.010 0.384 11762 Dihedral : 18.925 179.738 26996 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.51 % Rotamer: Outliers : 1.37 % Allowed : 15.52 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.94 (0.09), residues: 8173 helix: 1.51 (0.08), residues: 4321 sheet: 0.05 (0.24), residues: 428 loop : -0.39 (0.11), residues: 3424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.011 0.001 HIS p 51 PHE 0.028 0.002 PHE i 292 TYR 0.023 0.002 TYR l 587 ARG 0.008 0.000 ARG h 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1079 time to evaluate : 5.814 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: A 298 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: A 456 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 101 ASP cc_start: 0.9158 (m-30) cc_final: 0.8941 (m-30) REVERT: J 341 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8029 (tp40) REVERT: N 136 GLU cc_start: 0.8702 (pm20) cc_final: 0.8444 (mp0) REVERT: V 95 CYS cc_start: 0.8603 (m) cc_final: 0.8158 (t) REVERT: b 120 MET cc_start: 0.7647 (ttp) cc_final: 0.7220 (ttp) REVERT: c 149 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8124 (mp) outliers start: 98 outliers final: 75 residues processed: 1155 average time/residue: 1.6359 time to fit residues: 2415.2564 Evaluate side-chains 1142 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1064 time to evaluate : 5.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 336 GLU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 140 CYS Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 102 ASP Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain i residue 182 SER Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 288 THR Chi-restraints excluded: chain l residue 371 THR Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 489 THR Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain o residue 29 THR Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 3 LYS Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 212 LEU Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain u residue 153 GLU Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 95 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 0.9990 chunk 610 optimal weight: 0.8980 chunk 338 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 411 optimal weight: 3.9990 chunk 325 optimal weight: 8.9990 chunk 630 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 383 optimal weight: 4.9990 chunk 469 optimal weight: 6.9990 chunk 731 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN A 451 GLN G 103 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN J 269 ASN K 77 GLN K 79 HIS N 13 GLN N 112 ASN N 135 GLN ** T 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 ASN Y 83 HIS a 189 ASN h 27 HIS j 108 GLN l 59 GLN l 274 GLN ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 62 GLN p 66 GLN r 304 GLN s 258 ASN u 64 ASN u 73 GLN w 202 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 69816 Z= 0.193 Angle : 0.529 10.478 94395 Z= 0.268 Chirality : 0.041 0.241 10195 Planarity : 0.004 0.057 11762 Dihedral : 15.798 178.048 10961 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.46 % Rotamer: Outliers : 2.41 % Allowed : 14.85 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 1.04 (0.09), residues: 8173 helix: 1.58 (0.08), residues: 4331 sheet: 0.10 (0.25), residues: 428 loop : -0.33 (0.11), residues: 3414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.009 0.001 HIS p 51 PHE 0.027 0.001 PHE i 292 TYR 0.022 0.001 TYR l 587 ARG 0.006 0.000 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1109 time to evaluate : 5.912 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: A 456 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7608 (tm-30) REVERT: E 92 GLU cc_start: 0.8870 (tt0) cc_final: 0.8566 (tt0) REVERT: G 89 LEU cc_start: 0.8639 (mt) cc_final: 0.8296 (mp) REVERT: G 143 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7490 (mt-10) REVERT: I 101 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8864 (pt) REVERT: J 165 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8713 (mm) REVERT: M 464 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7118 (tp-100) REVERT: M 636 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.7554 (p90) REVERT: N 41 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: N 136 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: U 82 LYS cc_start: 0.8082 (ptmm) cc_final: 0.7835 (ptpt) REVERT: X 111 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7700 (p0) REVERT: a 160 MET cc_start: 0.9443 (OUTLIER) cc_final: 0.9097 (mtt) REVERT: b 120 MET cc_start: 0.7704 (ttp) cc_final: 0.7486 (ttp) REVERT: c 81 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8308 (mmm160) REVERT: c 113 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8735 (pt) REVERT: f 46 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8674 (mp) REVERT: f 60 LYS cc_start: 0.8541 (tmtp) cc_final: 0.8234 (mttt) REVERT: i 68 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8097 (mpp) REVERT: j 44 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7122 (tmm) REVERT: m 135 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8234 (t80) REVERT: r 48 ASN cc_start: 0.8315 (p0) cc_final: 0.8040 (p0) REVERT: r 103 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: r 271 MET cc_start: 0.9469 (mmp) cc_final: 0.9191 (mmp) REVERT: s 100 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9087 (mt) REVERT: w 354 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8579 (tp) outliers start: 172 outliers final: 70 residues processed: 1205 average time/residue: 1.6676 time to fit residues: 2611.7009 Evaluate side-chains 1166 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1079 time to evaluate : 5.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 464 GLN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain W residue 52 LYS Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 140 CYS Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 329 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 153 GLU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 354 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 608 optimal weight: 5.9990 chunk 497 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 732 optimal weight: 3.9990 chunk 791 optimal weight: 7.9990 chunk 652 optimal weight: 1.9990 chunk 726 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 587 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN I 110 GLN J 269 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS M 336 ASN M 540 ASN N 112 ASN N 135 GLN ** T 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 ASN Y 83 HIS i 36 ASN i 134 GLN j 108 GLN l 59 GLN l 320 ASN ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 117 GLN r 51 ASN r 304 GLN r 349 GLN u 64 ASN u 73 GLN w 132 GLN w 202 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 69816 Z= 0.371 Angle : 0.635 10.959 94395 Z= 0.324 Chirality : 0.047 0.219 10195 Planarity : 0.005 0.067 11762 Dihedral : 15.230 176.848 10878 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.08 % Rotamer: Outliers : 3.26 % Allowed : 14.54 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.68 (0.09), residues: 8173 helix: 1.25 (0.08), residues: 4334 sheet: 0.11 (0.25), residues: 416 loop : -0.48 (0.10), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP l 144 HIS 0.013 0.002 HIS J 37 PHE 0.056 0.002 PHE l 340 TYR 0.026 0.002 TYR J 180 ARG 0.008 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1099 time to evaluate : 6.114 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7860 (tppp) cc_final: 0.7645 (mmmm) REVERT: A 121 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: A 456 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7681 (tm-30) REVERT: B 114 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8947 (pt) REVERT: B 149 MET cc_start: 0.9557 (mmm) cc_final: 0.9249 (mmm) REVERT: C 49 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8414 (mmtm) REVERT: E 21 PHE cc_start: 0.8750 (m-80) cc_final: 0.8476 (m-80) REVERT: F 43 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: G 142 GLN cc_start: 0.7791 (tp40) cc_final: 0.7182 (tp40) REVERT: G 143 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7642 (mt-10) REVERT: H 66 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7436 (mptp) REVERT: I 101 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8882 (pt) REVERT: J 165 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8786 (mm) REVERT: J 303 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7227 (tpt-90) REVERT: J 341 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8028 (tp40) REVERT: L 154 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8164 (ptmm) REVERT: M 150 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8652 (mtp85) REVERT: M 427 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8826 (tp) REVERT: M 636 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.7615 (p90) REVERT: N 41 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: Q 197 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8184 (pmm) REVERT: V 82 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: W 98 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7672 (mmm) REVERT: X 74 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7232 (tt) REVERT: X 111 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7852 (p0) REVERT: Z 72 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7042 (tmtt) REVERT: a 160 MET cc_start: 0.9466 (OUTLIER) cc_final: 0.9245 (mtt) REVERT: c 81 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8277 (mmm160) REVERT: c 113 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8630 (pt) REVERT: c 159 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.7869 (tmtm) REVERT: f 60 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8226 (mttt) REVERT: f 68 GLU cc_start: 0.8904 (tp30) cc_final: 0.8645 (tp30) REVERT: i 28 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9102 (mm) REVERT: i 68 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8379 (mpp) REVERT: j 44 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7253 (tmm) REVERT: l 21 MET cc_start: 0.8774 (mtp) cc_final: 0.8526 (OUTLIER) REVERT: l 102 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: m 100 GLU cc_start: 0.8610 (tp30) cc_final: 0.8395 (tp30) REVERT: m 135 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8390 (t80) REVERT: p 63 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8553 (mp) REVERT: r 87 GLU cc_start: 0.8812 (tp30) cc_final: 0.8544 (tp30) REVERT: r 103 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8700 (tt0) REVERT: r 207 MET cc_start: 0.9006 (mmm) cc_final: 0.8700 (mmm) REVERT: r 355 MET cc_start: 0.9290 (tpp) cc_final: 0.8998 (tpp) REVERT: s 31 MET cc_start: 0.9490 (mtt) cc_final: 0.9286 (mtt) REVERT: s 108 MET cc_start: 0.9256 (mmp) cc_final: 0.8949 (mmp) REVERT: s 204 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7527 (tp30) REVERT: s 289 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9107 (mm) REVERT: v 106 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7160 (ttm170) REVERT: w 354 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8580 (tp) outliers start: 233 outliers final: 115 residues processed: 1241 average time/residue: 1.6105 time to fit residues: 2559.6538 Evaluate side-chains 1228 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1079 time to evaluate : 5.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 464 GLN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 336 GLU Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 82 GLU Chi-restraints excluded: chain W residue 52 LYS Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 140 CYS Chi-restraints excluded: chain Y residue 52 ARG Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 159 LYS Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 92 MET Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 28 LEU Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 182 SER Chi-restraints excluded: chain i residue 329 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 102 GLU Chi-restraints excluded: chain l residue 288 THR Chi-restraints excluded: chain l residue 371 THR Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain l residue 489 THR Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 94 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 63 LEU Chi-restraints excluded: chain r residue 3 LYS Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 130 LEU Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 290 SER Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 133 LEU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 289 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 165 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 106 ARG Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 354 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 0.7980 chunk 550 optimal weight: 10.0000 chunk 380 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 349 optimal weight: 8.9990 chunk 491 optimal weight: 0.4980 chunk 734 optimal weight: 9.9990 chunk 778 optimal weight: 4.9990 chunk 383 optimal weight: 3.9990 chunk 696 optimal weight: 0.9980 chunk 209 optimal weight: 8.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN G 103 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 110 ASN I 29 GLN I 110 GLN J 269 ASN K 77 GLN K 79 HIS M 336 ASN M 453 GLN M 540 ASN N 52 ASN N 112 ASN N 135 GLN ** T 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 ASN Y 83 HIS h 21 GLN i 322 GLN l 59 GLN l 320 ASN ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 117 GLN r 304 GLN u 16 GLN ** u 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN v 50 GLN w 202 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 69816 Z= 0.243 Angle : 0.549 10.578 94395 Z= 0.280 Chirality : 0.043 0.216 10195 Planarity : 0.005 0.061 11762 Dihedral : 14.643 178.160 10873 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 3.22 % Allowed : 15.07 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.84 (0.09), residues: 8173 helix: 1.41 (0.08), residues: 4325 sheet: 0.05 (0.25), residues: 410 loop : -0.42 (0.11), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP l 144 HIS 0.010 0.001 HIS J 37 PHE 0.027 0.002 PHE i 292 TYR 0.024 0.002 TYR l 587 ARG 0.008 0.000 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1102 time to evaluate : 6.376 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: A 52 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7206 (mtp-110) REVERT: A 54 LYS cc_start: 0.7801 (tppp) cc_final: 0.7597 (mmmm) REVERT: A 121 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: A 456 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7685 (tm-30) REVERT: B 114 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8925 (pt) REVERT: C 49 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8395 (mmtm) REVERT: G 133 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6516 (tp) REVERT: G 142 GLN cc_start: 0.7870 (tp40) cc_final: 0.7261 (tp40) REVERT: G 143 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7624 (mt-10) REVERT: H 96 ARG cc_start: 0.7331 (ttp80) cc_final: 0.7030 (ttm110) REVERT: I 101 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8885 (pt) REVERT: J 165 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8752 (mm) REVERT: J 341 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8006 (tp40) REVERT: L 154 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8130 (ptmm) REVERT: M 150 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8551 (mtp85) REVERT: M 636 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.7585 (p90) REVERT: N 41 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: O 209 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7966 (mtmp) REVERT: S 67 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: U 82 LYS cc_start: 0.8180 (ptmm) cc_final: 0.7878 (ptpt) REVERT: V 82 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: V 95 CYS cc_start: 0.8623 (m) cc_final: 0.8290 (m) REVERT: W 64 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7869 (t70) REVERT: W 98 MET cc_start: 0.7867 (mmm) cc_final: 0.7598 (mmm) REVERT: X 74 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7141 (tt) REVERT: X 111 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7807 (p0) REVERT: a 103 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: a 160 MET cc_start: 0.9452 (OUTLIER) cc_final: 0.9094 (mtt) REVERT: c 81 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8333 (mmm160) REVERT: c 113 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8589 (pt) REVERT: c 159 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.7895 (tmtm) REVERT: f 60 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8222 (mttt) REVERT: i 28 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9033 (mm) REVERT: i 68 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.8106 (mpp) REVERT: j 44 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7189 (tmm) REVERT: l 102 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: m 135 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8316 (t80) REVERT: r 87 GLU cc_start: 0.8771 (tp30) cc_final: 0.8529 (tp30) REVERT: r 103 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8675 (tt0) REVERT: s 24 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8040 (tp30) REVERT: s 151 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9214 (tp) REVERT: s 204 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7469 (tp30) REVERT: v 106 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7118 (ttm170) REVERT: w 55 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6748 (tt0) REVERT: w 354 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8580 (tp) outliers start: 230 outliers final: 114 residues processed: 1240 average time/residue: 1.6383 time to fit residues: 2605.8847 Evaluate side-chains 1235 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1086 time to evaluate : 5.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 464 GLN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 209 LYS Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 336 GLU Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 82 GLU Chi-restraints excluded: chain W residue 52 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 99 LYS Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 140 CYS Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 159 LYS Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain e residue 141 CYS Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 28 LEU Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 329 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 4 MET Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 102 GLU Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 551 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 130 LEU Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 349 GLN Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 106 ARG Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 354 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 8.9990 chunk 441 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 579 optimal weight: 10.0000 chunk 321 optimal weight: 6.9990 chunk 664 optimal weight: 6.9990 chunk 537 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 0.0040 chunk 698 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN B 59 GLN G 103 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 GLN I 110 GLN J 269 ASN K 79 HIS M 453 GLN N 52 ASN N 135 GLN ** T 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 ASN W 85 GLN j 108 GLN l 59 GLN l 320 ASN ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 117 GLN r 304 GLN u 16 GLN u 64 ASN u 73 GLN w 132 GLN w 202 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 69816 Z= 0.240 Angle : 0.548 10.615 94395 Z= 0.279 Chirality : 0.042 0.207 10195 Planarity : 0.005 0.062 11762 Dihedral : 14.271 179.723 10873 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.27 % Rotamer: Outliers : 3.26 % Allowed : 15.35 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.89 (0.09), residues: 8173 helix: 1.45 (0.08), residues: 4326 sheet: 0.05 (0.25), residues: 410 loop : -0.39 (0.11), residues: 3437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.009 0.001 HIS J 37 PHE 0.027 0.002 PHE i 292 TYR 0.023 0.002 TYR l 587 ARG 0.006 0.000 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1110 time to evaluate : 5.825 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: A 52 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7184 (mtp-110) REVERT: A 54 LYS cc_start: 0.7813 (tppp) cc_final: 0.7610 (mmmm) REVERT: A 121 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: A 174 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.6318 (ttm-80) REVERT: A 208 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8613 (tm-30) REVERT: A 271 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8636 (p) REVERT: A 298 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: A 456 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 114 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8911 (pt) REVERT: C 49 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8390 (mmtm) REVERT: C 101 ASP cc_start: 0.9143 (m-30) cc_final: 0.8925 (m-30) REVERT: E 92 GLU cc_start: 0.9021 (tt0) cc_final: 0.8723 (tt0) REVERT: G 133 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6589 (tp) REVERT: G 143 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7668 (mt-10) REVERT: I 101 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8883 (pt) REVERT: J 85 ARG cc_start: 0.9447 (OUTLIER) cc_final: 0.7631 (ppt-90) REVERT: J 165 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8739 (mm) REVERT: J 189 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8302 (mtpt) REVERT: J 303 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7395 (tpt-90) REVERT: J 341 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8028 (tp40) REVERT: L 154 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8129 (ptmm) REVERT: M 150 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8556 (mtp85) REVERT: M 427 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8806 (tp) REVERT: M 636 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.7581 (p90) REVERT: N 41 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: O 209 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7897 (mtmp) REVERT: Q 197 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.7586 (pmm) REVERT: S 67 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: U 82 LYS cc_start: 0.8176 (ptmm) cc_final: 0.7873 (ptpt) REVERT: V 82 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7290 (mm-30) REVERT: V 138 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: W 64 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7858 (t70) REVERT: X 74 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7132 (tt) REVERT: X 111 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7799 (p0) REVERT: Z 49 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: a 103 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7153 (mm-30) REVERT: a 160 MET cc_start: 0.9453 (OUTLIER) cc_final: 0.9091 (mtt) REVERT: c 43 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7266 (mmmm) REVERT: c 81 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8378 (mmm160) REVERT: c 113 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8656 (pt) REVERT: c 159 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.7890 (tmtm) REVERT: f 60 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8225 (mttt) REVERT: i 68 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8268 (mpp) REVERT: j 44 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7136 (tmm) REVERT: l 102 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: m 135 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8341 (t80) REVERT: o 25 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6650 (pp) REVERT: r 87 GLU cc_start: 0.8753 (tp30) cc_final: 0.8535 (tp30) REVERT: r 103 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8617 (tt0) REVERT: s 24 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.7976 (tp30) REVERT: s 204 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7460 (tp30) REVERT: s 289 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9044 (mm) REVERT: v 106 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7141 (ttm170) REVERT: w 354 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8584 (tp) outliers start: 233 outliers final: 129 residues processed: 1249 average time/residue: 1.6121 time to fit residues: 2587.6921 Evaluate side-chains 1257 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1082 time to evaluate : 5.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 464 GLN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 209 LYS Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 336 GLU Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 82 GLU Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 52 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 140 CYS Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 159 LYS Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain e residue 141 CYS Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 182 SER Chi-restraints excluded: chain i residue 329 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 4 MET Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 69 ILE Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 102 GLU Chi-restraints excluded: chain l residue 288 THR Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 371 THR Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 548 SER Chi-restraints excluded: chain l residue 551 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 29 THR Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 130 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 349 GLN Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 289 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain v residue 106 ARG Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 354 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 0.8980 chunk 700 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 456 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 778 optimal weight: 4.9990 chunk 646 optimal weight: 7.9990 chunk 360 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 408 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN B 59 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN J 269 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS M 453 GLN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 135 GLN ** T 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 ASN W 85 GLN l 59 GLN m 86 ASN o 117 GLN r 304 GLN s 258 ASN u 16 GLN u 64 ASN u 73 GLN w 202 HIS w 322 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 69816 Z= 0.302 Angle : 0.583 10.769 94395 Z= 0.297 Chirality : 0.044 0.198 10195 Planarity : 0.005 0.064 11762 Dihedral : 14.156 177.885 10871 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 3.47 % Allowed : 15.26 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.78 (0.09), residues: 8173 helix: 1.36 (0.08), residues: 4324 sheet: 0.01 (0.25), residues: 410 loop : -0.43 (0.11), residues: 3439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP u 86 HIS 0.010 0.001 HIS J 37 PHE 0.027 0.002 PHE i 292 TYR 0.023 0.002 TYR l 587 ARG 0.007 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1084 time to evaluate : 5.955 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: A 52 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7183 (mtp-110) REVERT: A 174 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.6314 (ttm-80) REVERT: A 298 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: A 456 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 49 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7231 (p0) REVERT: B 114 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8944 (pt) REVERT: C 49 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8408 (mmtm) REVERT: C 101 ASP cc_start: 0.9174 (m-30) cc_final: 0.8938 (m-30) REVERT: G 143 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7678 (mt-10) REVERT: H 96 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7123 (ttm110) REVERT: I 101 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8894 (pt) REVERT: J 85 ARG cc_start: 0.9461 (OUTLIER) cc_final: 0.7753 (ppt-90) REVERT: J 165 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8755 (mm) REVERT: J 189 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8397 (mtpt) REVERT: J 303 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7405 (tpt-90) REVERT: J 341 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8002 (tp40) REVERT: L 154 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8138 (ptmm) REVERT: M 150 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8624 (mtp85) REVERT: M 427 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8817 (tp) REVERT: M 636 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.7608 (p90) REVERT: N 41 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: O 209 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7917 (mtmp) REVERT: Q 197 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.7612 (pmm) REVERT: S 67 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: U 82 LYS cc_start: 0.8231 (ptmm) cc_final: 0.7933 (ptpt) REVERT: V 82 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: V 95 CYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8050 (m) REVERT: V 138 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: W 64 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7877 (t70) REVERT: W 98 MET cc_start: 0.7788 (mmm) cc_final: 0.7445 (mmm) REVERT: X 74 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7168 (tt) REVERT: X 111 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7811 (p0) REVERT: a 103 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7185 (mm-30) REVERT: a 160 MET cc_start: 0.9459 (OUTLIER) cc_final: 0.9096 (mtt) REVERT: c 43 LYS cc_start: 0.7920 (mttm) cc_final: 0.7290 (mmmm) REVERT: c 81 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8374 (mmm160) REVERT: c 113 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8612 (pt) REVERT: c 159 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.7965 (tmtm) REVERT: f 60 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8223 (mttt) REVERT: i 68 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.8311 (mpp) REVERT: j 44 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7171 (tmm) REVERT: l 102 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: m 78 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6809 (tpt) REVERT: m 135 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8401 (t80) REVERT: o 25 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6646 (pp) REVERT: r 66 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9142 (mt) REVERT: r 103 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8697 (tt0) REVERT: s 24 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8017 (tp30) REVERT: s 151 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9298 (tp) REVERT: s 204 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7471 (tp30) REVERT: s 289 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9039 (mm) REVERT: s 318 SER cc_start: 0.6881 (OUTLIER) cc_final: 0.6420 (t) REVERT: v 106 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7224 (ttm170) REVERT: w 55 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6768 (tt0) REVERT: w 319 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8585 (mt) REVERT: w 354 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8601 (tp) outliers start: 248 outliers final: 137 residues processed: 1234 average time/residue: 1.6165 time to fit residues: 2567.1202 Evaluate side-chains 1263 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1078 time to evaluate : 5.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 464 GLN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 209 LYS Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 336 GLU Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 82 GLU Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 52 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 99 LYS Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 140 CYS Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 159 LYS Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain e residue 141 CYS Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 182 SER Chi-restraints excluded: chain i residue 329 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 69 ILE Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 102 GLU Chi-restraints excluded: chain l residue 288 THR Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 371 THR Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain l residue 489 THR Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 548 SER Chi-restraints excluded: chain l residue 551 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 29 THR Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 130 LEU Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 349 GLN Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 133 LEU Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 289 LEU Chi-restraints excluded: chain s residue 318 SER Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain v residue 106 ARG Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 319 ILE Chi-restraints excluded: chain w residue 354 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 443 optimal weight: 1.9990 chunk 568 optimal weight: 1.9990 chunk 440 optimal weight: 0.9990 chunk 655 optimal weight: 6.9990 chunk 434 optimal weight: 9.9990 chunk 775 optimal weight: 6.9990 chunk 485 optimal weight: 8.9990 chunk 473 optimal weight: 10.0000 chunk 358 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN B 59 GLN G 103 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN I 29 GLN I 110 GLN J 269 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS M 453 GLN N 52 ASN N 135 GLN ** T 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 ASN W 85 GLN l 59 GLN o 117 GLN r 304 GLN ** u 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN ** v 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 124 ASN w 202 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 69816 Z= 0.322 Angle : 0.596 10.785 94395 Z= 0.304 Chirality : 0.045 0.189 10195 Planarity : 0.005 0.065 11762 Dihedral : 14.025 177.592 10871 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.12 % Rotamer: Outliers : 3.18 % Allowed : 15.72 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.73 (0.09), residues: 8173 helix: 1.31 (0.08), residues: 4325 sheet: 0.02 (0.25), residues: 409 loop : -0.46 (0.11), residues: 3439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP l 144 HIS 0.011 0.001 HIS J 37 PHE 0.036 0.002 PHE l 340 TYR 0.024 0.002 TYR l 587 ARG 0.009 0.001 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1084 time to evaluate : 7.296 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: A 52 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7175 (mtp-110) REVERT: A 121 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: A 174 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.6308 (ttm-80) REVERT: A 208 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8617 (tm-30) REVERT: A 298 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: A 456 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7681 (tm-30) REVERT: B 49 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7252 (p0) REVERT: B 114 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8947 (pt) REVERT: C 49 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8406 (mmtm) REVERT: C 101 ASP cc_start: 0.9182 (m-30) cc_final: 0.8944 (m-30) REVERT: G 143 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7674 (mt-10) REVERT: I 101 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8881 (pt) REVERT: J 85 ARG cc_start: 0.9468 (OUTLIER) cc_final: 0.7771 (ppt-90) REVERT: J 165 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8761 (mm) REVERT: J 189 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8396 (mtpt) REVERT: J 303 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7411 (tpt-90) REVERT: J 341 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8011 (tp40) REVERT: J 370 LYS cc_start: 0.7917 (tppt) cc_final: 0.7369 (ttpp) REVERT: L 154 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8141 (ptmm) REVERT: M 150 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8609 (mtp85) REVERT: M 427 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8820 (tp) REVERT: M 636 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.7617 (p90) REVERT: N 41 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: O 209 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7903 (mtmp) REVERT: Q 197 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8219 (pmm) REVERT: S 67 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: U 82 LYS cc_start: 0.8195 (ptmm) cc_final: 0.7907 (ptpt) REVERT: V 82 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7300 (mm-30) REVERT: V 95 CYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8022 (m) REVERT: V 138 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: W 64 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7882 (t70) REVERT: W 98 MET cc_start: 0.7808 (mmm) cc_final: 0.7511 (mmm) REVERT: X 74 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7190 (tt) REVERT: X 111 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7814 (p0) REVERT: a 103 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7212 (mm-30) REVERT: a 160 MET cc_start: 0.9462 (OUTLIER) cc_final: 0.9100 (mtt) REVERT: c 43 LYS cc_start: 0.7885 (mttm) cc_final: 0.7278 (mmmm) REVERT: c 113 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8687 (pt) REVERT: c 159 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.7848 (tmtm) REVERT: f 60 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8213 (mttt) REVERT: f 68 GLU cc_start: 0.8920 (tp30) cc_final: 0.8620 (tp30) REVERT: i 28 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9071 (mm) REVERT: i 68 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8362 (mpp) REVERT: j 44 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7175 (tmm) REVERT: l 102 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: m 78 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6946 (tpt) REVERT: m 135 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8343 (t80) REVERT: o 25 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6673 (pp) REVERT: r 66 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9143 (mt) REVERT: r 103 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8697 (tt0) REVERT: s 24 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8035 (tp30) REVERT: s 151 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9311 (tp) REVERT: s 204 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7489 (tp30) REVERT: s 318 SER cc_start: 0.6879 (OUTLIER) cc_final: 0.6408 (t) REVERT: v 106 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7359 (ttm170) REVERT: v 115 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6552 (ptm160) REVERT: w 55 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6755 (tt0) REVERT: w 319 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8582 (mt) REVERT: w 354 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8603 (tp) outliers start: 227 outliers final: 134 residues processed: 1219 average time/residue: 1.6172 time to fit residues: 2535.9226 Evaluate side-chains 1246 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1062 time to evaluate : 5.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 464 GLN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 633 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 209 LYS Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 197 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 336 GLU Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 67 GLU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 82 GLU Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 52 LYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 99 LYS Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 140 CYS Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 159 LYS Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 141 CYS Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 28 LEU Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 182 SER Chi-restraints excluded: chain i residue 329 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 69 ILE Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 102 GLU Chi-restraints excluded: chain l residue 288 THR Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 371 THR Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 442 LEU Chi-restraints excluded: chain l residue 489 THR Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 551 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 78 MET Chi-restraints excluded: chain m residue 94 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 29 THR Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 130 LEU Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 349 GLN Chi-restraints excluded: chain r residue 420 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 133 LEU Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 318 SER Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain v residue 106 ARG Chi-restraints excluded: chain v residue 115 ARG Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 319 ILE Chi-restraints excluded: chain w residue 354 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 0.6980 chunk 309 optimal weight: 0.9980 chunk 463 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 493 optimal weight: 6.9990 chunk 528 optimal weight: 0.9990 chunk 383 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 609 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN B 59 GLN G 103 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN I 29 GLN I 110 GLN J 269 ASN K 77 GLN K 79 HIS M 453 GLN N 52 ASN N 135 GLN T 123 HIS W 24 ASN W 85 GLN i 204 ASN l 59 GLN l 320 ASN o 117 GLN ** p 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN ** u 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 GLN w 124 ASN w 202 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 69816 Z= 0.148 Angle : 0.505 10.624 94395 Z= 0.255 Chirality : 0.040 0.181 10195 Planarity : 0.004 0.057 11762 Dihedral : 13.123 179.093 10870 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 2.27 % Allowed : 16.89 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 1.08 (0.09), residues: 8173 helix: 1.62 (0.08), residues: 4321 sheet: -0.00 (0.24), residues: 442 loop : -0.30 (0.11), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP l 144 HIS 0.008 0.001 HIS p 51 PHE 0.029 0.001 PHE i 292 TYR 0.021 0.001 TYR e 128 ARG 0.008 0.000 ARG I 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1283 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1121 time to evaluate : 7.238 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: A 38 GLU cc_start: 0.7773 (pt0) cc_final: 0.7242 (pm20) REVERT: A 52 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7164 (mtp-110) REVERT: A 174 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.6789 (ttm-80) REVERT: A 208 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8586 (tm-30) REVERT: A 456 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7631 (tm-30) REVERT: B 49 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7179 (p0) REVERT: C 101 ASP cc_start: 0.9078 (m-30) cc_final: 0.8844 (m-30) REVERT: G 89 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8360 (mt) REVERT: G 133 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6485 (tp) REVERT: G 143 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7589 (mt-10) REVERT: H 94 MET cc_start: 0.8231 (mmm) cc_final: 0.8023 (mtp) REVERT: I 29 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8122 (tp40) REVERT: I 101 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8844 (pt) REVERT: J 85 ARG cc_start: 0.9450 (OUTLIER) cc_final: 0.8035 (ppt-90) REVERT: J 373 LYS cc_start: 0.8090 (mptt) cc_final: 0.7860 (mmtt) REVERT: L 112 MET cc_start: 0.8310 (mmp) cc_final: 0.7998 (mmp) REVERT: N 136 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: O 141 MET cc_start: 0.8622 (tmm) cc_final: 0.8258 (tmt) REVERT: O 209 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7935 (mtmp) REVERT: U 82 LYS cc_start: 0.8134 (ptmm) cc_final: 0.7851 (ptpt) REVERT: V 82 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: V 95 CYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7827 (m) REVERT: X 111 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7774 (p0) REVERT: Z 49 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.6926 (mm-30) REVERT: a 160 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.9067 (mtt) REVERT: c 43 LYS cc_start: 0.7865 (mttm) cc_final: 0.7256 (mmmm) REVERT: c 81 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8269 (mmm160) REVERT: c 113 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8608 (pt) REVERT: c 159 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.7923 (tmtm) REVERT: f 60 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8212 (mttt) REVERT: i 68 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8066 (mpp) REVERT: j 44 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7116 (tmm) REVERT: m 135 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8088 (t80) REVERT: o 25 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6659 (pp) REVERT: p 57 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7174 (mmm) REVERT: r 271 MET cc_start: 0.9448 (mmp) cc_final: 0.9129 (mmp) REVERT: s 24 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: s 204 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7385 (tp30) REVERT: s 318 SER cc_start: 0.6449 (OUTLIER) cc_final: 0.6153 (t) REVERT: u 65 GLN cc_start: 0.7695 (tp-100) cc_final: 0.7489 (tp-100) REVERT: w 253 CYS cc_start: 0.4372 (OUTLIER) cc_final: 0.2933 (p) REVERT: w 319 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8518 (mt) outliers start: 162 outliers final: 76 residues processed: 1225 average time/residue: 1.6282 time to fit residues: 2567.4236 Evaluate side-chains 1184 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1079 time to evaluate : 7.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 464 GLN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 209 LYS Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 336 GLU Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 82 GLU Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain W residue 52 LYS Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 99 LYS Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 159 LYS Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 329 MET Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 130 LEU Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 313 SER Chi-restraints excluded: chain s residue 318 SER Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 319 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.6980 chunk 743 optimal weight: 0.7980 chunk 678 optimal weight: 0.8980 chunk 723 optimal weight: 2.9990 chunk 435 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 567 optimal weight: 5.9990 chunk 221 optimal weight: 0.5980 chunk 653 optimal weight: 4.9990 chunk 683 optimal weight: 0.9980 chunk 720 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN B 59 GLN ** F 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN I 29 GLN I 110 GLN J 269 ASN K 79 HIS M 453 GLN N 52 ASN N 135 GLN P 247 GLN W 24 ASN W 85 GLN j 108 GLN l 59 GLN o 117 GLN ** p 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN s 258 ASN u 16 GLN u 64 ASN u 73 GLN u 77 HIS v 44 GLN w 124 ASN w 202 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 69816 Z= 0.149 Angle : 0.506 11.387 94395 Z= 0.254 Chirality : 0.040 0.171 10195 Planarity : 0.004 0.054 11762 Dihedral : 12.686 179.751 10864 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 1.88 % Allowed : 17.52 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.09), residues: 8173 helix: 1.73 (0.08), residues: 4314 sheet: 0.11 (0.24), residues: 433 loop : -0.26 (0.11), residues: 3426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP l 144 HIS 0.009 0.001 HIS p 51 PHE 0.028 0.001 PHE i 292 TYR 0.024 0.001 TYR A 63 ARG 0.007 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1103 time to evaluate : 5.940 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: A 38 GLU cc_start: 0.7711 (pt0) cc_final: 0.7188 (pm20) REVERT: A 52 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7260 (mtp-110) REVERT: A 174 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.6750 (ttm-80) REVERT: A 208 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8593 (tm-30) REVERT: A 456 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7624 (tm-30) REVERT: B 49 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7190 (p0) REVERT: C 101 ASP cc_start: 0.9114 (m-30) cc_final: 0.8857 (m-30) REVERT: G 89 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8363 (mt) REVERT: G 143 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7592 (mt-10) REVERT: H 94 MET cc_start: 0.8251 (mmm) cc_final: 0.7983 (mtp) REVERT: I 101 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8837 (pt) REVERT: J 85 ARG cc_start: 0.9436 (OUTLIER) cc_final: 0.8049 (ppt-90) REVERT: J 117 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7752 (ttp-110) REVERT: L 112 MET cc_start: 0.8283 (mmp) cc_final: 0.7980 (mmp) REVERT: M 464 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7159 (tp-100) REVERT: M 707 MET cc_start: 0.9230 (mmp) cc_final: 0.8794 (mmp) REVERT: N 136 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: O 141 MET cc_start: 0.8604 (tmm) cc_final: 0.8241 (tmt) REVERT: O 209 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7951 (mtmp) REVERT: U 82 LYS cc_start: 0.8125 (ptmm) cc_final: 0.7853 (ptpt) REVERT: V 95 CYS cc_start: 0.8177 (t) cc_final: 0.7829 (m) REVERT: W 98 MET cc_start: 0.7842 (mmm) cc_final: 0.7589 (mmm) REVERT: X 74 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7280 (tt) REVERT: X 111 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7759 (p0) REVERT: Z 49 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.6929 (mm-30) REVERT: a 160 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.9057 (mtt) REVERT: c 43 LYS cc_start: 0.7868 (mttm) cc_final: 0.7248 (mmmm) REVERT: c 113 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8643 (pt) REVERT: c 159 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.7929 (tmtm) REVERT: f 60 LYS cc_start: 0.8532 (tmtp) cc_final: 0.8242 (mttt) REVERT: j 44 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7077 (tmm) REVERT: l 102 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: m 135 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8128 (t80) REVERT: o 25 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6676 (pp) REVERT: r 103 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: r 271 MET cc_start: 0.9444 (mmp) cc_final: 0.9148 (mmp) REVERT: s 24 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: s 62 ARG cc_start: 0.8283 (mtp180) cc_final: 0.8063 (mtp180) REVERT: s 204 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7381 (tp30) REVERT: s 318 SER cc_start: 0.6417 (OUTLIER) cc_final: 0.6133 (t) REVERT: w 55 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6627 (tt0) REVERT: w 253 CYS cc_start: 0.4353 (OUTLIER) cc_final: 0.3337 (p) REVERT: w 319 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8527 (mt) REVERT: w 354 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8613 (tp) outliers start: 134 outliers final: 76 residues processed: 1189 average time/residue: 1.6549 time to fit residues: 2529.8614 Evaluate side-chains 1184 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1081 time to evaluate : 5.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 464 GLN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 209 LYS Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 336 GLU Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain W residue 52 LYS Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 99 LYS Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 159 LYS Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 329 MET Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 102 GLU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 130 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain s residue 313 SER Chi-restraints excluded: chain s residue 318 SER Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 319 ILE Chi-restraints excluded: chain w residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 8.9990 chunk 764 optimal weight: 10.0000 chunk 466 optimal weight: 0.7980 chunk 362 optimal weight: 0.5980 chunk 531 optimal weight: 0.9980 chunk 801 optimal weight: 3.9990 chunk 738 optimal weight: 0.9980 chunk 638 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 493 optimal weight: 5.9990 chunk 391 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN F 25 GLN ** F 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN J 269 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS M 453 GLN N 135 GLN P 247 GLN W 24 ASN W 85 GLN j 108 GLN l 59 GLN ** p 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN u 16 GLN u 64 ASN u 73 GLN u 77 HIS w 124 ASN w 202 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.143 69816 Z= 0.165 Angle : 0.560 59.129 94395 Z= 0.295 Chirality : 0.040 0.492 10195 Planarity : 0.004 0.067 11762 Dihedral : 12.681 179.751 10863 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 1.72 % Allowed : 17.89 % Favored : 80.39 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.09), residues: 8173 helix: 1.73 (0.08), residues: 4314 sheet: 0.12 (0.24), residues: 433 loop : -0.26 (0.11), residues: 3426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP l 144 HIS 0.007 0.001 HIS p 51 PHE 0.028 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.007 0.000 ARG I 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1079 time to evaluate : 5.909 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: A 38 GLU cc_start: 0.7712 (pt0) cc_final: 0.7188 (pm20) REVERT: A 52 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7260 (mtp-110) REVERT: A 174 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.6751 (ttm-80) REVERT: A 208 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8594 (tm-30) REVERT: A 456 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 49 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7189 (p0) REVERT: C 101 ASP cc_start: 0.9114 (m-30) cc_final: 0.8857 (m-30) REVERT: G 89 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8364 (mt) REVERT: G 143 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7600 (mt-10) REVERT: H 94 MET cc_start: 0.8251 (mmm) cc_final: 0.7984 (mtp) REVERT: I 101 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8837 (pt) REVERT: J 85 ARG cc_start: 0.9436 (OUTLIER) cc_final: 0.8049 (ppt-90) REVERT: J 117 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7756 (ttp-110) REVERT: L 112 MET cc_start: 0.8284 (mmp) cc_final: 0.7987 (mmp) REVERT: M 464 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7161 (tp-100) REVERT: M 707 MET cc_start: 0.9231 (mmp) cc_final: 0.8794 (mmp) REVERT: N 136 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: O 141 MET cc_start: 0.8605 (tmm) cc_final: 0.8239 (tmt) REVERT: O 209 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7951 (mtmp) REVERT: U 82 LYS cc_start: 0.8128 (ptmm) cc_final: 0.7853 (ptpt) REVERT: V 95 CYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7829 (m) REVERT: W 98 MET cc_start: 0.7843 (mmm) cc_final: 0.7631 (mmm) REVERT: X 74 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7279 (tt) REVERT: X 111 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7759 (p0) REVERT: Z 49 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.6928 (mm-30) REVERT: a 160 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.9057 (mtt) REVERT: c 43 LYS cc_start: 0.7866 (mttm) cc_final: 0.7251 (mmmm) REVERT: c 113 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8644 (pt) REVERT: c 159 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.7928 (tmtm) REVERT: f 60 LYS cc_start: 0.8524 (tmtp) cc_final: 0.8243 (mttt) REVERT: j 44 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7078 (tmm) REVERT: l 102 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: m 135 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8128 (t80) REVERT: o 25 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6676 (pp) REVERT: r 103 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: r 271 MET cc_start: 0.9444 (mmp) cc_final: 0.9147 (mmp) REVERT: s 24 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.7759 (tp30) REVERT: s 204 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7380 (tp30) REVERT: s 318 SER cc_start: 0.6420 (OUTLIER) cc_final: 0.6134 (t) REVERT: w 55 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6628 (tt0) REVERT: w 253 CYS cc_start: 0.4352 (OUTLIER) cc_final: 0.3336 (p) REVERT: w 319 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8528 (mt) REVERT: w 354 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8612 (tp) outliers start: 123 outliers final: 78 residues processed: 1163 average time/residue: 1.6656 time to fit residues: 2493.7315 Evaluate side-chains 1182 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1076 time to evaluate : 5.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain M residue 44 GLU Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 464 GLN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 209 LYS Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 336 GLU Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain W residue 52 LYS Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 99 LYS Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 159 LYS Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 329 MET Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 102 GLU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 130 LEU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 313 SER Chi-restraints excluded: chain s residue 318 SER Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 314 LEU Chi-restraints excluded: chain w residue 319 ILE Chi-restraints excluded: chain w residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 0.0370 chunk 680 optimal weight: 0.9980 chunk 195 optimal weight: 8.9990 chunk 588 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 177 optimal weight: 0.3980 chunk 639 optimal weight: 9.9990 chunk 267 optimal weight: 7.9990 chunk 656 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN F 25 GLN ** F 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN J 269 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS M 453 GLN N 135 GLN P 247 GLN W 24 ASN W 85 GLN j 108 GLN l 59 GLN ** p 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN u 16 GLN u 64 ASN u 73 GLN u 77 HIS w 124 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.095793 restraints weight = 83183.946| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.26 r_work: 0.2914 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 69816 Z= 0.168 Angle : 0.559 59.185 94395 Z= 0.293 Chirality : 0.040 0.169 10195 Planarity : 0.004 0.053 11762 Dihedral : 12.681 179.735 10863 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.41 % Favored : 96.51 % Rotamer: Outliers : 1.88 % Allowed : 17.73 % Favored : 80.39 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.09), residues: 8173 helix: 1.73 (0.08), residues: 4314 sheet: 0.05 (0.24), residues: 440 loop : -0.25 (0.11), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.006 0.001 HIS J 37 PHE 0.028 0.001 PHE i 292 TYR 0.020 0.001 TYR l 422 ARG 0.005 0.000 ARG B 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33430.84 seconds wall clock time: 577 minutes 18.99 seconds (34638.99 seconds total)