Starting phenix.real_space_refine on Mon Feb 19 23:57:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a1g_11608/02_2024/7a1g_11608_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a1g_11608/02_2024/7a1g_11608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a1g_11608/02_2024/7a1g_11608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a1g_11608/02_2024/7a1g_11608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a1g_11608/02_2024/7a1g_11608_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a1g_11608/02_2024/7a1g_11608_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 8 7.16 5 Zn 2 6.06 5 P 1773 5.49 5 Mg 80 5.21 5 S 122 5.16 5 C 44727 2.51 5 N 14838 2.21 5 O 20316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 12": "OE1" <-> "OE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P ARG 41": "NH1" <-> "NH2" Residue "P GLU 55": "OE1" <-> "OE2" Residue "P GLU 117": "OE1" <-> "OE2" Residue "P ARG 191": "NH1" <-> "NH2" Residue "P ARG 205": "NH1" <-> "NH2" Residue "Q PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 41": "NH1" <-> "NH2" Residue "Q GLU 77": "OE1" <-> "OE2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "Q GLU 90": "OE1" <-> "OE2" Residue "Q TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 144": "NH1" <-> "NH2" Residue "Q ARG 152": "NH1" <-> "NH2" Residue "Q GLU 196": "OE1" <-> "OE2" Residue "Q ARG 213": "NH1" <-> "NH2" Residue "R GLU 54": "OE1" <-> "OE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "R ARG 91": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "S ARG 11": "NH1" <-> "NH2" Residue "S ARG 30": "NH1" <-> "NH2" Residue "S GLU 40": "OE1" <-> "OE2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S ARG 59": "NH1" <-> "NH2" Residue "S GLU 60": "OE1" <-> "OE2" Residue "S ARG 108": "NH1" <-> "NH2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S ARG 187": "NH1" <-> "NH2" Residue "S ARG 200": "NH1" <-> "NH2" Residue "S ARG 252": "NH1" <-> "NH2" Residue "T ARG 23": "NH1" <-> "NH2" Residue "T ARG 92": "NH1" <-> "NH2" Residue "T ARG 98": "NH1" <-> "NH2" Residue "T ARG 137": "NH1" <-> "NH2" Residue "T ARG 183": "NH1" <-> "NH2" Residue "T ARG 191": "NH1" <-> "NH2" Residue "T ARG 227": "NH1" <-> "NH2" Residue "U GLU 17": "OE1" <-> "OE2" Residue "U ARG 39": "NH1" <-> "NH2" Residue "U GLU 48": "OE1" <-> "OE2" Residue "U ARG 79": "NH1" <-> "NH2" Residue "U PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 104": "NH1" <-> "NH2" Residue "V ARG 8": "NH1" <-> "NH2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ARG 47": "NH1" <-> "NH2" Residue "V ARG 59": "NH1" <-> "NH2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "V GLU 89": "OE1" <-> "OE2" Residue "V ARG 110": "NH1" <-> "NH2" Residue "V GLU 140": "OE1" <-> "OE2" Residue "V ARG 164": "NH1" <-> "NH2" Residue "V ARG 178": "NH1" <-> "NH2" Residue "W ARG 3": "NH1" <-> "NH2" Residue "W ARG 17": "NH1" <-> "NH2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "W ARG 54": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 78": "NH1" <-> "NH2" Residue "W ARG 168": "NH1" <-> "NH2" Residue "W ARG 174": "NH1" <-> "NH2" Residue "W ARG 175": "NH1" <-> "NH2" Residue "X ARG 30": "NH1" <-> "NH2" Residue "X ARG 33": "NH1" <-> "NH2" Residue "X TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "X ARG 116": "NH1" <-> "NH2" Residue "Y GLU 31": "OE1" <-> "OE2" Residue "Y ARG 104": "NH1" <-> "NH2" Residue "Y ARG 106": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "Z ARG 90": "NH1" <-> "NH2" Residue "Z ARG 103": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "a ARG 60": "NH1" <-> "NH2" Residue "a ARG 71": "NH1" <-> "NH2" Residue "b GLU 18": "OE1" <-> "OE2" Residue "c ARG 16": "NH1" <-> "NH2" Residue "c ARG 19": "NH1" <-> "NH2" Residue "c ARG 144": "NH1" <-> "NH2" Residue "d ARG 20": "NH1" <-> "NH2" Residue "d ARG 32": "NH1" <-> "NH2" Residue "d GLU 39": "OE1" <-> "OE2" Residue "d ARG 93": "NH1" <-> "NH2" Residue "d ARG 131": "NH1" <-> "NH2" Residue "e ARG 5": "NH1" <-> "NH2" Residue "e ARG 10": "NH1" <-> "NH2" Residue "e ARG 51": "NH1" <-> "NH2" Residue "f GLU 15": "OE1" <-> "OE2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "g ARG 54": "NH1" <-> "NH2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "F ARG 66": "NH1" <-> "NH2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "I PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 88": "NH1" <-> "NH2" Residue "I GLU 106": "OE1" <-> "OE2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "I ARG 120": "NH1" <-> "NH2" Residue "I ARG 144": "NH1" <-> "NH2" Residue "I ARG 145": "NH1" <-> "NH2" Residue "J ARG 130": "NH1" <-> "NH2" Residue "K ARG 57": "NH1" <-> "NH2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "K TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 103": "NH1" <-> "NH2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "N ARG 119": "NH1" <-> "NH2" Residue "O GLU 239": "OE1" <-> "OE2" Residue "O ARG 249": "NH1" <-> "NH2" Residue "O GLU 286": "OE1" <-> "OE2" Residue "h ARG 18": "NH1" <-> "NH2" Residue "h ARG 38": "NH1" <-> "NH2" Residue "h ARG 61": "NH1" <-> "NH2" Residue "z ARG 148": "NH1" <-> "NH2" Residue "z ARG 154": "NH1" <-> "NH2" Residue "z ARG 194": "NH1" <-> "NH2" Residue "z ARG 209": "NH1" <-> "NH2" Residue "z ARG 220": "NH1" <-> "NH2" Residue "y ARG 148": "NH1" <-> "NH2" Residue "y ARG 154": "NH1" <-> "NH2" Residue "y ARG 194": "NH1" <-> "NH2" Residue "y ARG 209": "NH1" <-> "NH2" Residue "x ARG 22": "NH1" <-> "NH2" Residue "x ARG 27": "NH1" <-> "NH2" Residue "x GLU 52": "OE1" <-> "OE2" Residue "x ARG 96": "NH1" <-> "NH2" Residue "x ARG 133": "NH1" <-> "NH2" Residue "x ARG 178": "NH1" <-> "NH2" Residue "x ARG 204": "NH1" <-> "NH2" Residue "x ARG 311": "NH1" <-> "NH2" Residue "x ARG 328": "NH1" <-> "NH2" Residue "x ARG 330": "NH1" <-> "NH2" Residue "x ARG 456": "NH1" <-> "NH2" Residue "x GLU 501": "OE1" <-> "OE2" Residue "x ARG 511": "NH1" <-> "NH2" Residue "x ARG 552": "NH1" <-> "NH2" Residue "x ARG 573": "NH1" <-> "NH2" Residue "x ARG 574": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 81866 Number of models: 1 Model: "" Number of chains: 44 Chain: "2" Number of atoms: 37739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1771, 37739 Classifications: {'RNA': 1771} Modifications used: {'rna2p_pur': 116, 'rna2p_pyr': 110, 'rna3p_pur': 817, 'rna3p_pyr': 728} Link IDs: {'rna2p': 225, 'rna3p': 1545} Chain breaks: 2 Chain: "P" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1603 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 189} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 5, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1626 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain: "S" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2056 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 12, 'TRANS': 245} Chain: "T" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1815 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 218} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 173} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1479 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 175} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1142 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} 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: "Y" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 142} Chain: "Z" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 923 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "a" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 673 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 84} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "c" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "d" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "e" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 765 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 90} 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: "f" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "g" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 472 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 54} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 916 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 108} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1729 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 9, 'TRANS': 212} Chain: "B" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1605 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 197} 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: "C" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 754 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 88} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 875 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 948 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1188 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} 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: "J" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "K" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 797 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "L" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 651 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 79} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 442 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 560 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2383 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 303} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "h" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 491 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "z" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 896 Classifications: {'peptide': 120} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 31 Chain: "y" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 74} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "x" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4608 Classifications: {'peptide': 582} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 547} Chain breaks: 1 Chain: "2" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Unusual residues: {' MG': 76} Classifications: {'undetermined': 76} Link IDs: {None: 75} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' MG': 1, 'ADP': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 71892 SG CYS M 21 150.140 167.510 72.795 1.00 5.00 S ATOM 71916 SG CYS M 24 147.133 165.609 71.648 1.00 4.65 S ATOM 72030 SG CYS M 39 146.588 168.438 74.153 1.00 5.00 S ATOM 72056 SG CYS M 42 147.830 165.448 75.402 1.00 5.00 S ATOM 72540 SG CYS N 126 173.705 159.671 31.309 1.00 22.54 S ATOM 72675 SG CYS N 144 170.703 161.474 32.145 1.00 16.36 S ATOM 77269 SG CYS x 21 68.267 115.472 63.271 1.00 11.67 S ATOM 77336 SG CYS x 29 82.280 114.988 62.238 1.00 5.00 S ATOM 77529 SG CYS x 55 83.640 108.504 60.745 1.00 6.00 S ATOM 77565 SG CYS x 61 79.045 109.853 64.779 1.00 5.00 S ATOM 77547 SG CYS x 58 84.722 111.441 66.291 1.00 4.70 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A 21756 " occ=0.55 ... (20 atoms not shown) pdb=" C4 A 21756 " occ=0.55 Time building chain proxies: 31.98, per 1000 atoms: 0.39 Number of scatterers: 81866 At special positions: 0 Unit cell: (203.328, 259.455, 209.682, 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 2 29.99 Fe 8 26.01 S 122 16.00 P 1773 15.00 Mg 80 11.99 O 20316 8.00 N 14838 7.00 C 44727 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 30.55 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 x 701 " pdb="FE1 SF4 x 701 " - pdb=" SG CYS x 21 " pdb="FE4 SF4 x 701 " - pdb=" SG CYS x 65 " pdb="FE3 SF4 x 701 " - pdb=" SG CYS x 16 " pdb=" SF4 x 702 " pdb="FE3 SF4 x 702 " - pdb=" SG CYS x 61 " pdb="FE4 SF4 x 702 " - pdb=" SG CYS x 58 " pdb="FE2 SF4 x 702 " - pdb=" SG CYS x 55 " pdb="FE1 SF4 x 702 " - pdb=" SG CYS x 29 " Number of angles added : 21 Zn2+ tetrahedral coordination pdb=" ZN M 101 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 39 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 42 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 21 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 144 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 126 " Number of angles added : 6 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 187 helices and 59 sheets defined 31.5% alpha, 13.9% beta 511 base pairs and 929 stacking pairs defined. Time for finding SS restraints: 31.83 Creating SS restraints... Processing helix chain 'P' and resid 11 through 19 Processing helix chain 'P' and resid 50 through 65 Processing helix chain 'P' and resid 70 through 72 No H-bonds generated for 'chain 'P' and resid 70 through 72' Processing helix chain 'P' and resid 80 through 92 removed outlier: 4.569A pdb=" N ARG P 84 " --> pdb=" O THR P 80 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA P 85 " --> pdb=" O PHE P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 138 removed outlier: 3.866A pdb=" N TYR P 138 " --> pdb=" O LYS P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 185 removed outlier: 3.575A pdb=" N GLY P 171 " --> pdb=" O LYS P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 199 through 202 removed outlier: 3.507A pdb=" N TYR P 202 " --> pdb=" O PRO P 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 199 through 202' Processing helix chain 'Q' and resid 58 through 61 No H-bonds generated for 'chain 'Q' and resid 58 through 61' Processing helix chain 'Q' and resid 70 through 74 Processing helix chain 'Q' and resid 107 through 113 Processing helix chain 'Q' and resid 160 through 176 Processing helix chain 'Q' and resid 181 through 188 Processing helix chain 'Q' and resid 192 through 201 Processing helix chain 'Q' and resid 225 through 231 removed outlier: 3.729A pdb=" N LEU Q 231 " --> pdb=" O ALA Q 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 47 Processing helix chain 'R' and resid 54 through 59 Processing helix chain 'R' and resid 66 through 72 Processing helix chain 'R' and resid 121 through 134 Processing helix chain 'R' and resid 182 through 191 Processing helix chain 'R' and resid 207 through 222 removed outlier: 4.015A pdb=" N THR R 221 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR R 222 " --> pdb=" O ILE R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 229 No H-bonds generated for 'chain 'R' and resid 227 through 229' Processing helix chain 'R' and resid 239 through 242 No H-bonds generated for 'chain 'R' and resid 239 through 242' Processing helix chain 'R' and resid 244 through 246 No H-bonds generated for 'chain 'R' and resid 244 through 246' Processing helix chain 'S' and resid 16 through 18 No H-bonds generated for 'chain 'S' and resid 16 through 18' Processing helix chain 'S' and resid 44 through 49 Processing helix chain 'S' and resid 58 through 67 removed outlier: 4.016A pdb=" N GLN S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 118 through 120 No H-bonds generated for 'chain 'S' and resid 118 through 120' Processing helix chain 'S' and resid 133 through 135 No H-bonds generated for 'chain 'S' and resid 133 through 135' Processing helix chain 'S' and resid 222 through 224 No H-bonds generated for 'chain 'S' and resid 222 through 224' Processing helix chain 'S' and resid 248 through 257 Processing helix chain 'T' and resid 24 through 27 Processing helix chain 'T' and resid 38 through 41 No H-bonds generated for 'chain 'T' and resid 38 through 41' Processing helix chain 'T' and resid 58 through 60 No H-bonds generated for 'chain 'T' and resid 58 through 60' Processing helix chain 'T' and resid 138 through 144 Processing helix chain 'T' and resid 153 through 155 No H-bonds generated for 'chain 'T' and resid 153 through 155' Processing helix chain 'T' and resid 181 through 225 removed outlier: 3.582A pdb=" N VAL T 195 " --> pdb=" O ARG T 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 8 No H-bonds generated for 'chain 'U' and resid 5 through 8' Processing helix chain 'U' and resid 15 through 28 Processing helix chain 'U' and resid 64 through 84 removed outlier: 4.666A pdb=" N ALA U 68 " --> pdb=" O VAL U 64 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY U 69 " --> pdb=" O PRO U 65 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL U 73 " --> pdb=" O GLY U 69 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N THR U 75 " --> pdb=" O HIS U 71 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS U 76 " --> pdb=" O LYS U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 116 No H-bonds generated for 'chain 'U' and resid 114 through 116' Processing helix chain 'U' and resid 118 through 128 Processing helix chain 'U' and resid 159 through 161 No H-bonds generated for 'chain 'U' and resid 159 through 161' Processing helix chain 'U' and resid 166 through 177 Processing helix chain 'V' and resid 26 through 28 No H-bonds generated for 'chain 'V' and resid 26 through 28' Processing helix chain 'V' and resid 88 through 92 Processing helix chain 'V' and resid 107 through 117 Processing helix chain 'V' and resid 137 through 145 Processing helix chain 'V' and resid 155 through 162 Processing helix chain 'V' and resid 173 through 176 No H-bonds generated for 'chain 'V' and resid 173 through 176' Processing helix chain 'V' and resid 186 through 197 Processing helix chain 'W' and resid 21 through 34 Processing helix chain 'W' and resid 39 through 61 removed outlier: 3.510A pdb=" N THR W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 83 Processing helix chain 'W' and resid 101 through 107 removed outlier: 4.340A pdb=" N ARG W 107 " --> pdb=" O ASP W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 109 through 116 Processing helix chain 'W' and resid 122 through 130 Processing helix chain 'W' and resid 153 through 155 No H-bonds generated for 'chain 'W' and resid 153 through 155' Processing helix chain 'W' and resid 171 through 184 Processing helix chain 'X' and resid 46 through 50 Processing helix chain 'Y' and resid 30 through 42 Processing helix chain 'Y' and resid 47 through 56 Processing helix chain 'Y' and resid 63 through 66 No H-bonds generated for 'chain 'Y' and resid 63 through 66' Processing helix chain 'Y' and resid 71 through 78 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 109 through 131 Processing helix chain 'Y' and resid 143 through 149 removed outlier: 4.275A pdb=" N ALA Y 148 " --> pdb=" O ALA Y 144 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 46 No H-bonds generated for 'chain 'Z' and resid 44 through 46' Processing helix chain 'Z' and resid 53 through 55 No H-bonds generated for 'chain 'Z' and resid 53 through 55' Processing helix chain 'Z' and resid 57 through 74 Processing helix chain 'Z' and resid 98 through 107 Processing helix chain 'a' and resid 57 through 61 Processing helix chain 'a' and resid 65 through 75 Processing helix chain 'b' and resid 6 through 20 Processing helix chain 'b' and resid 32 through 43 Processing helix chain 'b' and resid 83 through 93 removed outlier: 3.967A pdb=" N GLU b 87 " --> pdb=" O ILE b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 119 Processing helix chain 'c' and resid 12 through 23 Processing helix chain 'c' and resid 28 through 34 Processing helix chain 'c' and resid 36 through 39 No H-bonds generated for 'chain 'c' and resid 36 through 39' Processing helix chain 'c' and resid 92 through 95 Processing helix chain 'c' and resid 132 through 136 Processing helix chain 'd' and resid 37 through 48 Processing helix chain 'd' and resid 79 through 85 Processing helix chain 'd' and resid 88 through 93 Processing helix chain 'd' and resid 105 through 117 removed outlier: 3.780A pdb=" N LYS d 117 " --> pdb=" O ASN d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 134 removed outlier: 5.152A pdb=" N ALA d 134 " --> pdb=" O ALA d 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 56 Processing helix chain 'e' and resid 75 through 80 Processing helix chain 'e' and resid 89 through 91 No H-bonds generated for 'chain 'e' and resid 89 through 91' Processing helix chain 'f' and resid 12 through 17 Processing helix chain 'g' and resid 8 through 10 No H-bonds generated for 'chain 'g' and resid 8 through 10' Processing helix chain 'g' and resid 13 through 17 Processing helix chain 'g' and resid 33 through 43 Processing helix chain 'E' and resid 17 through 19 No H-bonds generated for 'chain 'E' and resid 17 through 19' Processing helix chain 'E' and resid 22 through 27 removed outlier: 5.790A pdb=" N GLU E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 52 through 66 removed outlier: 3.637A pdb=" N PHE E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 116 through 119 Processing helix chain 'A' and resid 7 through 28 Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 61 through 77 removed outlier: 6.402A pdb=" N ARG A 65 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 67 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 76 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 77 " --> pdb=" O GLN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.618A pdb=" N ASP A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.712A pdb=" N LEU B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 124 Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.514A pdb=" N THR B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 182 removed outlier: 3.544A pdb=" N GLY B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 203 removed outlier: 3.602A pdb=" N GLU B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 39 through 52 removed outlier: 4.006A pdb=" N LYS C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 80 Processing helix chain 'D' and resid 27 through 38 removed outlier: 3.651A pdb=" N VAL D 31 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 33 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR D 34 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 37 " --> pdb=" O THR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.748A pdb=" N GLU D 76 " --> pdb=" O ILE D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 4.251A pdb=" N GLU D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 removed outlier: 3.805A pdb=" N MET D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU D 138 " --> pdb=" O SER D 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 38 No H-bonds generated for 'chain 'F' and resid 36 through 38' Processing helix chain 'F' and resid 42 through 55 removed outlier: 4.133A pdb=" N PHE F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS F 47 " --> pdb=" O ILE F 43 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU F 50 " --> pdb=" O PHE F 46 " (cutoff:3.500A) Proline residue: F 51 - end of helix Processing helix chain 'F' and resid 57 through 60 Processing helix chain 'F' and resid 74 through 95 removed outlier: 3.507A pdb=" N TYR F 79 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 112 Processing helix chain 'F' and resid 114 through 116 No H-bonds generated for 'chain 'F' and resid 114 through 116' Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.772A pdb=" N LYS H 14 " --> pdb=" O LYS H 10 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 38 removed outlier: 4.101A pdb=" N ASP H 36 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 62 removed outlier: 3.620A pdb=" N LYS H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG H 60 " --> pdb=" O HIS H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 removed outlier: 3.595A pdb=" N GLU H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 113 Processing helix chain 'I' and resid 28 through 34 removed outlier: 3.702A pdb=" N THR I 33 " --> pdb=" O VAL I 29 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR I 34 " --> pdb=" O TYR I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 49 removed outlier: 3.502A pdb=" N CYS I 47 " --> pdb=" O SER I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 74 removed outlier: 3.653A pdb=" N GLU I 67 " --> pdb=" O GLN I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 79 No H-bonds generated for 'chain 'I' and resid 77 through 79' Processing helix chain 'I' and resid 104 through 118 removed outlier: 3.561A pdb=" N LEU I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU I 116 " --> pdb=" O ASP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 129 Processing helix chain 'J' and resid 11 through 25 Processing helix chain 'J' and resid 54 through 67 Processing helix chain 'J' and resid 73 through 79 Processing helix chain 'J' and resid 98 through 111 Processing helix chain 'J' and resid 128 through 140 removed outlier: 3.525A pdb=" N LEU J 132 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP J 133 " --> pdb=" O GLN J 129 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG J 134 " --> pdb=" O ARG J 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 47 removed outlier: 3.641A pdb=" N ASN K 36 " --> pdb=" O LYS K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 105 removed outlier: 3.741A pdb=" N THR K 104 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 53 removed outlier: 3.607A pdb=" N ARG L 49 " --> pdb=" O GLU L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 69 Processing helix chain 'L' and resid 73 through 86 removed outlier: 3.546A pdb=" N GLU L 84 " --> pdb=" O LEU L 80 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS L 85 " --> pdb=" O ARG L 81 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU L 86 " --> pdb=" O HIS L 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 35 No H-bonds generated for 'chain 'M' and resid 33 through 35' Processing helix chain 'M' and resid 40 through 50 removed outlier: 3.519A pdb=" N ARG M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU M 45 " --> pdb=" O GLN M 41 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASN M 48 " --> pdb=" O ARG M 44 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASP M 49 " --> pdb=" O GLU M 45 " (cutoff:3.500A) Processing helix chain 'z' and resid 147 through 165 removed outlier: 4.081A pdb=" N ASP z 152 " --> pdb=" O ARG z 148 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU z 153 " --> pdb=" O GLU z 149 " (cutoff:3.500A) Proline residue: z 163 - end of helix Processing helix chain 'z' and resid 169 through 175 Processing helix chain 'z' and resid 177 through 186 Processing helix chain 'z' and resid 190 through 218 removed outlier: 3.579A pdb=" N LEU z 216 " --> pdb=" O ARG z 212 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG z 218 " --> pdb=" O ALA z 214 " (cutoff:3.500A) Processing helix chain 'z' and resid 226 through 228 No H-bonds generated for 'chain 'z' and resid 226 through 228' Processing helix chain 'y' and resid 147 through 167 removed outlier: 3.535A pdb=" N THR y 162 " --> pdb=" O THR y 158 " (cutoff:3.500A) Proline residue: y 163 - end of helix removed outlier: 4.018A pdb=" N LYS y 166 " --> pdb=" O THR y 162 " (cutoff:3.500A) Processing helix chain 'y' and resid 169 through 172 No H-bonds generated for 'chain 'y' and resid 169 through 172' Processing helix chain 'y' and resid 175 through 186 removed outlier: 3.705A pdb=" N ASP y 179 " --> pdb=" O SER y 175 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU y 180 " --> pdb=" O LEU y 176 " (cutoff:3.500A) Processing helix chain 'y' and resid 190 through 215 Processing helix chain 'x' and resid 18 through 20 No H-bonds generated for 'chain 'x' and resid 18 through 20' Processing helix chain 'x' and resid 24 through 28 Processing helix chain 'x' and resid 30 through 33 No H-bonds generated for 'chain 'x' and resid 30 through 33' Processing helix chain 'x' and resid 60 through 63 No H-bonds generated for 'chain 'x' and resid 60 through 63' Processing helix chain 'x' and resid 116 through 124 removed outlier: 3.586A pdb=" N LEU x 120 " --> pdb=" O LYS x 116 " (cutoff:3.500A) Processing helix chain 'x' and resid 140 through 146 Processing helix chain 'x' and resid 151 through 160 Processing helix chain 'x' and resid 173 through 176 No H-bonds generated for 'chain 'x' and resid 173 through 176' Processing helix chain 'x' and resid 187 through 193 removed outlier: 3.522A pdb=" N LEU x 191 " --> pdb=" O VAL x 187 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU x 193 " --> pdb=" O GLU x 189 " (cutoff:3.500A) Processing helix chain 'x' and resid 205 through 208 No H-bonds generated for 'chain 'x' and resid 205 through 208' Processing helix chain 'x' and resid 213 through 215 No H-bonds generated for 'chain 'x' and resid 213 through 215' Processing helix chain 'x' and resid 219 through 221 No H-bonds generated for 'chain 'x' and resid 219 through 221' Processing helix chain 'x' and resid 224 through 237 removed outlier: 4.140A pdb=" N ARG x 229 " --> pdb=" O GLY x 225 " (cutoff:3.500A) Processing helix chain 'x' and resid 254 through 267 removed outlier: 3.636A pdb=" N ILE x 264 " --> pdb=" O ALA x 260 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG x 265 " --> pdb=" O ALA x 261 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU x 267 " --> pdb=" O ILE x 263 " (cutoff:3.500A) Processing helix chain 'x' and resid 281 through 287 removed outlier: 3.522A pdb=" N ASP x 285 " --> pdb=" O LEU x 281 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR x 286 " --> pdb=" O SER x 282 " (cutoff:3.500A) Processing helix chain 'x' and resid 310 through 319 removed outlier: 3.501A pdb=" N ASN x 315 " --> pdb=" O ARG x 311 " (cutoff:3.500A) Processing helix chain 'x' and resid 391 through 398 removed outlier: 3.584A pdb=" N ILE x 395 " --> pdb=" O LYS x 391 " (cutoff:3.500A) Processing helix chain 'x' and resid 430 through 436 Processing helix chain 'x' and resid 448 through 454 removed outlier: 3.662A pdb=" N LYS x 453 " --> pdb=" O THR x 449 " (cutoff:3.500A) Proline residue: x 454 - end of helix Processing helix chain 'x' and resid 456 through 460 Processing helix chain 'x' and resid 470 through 483 Processing helix chain 'x' and resid 500 through 516 removed outlier: 3.730A pdb=" N HIS x 516 " --> pdb=" O ARG x 512 " (cutoff:3.500A) Processing helix chain 'x' and resid 529 through 534 Processing helix chain 'x' and resid 557 through 566 removed outlier: 3.593A pdb=" N ASN x 562 " --> pdb=" O LEU x 558 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE x 564 " --> pdb=" O GLY x 560 " (cutoff:3.500A) Processing helix chain 'x' and resid 589 through 597 Processing sheet with id= A, first strand: chain 'P' and resid 96 through 99 removed outlier: 6.679A pdb=" N LEU P 120 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE P 76 " --> pdb=" O LEU P 120 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE P 122 " --> pdb=" O ILE P 76 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL P 123 " --> pdb=" O PRO P 142 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE P 144 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL P 158 " --> pdb=" O ALA P 145 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR P 147 " --> pdb=" O VAL P 158 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE P 160 " --> pdb=" O THR P 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'Q' and resid 65 through 69 removed outlier: 5.432A pdb=" N ARG Q 87 " --> pdb=" O PHE Q 100 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE Q 100 " --> pdb=" O ARG Q 87 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'Q' and resid 120 through 125 removed outlier: 3.753A pdb=" N LYS Q 219 " --> pdb=" O VAL Q 134 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG Q 136 " --> pdb=" O LEU Q 217 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU Q 217 " --> pdb=" O ARG Q 136 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE Q 138 " --> pdb=" O VAL Q 215 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL Q 215 " --> pdb=" O PHE Q 138 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'Q' and resid 27 through 33 removed outlier: 4.348A pdb=" N GLY Q 44 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'R' and resid 77 through 80 removed outlier: 3.851A pdb=" N HIS R 110 " --> pdb=" O ASP R 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 83 through 90 removed outlier: 4.040A pdb=" N GLY R 93 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 158 through 162 Processing sheet with id= H, first strand: chain 'S' and resid 70 through 72 Processing sheet with id= I, first strand: chain 'S' and resid 122 through 125 Processing sheet with id= J, first strand: chain 'S' and resid 128 through 131 removed outlier: 3.688A pdb=" N LYS S 128 " --> pdb=" O VAL S 140 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 225 through 230 removed outlier: 6.040A pdb=" N LEU S 180 " --> pdb=" O ILE S 228 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS S 179 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY S 193 " --> pdb=" O VAL S 181 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N HIS S 209 " --> pdb=" O VAL S 196 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS S 198 " --> pdb=" O LEU S 207 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU S 207 " --> pdb=" O LYS S 198 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 12 through 17 removed outlier: 3.633A pdb=" N VAL T 114 " --> pdb=" O VAL T 49 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL T 49 " --> pdb=" O VAL T 114 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 72 through 77 Processing sheet with id= N, first strand: chain 'T' and resid 54 through 57 Processing sheet with id= O, first strand: chain 'U' and resid 88 through 94 removed outlier: 7.237A pdb=" N LYS U 56 " --> pdb=" O HIS U 89 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N ILE U 91 " --> pdb=" O LYS U 56 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU U 58 " --> pdb=" O ILE U 91 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU U 93 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE U 60 " --> pdb=" O LEU U 93 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER U 45 " --> pdb=" O PHE U 61 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'U' and resid 181 through 185 removed outlier: 8.319A pdb=" N VAL U 182 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN U 150 " --> pdb=" O VAL U 182 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLU U 184 " --> pdb=" O GLN U 150 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL U 152 " --> pdb=" O GLU U 184 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 42 through 46 Processing sheet with id= R, first strand: chain 'V' and resid 62 through 67 Processing sheet with id= S, first strand: chain 'V' and resid 181 through 183 removed outlier: 3.640A pdb=" N GLY V 80 " --> pdb=" O GLN V 103 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 99 through 110 removed outlier: 3.502A pdb=" N ARG X 99 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG X 87 " --> pdb=" O VAL X 75 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL X 75 " --> pdb=" O ARG X 87 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA X 89 " --> pdb=" O GLY X 73 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N GLY X 73 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 15.402A pdb=" N LEU X 91 " --> pdb=" O LEU X 71 " (cutoff:3.500A) removed outlier: 16.560A pdb=" N LEU X 71 " --> pdb=" O LEU X 91 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLY X 126 " --> pdb=" O VAL X 139 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL X 139 " --> pdb=" O GLY X 126 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'Z' and resid 14 through 16 removed outlier: 6.371A pdb=" N ALA Z 78 " --> pdb=" O GLY Z 15 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG Z 111 " --> pdb=" O VAL Z 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'Z' and resid 27 through 31 removed outlier: 3.829A pdb=" N VAL Z 30 " --> pdb=" O ALA Z 40 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA Z 40 " --> pdb=" O VAL Z 30 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'a' and resid 32 through 37 Processing sheet with id= X, first strand: chain 'b' and resid 24 through 27 Processing sheet with id= Y, first strand: chain 'b' and resid 72 through 74 removed outlier: 6.971A pdb=" N ILE b 103 " --> pdb=" O LEU b 126 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE b 128 " --> pdb=" O TYR b 101 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR b 101 " --> pdb=" O PHE b 128 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'c' and resid 82 through 86 removed outlier: 3.658A pdb=" N GLU c 55 " --> pdb=" O ARG c 73 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN c 75 " --> pdb=" O VAL c 53 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL c 53 " --> pdb=" O GLN c 75 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS c 126 " --> pdb=" O LEU c 103 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA c 105 " --> pdb=" O VAL c 124 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL c 124 " --> pdb=" O ALA c 105 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'd' and resid 7 through 10 Processing sheet with id= AB, first strand: chain 'd' and resid 13 through 15 Processing sheet with id= AC, first strand: chain 'e' and resid 20 through 22 Processing sheet with id= AD, first strand: chain 'e' and resid 38 through 43 Processing sheet with id= AE, first strand: chain 'f' and resid 44 through 47 Processing sheet with id= AF, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= AG, first strand: chain 'A' and resid 37 through 42 Processing sheet with id= AH, first strand: chain 'A' and resid 148 through 155 removed outlier: 6.530A pdb=" N MET A 189 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS A 134 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS A 187 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A 136 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS A 185 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 138 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A 183 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY A 140 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL A 181 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 144 through 149 Processing sheet with id= AJ, first strand: chain 'C' and resid 20 through 22 Processing sheet with id= AK, first strand: chain 'D' and resid 121 through 123 removed outlier: 3.878A pdb=" N LEU D 59 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE D 89 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 6 through 12 Processing sheet with id= AM, first strand: chain 'H' and resid 100 through 102 Processing sheet with id= AN, first strand: chain 'I' and resid 14 through 17 removed outlier: 3.699A pdb=" N LEU I 17 " --> pdb=" O THR I 20 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'J' and resid 82 through 84 removed outlier: 3.559A pdb=" N GLY J 82 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS J 92 " --> pdb=" O LYS J 84 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'J' and resid 114 through 116 Processing sheet with id= AQ, first strand: chain 'K' and resid 89 through 93 Processing sheet with id= AR, first strand: chain 'K' and resid 61 through 68 Processing sheet with id= AS, first strand: chain 'L' and resid 89 through 95 removed outlier: 6.937A pdb=" N ILE L 100 " --> pdb=" O ILE L 92 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LYS L 94 " --> pdb=" O GLN L 98 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLN L 98 " --> pdb=" O LYS L 94 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'O' and resid 20 through 24 removed outlier: 6.745A pdb=" N ALA O 36 " --> pdb=" O THR O 21 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU O 23 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU O 34 " --> pdb=" O LEU O 23 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG O 59 " --> pdb=" O SER O 44 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LYS O 46 " --> pdb=" O PRO O 57 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'O' and resid 101 through 104 removed outlier: 4.037A pdb=" N GLN O 101 " --> pdb=" O LEU O 91 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR O 88 " --> pdb=" O SER O 84 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'O' and resid 110 through 115 removed outlier: 7.101A pdb=" N GLY O 125 " --> pdb=" O MET O 111 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL O 113 " --> pdb=" O ILE O 123 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE O 123 " --> pdb=" O VAL O 113 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL O 133 " --> pdb=" O ALA O 142 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA O 142 " --> pdb=" O VAL O 133 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'O' and resid 151 through 156 removed outlier: 6.812A pdb=" N ALA O 172 " --> pdb=" O SER O 152 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL O 154 " --> pdb=" O ILE O 170 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE O 170 " --> pdb=" O VAL O 154 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL O 156 " --> pdb=" O THR O 168 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR O 168 " --> pdb=" O VAL O 156 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY O 173 " --> pdb=" O MET O 177 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N MET O 177 " --> pdb=" O GLY O 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL O 178 " --> pdb=" O PHE O 192 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA O 190 " --> pdb=" O ALA O 180 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASN O 182 " --> pdb=" O ILE O 188 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE O 188 " --> pdb=" O ASN O 182 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'O' and resid 199 through 204 removed outlier: 7.033A pdb=" N ALA O 214 " --> pdb=" O ASN O 200 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU O 202 " --> pdb=" O ALA O 212 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA O 212 " --> pdb=" O LEU O 202 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA O 204 " --> pdb=" O LEU O 210 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU O 210 " --> pdb=" O ALA O 204 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY O 215 " --> pdb=" O GLU O 219 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLU O 219 " --> pdb=" O GLY O 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR O 232 " --> pdb=" O LEU O 222 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN O 224 " --> pdb=" O ALA O 230 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ALA O 230 " --> pdb=" O ASN O 224 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'O' and resid 243 through 245 Processing sheet with id= AZ, first strand: chain 'O' and resid 310 through 314 removed outlier: 3.519A pdb=" N SER O 291 " --> pdb=" O GLY O 304 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'h' and resid 53 through 56 removed outlier: 7.272A pdb=" N ARG h 29 " --> pdb=" O ILE h 13 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL h 15 " --> pdb=" O GLN h 27 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLN h 27 " --> pdb=" O VAL h 15 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE h 40 " --> pdb=" O VAL h 30 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'h' and resid 17 through 19 Processing sheet with id= BC, first strand: chain 'x' and resid 6 through 11 removed outlier: 3.813A pdb=" N SER x 6 " --> pdb=" O LEU x 75 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'x' and resid 290 through 293 removed outlier: 7.320A pdb=" N VAL x 274 " --> pdb=" O LEU x 106 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N LEU x 108 " --> pdb=" O VAL x 274 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N CYS x 276 " --> pdb=" O LEU x 108 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'x' and resid 415 through 417 removed outlier: 7.233A pdb=" N ILE x 488 " --> pdb=" O SER x 416 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'x' and resid 537 through 539 Processing sheet with id= BG, first strand: chain 'x' and resid 572 through 574 1373 hydrogen bonds defined for protein. 3933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1249 hydrogen bonds 2006 hydrogen bond angles 0 basepair planarities 511 basepair parallelities 929 stacking parallelities Total time for adding SS restraints: 59.59 Time building geometry restraints manager: 33.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.39: 32397 1.39 - 1.61: 54310 1.61 - 1.83: 276 1.83 - 2.06: 0 2.06 - 2.28: 24 Bond restraints: 87007 Sorted by residual: bond pdb=" CB VAL R 111 " pdb=" CG1 VAL R 111 " ideal model delta sigma weight residual 1.521 1.396 0.125 3.30e-02 9.18e+02 1.44e+01 bond pdb=" CB ILE S 210 " pdb=" CG2 ILE S 210 " ideal model delta sigma weight residual 1.521 1.412 0.109 3.30e-02 9.18e+02 1.09e+01 bond pdb=" C LYS z 186 " pdb=" N PRO z 187 " ideal model delta sigma weight residual 1.334 1.411 -0.077 2.34e-02 1.83e+03 1.07e+01 bond pdb=" CB VAL x 310 " pdb=" CG1 VAL x 310 " ideal model delta sigma weight residual 1.521 1.421 0.100 3.30e-02 9.18e+02 9.13e+00 bond pdb=" CB ARG V 56 " pdb=" CG ARG V 56 " ideal model delta sigma weight residual 1.520 1.433 0.087 3.00e-02 1.11e+03 8.41e+00 ... (remaining 87002 not shown) Histogram of bond angle deviations from ideal: 73.63 - 86.80: 24 86.80 - 99.98: 33 99.98 - 113.15: 58620 113.15 - 126.32: 61525 126.32 - 139.49: 5928 Bond angle restraints: 126130 Sorted by residual: angle pdb=" O GLN y 213 " pdb=" C GLN y 213 " pdb=" N ALA y 214 " ideal model delta sigma weight residual 122.07 108.31 13.76 1.03e+00 9.43e-01 1.79e+02 angle pdb=" N LEU y 176 " pdb=" CA LEU y 176 " pdb=" C LEU y 176 " ideal model delta sigma weight residual 111.07 122.25 -11.18 1.07e+00 8.73e-01 1.09e+02 angle pdb=" C ALA Y 22 " pdb=" N PRO Y 23 " pdb=" CD PRO Y 23 " ideal model delta sigma weight residual 120.60 103.80 16.80 2.20e+00 2.07e-01 5.83e+01 angle pdb=" N SER y 175 " pdb=" CA SER y 175 " pdb=" C SER y 175 " ideal model delta sigma weight residual 111.28 119.55 -8.27 1.09e+00 8.42e-01 5.75e+01 angle pdb=" N GLY P 44 " pdb=" CA GLY P 44 " pdb=" C GLY P 44 " ideal model delta sigma weight residual 114.95 104.49 10.46 1.41e+00 5.03e-01 5.50e+01 ... (remaining 126125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 49927 35.80 - 71.59: 4466 71.59 - 107.39: 468 107.39 - 143.19: 15 143.19 - 178.98: 39 Dihedral angle restraints: 54915 sinusoidal: 38723 harmonic: 16192 Sorted by residual: dihedral pdb=" O4' U 2 767 " pdb=" C1' U 2 767 " pdb=" N1 U 2 767 " pdb=" C2 U 2 767 " ideal model delta sinusoidal sigma weight residual 200.00 24.15 175.85 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 21145 " pdb=" C1' U 21145 " pdb=" N1 U 21145 " pdb=" C2 U 21145 " ideal model delta sinusoidal sigma weight residual 200.00 25.38 174.62 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U 21489 " pdb=" C1' U 21489 " pdb=" N1 U 21489 " pdb=" C2 U 21489 " ideal model delta sinusoidal sigma weight residual 200.00 26.73 173.27 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 54912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 15114 0.153 - 0.306: 539 0.306 - 0.459: 37 0.459 - 0.612: 6 0.612 - 0.765: 2 Chirality restraints: 15698 Sorted by residual: chirality pdb=" CB ILE B 40 " pdb=" CA ILE B 40 " pdb=" CG1 ILE B 40 " pdb=" CG2 ILE B 40 " both_signs ideal model delta sigma weight residual False 2.64 1.88 0.77 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CG LEU D 88 " pdb=" CB LEU D 88 " pdb=" CD1 LEU D 88 " pdb=" CD2 LEU D 88 " both_signs ideal model delta sigma weight residual False -2.59 -1.95 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C3' A 21791 " pdb=" C4' A 21791 " pdb=" O3' A 21791 " pdb=" C2' A 21791 " both_signs ideal model delta sigma weight residual False -2.74 -2.17 -0.57 2.00e-01 2.50e+01 8.21e+00 ... (remaining 15695 not shown) Planarity restraints: 9479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN y 213 " -0.074 2.00e-02 2.50e+03 1.37e-01 1.87e+02 pdb=" C GLN y 213 " 0.237 2.00e-02 2.50e+03 pdb=" O GLN y 213 " -0.086 2.00e-02 2.50e+03 pdb=" N ALA y 214 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN R 233 " 0.070 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO R 234 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO R 234 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO R 234 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 150 " -0.030 2.00e-02 2.50e+03 2.62e-02 1.72e+01 pdb=" CG TRP O 150 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP O 150 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP O 150 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP O 150 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP O 150 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP O 150 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 150 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 150 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP O 150 " -0.001 2.00e-02 2.50e+03 ... (remaining 9476 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 31 2.20 - 2.88: 27577 2.88 - 3.55: 111816 3.55 - 4.23: 236684 4.23 - 4.90: 337598 Nonbonded interactions: 713706 Sorted by model distance: nonbonded pdb=" CB CYS x 21 " pdb=" S2 SF4 x 701 " model vdw 1.525 3.040 nonbonded pdb=" OG SER x 117 " pdb="MG MG x 704 " model vdw 1.763 2.170 nonbonded pdb=" SG CYS x 25 " pdb=" S3 SF4 x 701 " model vdw 2.009 3.760 nonbonded pdb=" OP2 U 2 101 " pdb="MG MG 21805 " model vdw 2.057 2.170 nonbonded pdb=" OP1 G 21768 " pdb="MG MG 21874 " model vdw 2.064 2.170 ... (remaining 713701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.55 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: 4.720 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: 0.080 Extract box with map and model: 20.870 Check model and map are aligned: 0.920 Set scattering table: 0.600 Process input model: 244.010 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 283.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.009 0.125 87007 Z= 0.564 Angle : 1.248 19.806 126130 Z= 0.651 Chirality : 0.069 0.765 15698 Planarity : 0.009 0.137 9479 Dihedral : 22.231 178.983 44455 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 0.80 % Favored : 99.13 % Rotamer: Outliers : 0.19 % Allowed : 1.17 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -2.80 (0.10), residues: 5532 helix: -1.32 (0.10), residues: 1740 sheet: -1.66 (0.15), residues: 986 loop : -2.27 (0.10), residues: 2806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.004 TRP O 150 HIS 0.026 0.003 HIS P 32 PHE 0.064 0.005 PHE F 46 TYR 0.060 0.004 TYR Q 133 ARG 0.035 0.002 ARG d 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 796 time to evaluate : 5.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 175 GLU cc_start: 0.5835 (mt-10) cc_final: 0.5499 (mt-10) REVERT: Y 138 ASN cc_start: 0.6618 (p0) cc_final: 0.6409 (p0) REVERT: A 177 MET cc_start: 0.8041 (mmt) cc_final: 0.7814 (mmt) REVERT: C 80 LEU cc_start: 0.7308 (mt) cc_final: 0.7096 (mt) REVERT: N 140 TYR cc_start: 0.6199 (OUTLIER) cc_final: 0.5850 (t80) outliers start: 9 outliers final: 3 residues processed: 802 average time/residue: 1.8136 time to fit residues: 1891.7136 Evaluate side-chains 565 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 561 time to evaluate : 4.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 CYS Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 140 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 611 optimal weight: 9.9990 chunk 548 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 370 optimal weight: 5.9990 chunk 293 optimal weight: 0.9990 chunk 567 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 345 optimal weight: 0.0870 chunk 422 optimal weight: 2.9990 chunk 657 optimal weight: 3.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 ASN P 168 HIS ** R 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN S 258 GLN U 11 GLN U 174 ASN V 111 GLN V 159 GLN Y 36 GLN Y 62 GLN a 7 GLN d 34 ASN e 69 ASN A 67 ASN A 74 GLN B 35 GLN C 13 GLN C 28 ASN D 96 GLN D 139 HIS I 25 ASN I 71 GLN J 64 HIS L 98 GLN N 95 HIS ** O 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 51 ASN y 171 ASN y 213 GLN x 238 GLN x 363 GLN x 444 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 87007 Z= 0.183 Angle : 0.670 12.187 126130 Z= 0.347 Chirality : 0.042 0.335 15698 Planarity : 0.005 0.082 9479 Dihedral : 23.068 179.276 33503 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 2.04 % Allowed : 12.71 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -1.61 (0.10), residues: 5532 helix: 0.07 (0.12), residues: 1781 sheet: -1.05 (0.16), residues: 960 loop : -1.85 (0.11), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP O 150 HIS 0.005 0.001 HIS P 46 PHE 0.033 0.002 PHE x 447 TYR 0.020 0.001 TYR F 96 ARG 0.007 0.000 ARG J 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 633 time to evaluate : 5.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 77 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.6729 (pp30) REVERT: R 87 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: Y 3 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7303 (mpp-170) REVERT: a 4 ASP cc_start: 0.6766 (p0) cc_final: 0.6539 (p0) REVERT: a 44 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6859 (mmt-90) REVERT: F 46 PHE cc_start: 0.6015 (OUTLIER) cc_final: 0.5326 (t80) REVERT: J 127 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.7172 (m-40) REVERT: N 83 LYS cc_start: 0.3788 (mmtt) cc_final: 0.3375 (mmpt) outliers start: 96 outliers final: 21 residues processed: 680 average time/residue: 1.8012 time to fit residues: 1610.0082 Evaluate side-chains 580 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 553 time to evaluate : 4.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 GLN Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 163 ASP Chi-restraints excluded: chain Y residue 3 ARG Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Z residue 66 ASP Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain x residue 186 LYS Chi-restraints excluded: chain x residue 189 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 365 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 547 optimal weight: 10.0000 chunk 447 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 658 optimal weight: 40.0000 chunk 711 optimal weight: 6.9990 chunk 586 optimal weight: 9.9990 chunk 653 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 528 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 21 ASN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** Q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 152 HIS ** R 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 258 GLN U 160 GLN U 174 ASN V 111 GLN V 159 GLN X 110 HIS a 81 ASN d 34 ASN d 110 GLN e 69 ASN A 67 ASN A 74 GLN B 35 GLN C 28 ASN F 93 HIS K 33 GLN K 40 ASN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS N 93 HIS ** N 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 51 ASN y 213 GLN x 584 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 87007 Z= 0.344 Angle : 0.700 11.576 126130 Z= 0.361 Chirality : 0.044 0.403 15698 Planarity : 0.006 0.085 9479 Dihedral : 22.888 179.739 33500 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.60 % Allowed : 15.61 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -1.26 (0.11), residues: 5532 helix: 0.42 (0.12), residues: 1819 sheet: -0.85 (0.16), residues: 949 loop : -1.70 (0.11), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP O 150 HIS 0.023 0.001 HIS I 78 PHE 0.030 0.002 PHE c 107 TYR 0.031 0.002 TYR P 202 ARG 0.015 0.001 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 590 time to evaluate : 5.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 77 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.6681 (pp30) REVERT: W 138 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.7046 (ptmt) REVERT: X 143 SER cc_start: 0.6927 (m) cc_final: 0.6543 (t) REVERT: Y 3 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7390 (mpp-170) REVERT: a 4 ASP cc_start: 0.6919 (p0) cc_final: 0.6545 (p0) REVERT: a 44 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6983 (mmt-90) REVERT: b 117 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7172 (mpp80) REVERT: d 38 ASP cc_start: 0.6647 (t0) cc_final: 0.5616 (t0) REVERT: f 33 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7800 (mt) REVERT: C 13 GLN cc_start: 0.6064 (OUTLIER) cc_final: 0.5780 (tm130) REVERT: F 46 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.5468 (t80) REVERT: F 103 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7297 (m110) REVERT: N 83 LYS cc_start: 0.4334 (mmtt) cc_final: 0.4094 (mptt) REVERT: O 292 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7727 (pp) outliers start: 169 outliers final: 72 residues processed: 692 average time/residue: 1.6950 time to fit residues: 1552.6529 Evaluate side-chains 632 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 550 time to evaluate : 4.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 77 GLN Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 138 LYS Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 3 ARG Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain b residue 88 LYS Chi-restraints excluded: chain b residue 117 ARG Chi-restraints excluded: chain c residue 26 GLU Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 8 ARG Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain e residue 27 SER Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain N residue 93 HIS Chi-restraints excluded: chain N residue 119 ARG Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain z residue 202 VAL Chi-restraints excluded: chain y residue 155 LYS Chi-restraints excluded: chain y residue 196 THR Chi-restraints excluded: chain x residue 189 GLU Chi-restraints excluded: chain x residue 277 VAL Chi-restraints excluded: chain x residue 435 PHE Chi-restraints excluded: chain x residue 478 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 650 optimal weight: 3.9990 chunk 495 optimal weight: 0.9990 chunk 341 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 314 optimal weight: 5.9990 chunk 442 optimal weight: 1.9990 chunk 661 optimal weight: 4.9990 chunk 699 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 chunk 626 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 21 ASN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** R 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 GLN V 111 GLN a 81 ASN d 110 GLN e 69 ASN E 15 HIS A 67 ASN A 74 GLN B 35 GLN ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN L 82 HIS N 93 HIS N 95 HIS y 213 GLN x 526 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 87007 Z= 0.212 Angle : 0.617 13.136 126130 Z= 0.319 Chirality : 0.040 0.334 15698 Planarity : 0.005 0.076 9479 Dihedral : 22.783 179.937 33499 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.89 % Favored : 94.09 % Rotamer: Outliers : 3.30 % Allowed : 18.25 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.11), residues: 5532 helix: 0.75 (0.12), residues: 1804 sheet: -0.67 (0.16), residues: 930 loop : -1.53 (0.11), residues: 2798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP O 150 HIS 0.035 0.001 HIS N 93 PHE 0.026 0.001 PHE A 107 TYR 0.019 0.001 TYR P 202 ARG 0.011 0.000 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 606 time to evaluate : 5.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 3 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7456 (mpp-170) REVERT: a 44 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6828 (mmt-90) REVERT: F 46 PHE cc_start: 0.6222 (OUTLIER) cc_final: 0.5413 (t80) REVERT: N 136 LYS cc_start: 0.5833 (mmpt) cc_final: 0.5544 (mppt) REVERT: y 188 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7312 (mtm) REVERT: y 207 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7112 (ttpp) outliers start: 155 outliers final: 64 residues processed: 694 average time/residue: 1.6892 time to fit residues: 1557.6322 Evaluate side-chains 636 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 567 time to evaluate : 7.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 67 GLU Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain R residue 119 LYS Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain V residue 164 ARG Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 3 ARG Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain e residue 27 SER Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 41 THR Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain N residue 119 ARG Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 286 GLU Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain z residue 184 VAL Chi-restraints excluded: chain y residue 188 MET Chi-restraints excluded: chain y residue 196 THR Chi-restraints excluded: chain y residue 207 LYS Chi-restraints excluded: chain x residue 180 ILE Chi-restraints excluded: chain x residue 189 GLU Chi-restraints excluded: chain x residue 277 VAL Chi-restraints excluded: chain x residue 310 VAL Chi-restraints excluded: chain x residue 451 VAL Chi-restraints excluded: chain x residue 520 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 582 optimal weight: 5.9990 chunk 397 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 521 optimal weight: 7.9990 chunk 288 optimal weight: 4.9990 chunk 597 optimal weight: 9.9990 chunk 483 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 357 optimal weight: 2.9990 chunk 628 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN P 131 GLN ** R 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 GLN a 81 ASN b 56 HIS e 69 ASN A 67 ASN A 74 GLN B 35 GLN C 13 GLN C 17 GLN C 28 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS N 93 HIS ** y 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 526 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 87007 Z= 0.364 Angle : 0.685 14.043 126130 Z= 0.352 Chirality : 0.044 0.410 15698 Planarity : 0.005 0.084 9479 Dihedral : 22.760 179.904 33499 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.36 % Favored : 93.62 % Rotamer: Outliers : 4.19 % Allowed : 18.88 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -0.92 (0.11), residues: 5532 helix: 0.75 (0.12), residues: 1803 sheet: -0.69 (0.16), residues: 956 loop : -1.53 (0.11), residues: 2773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP O 150 HIS 0.007 0.001 HIS N 93 PHE 0.026 0.002 PHE c 107 TYR 0.025 0.002 TYR P 202 ARG 0.010 0.001 ARG O 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 575 time to evaluate : 5.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 143 SER cc_start: 0.6896 (m) cc_final: 0.6502 (t) REVERT: Y 3 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.7465 (mpp-170) REVERT: a 44 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6945 (mmt-90) REVERT: F 46 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5334 (t80) REVERT: y 188 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7375 (mtm) REVERT: y 207 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7347 (ttpp) outliers start: 197 outliers final: 116 residues processed: 697 average time/residue: 1.6108 time to fit residues: 1502.8419 Evaluate side-chains 669 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 548 time to evaluate : 4.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 119 LYS Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 50 ASP Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 105 ASP Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 3 ARG Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Z residue 26 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain c residue 26 GLU Chi-restraints excluded: chain c residue 79 ASN Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 42 GLU Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain e residue 27 SER Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 54 SER Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 41 THR Chi-restraints excluded: chain g residue 42 ARG Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain N residue 93 HIS Chi-restraints excluded: chain N residue 119 ARG Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 57 MET Chi-restraints excluded: chain z residue 162 THR Chi-restraints excluded: chain z residue 184 VAL Chi-restraints excluded: chain z residue 202 VAL Chi-restraints excluded: chain z residue 210 GLU Chi-restraints excluded: chain y residue 188 MET Chi-restraints excluded: chain y residue 196 THR Chi-restraints excluded: chain y residue 207 LYS Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 180 ILE Chi-restraints excluded: chain x residue 189 GLU Chi-restraints excluded: chain x residue 195 MET Chi-restraints excluded: chain x residue 277 VAL Chi-restraints excluded: chain x residue 310 VAL Chi-restraints excluded: chain x residue 408 GLN Chi-restraints excluded: chain x residue 451 VAL Chi-restraints excluded: chain x residue 476 VAL Chi-restraints excluded: chain x residue 478 ILE Chi-restraints excluded: chain x residue 520 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 235 optimal weight: 5.9990 chunk 630 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 410 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 700 optimal weight: 5.9990 chunk 581 optimal weight: 0.9990 chunk 324 optimal weight: 0.4980 chunk 58 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 367 optimal weight: 0.9980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 199 GLN S 67 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 GLN a 81 ASN e 69 ASN E 15 HIS A 67 ASN A 74 GLN B 35 GLN C 17 GLN C 28 ASN F 32 ASN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS N 93 HIS ** y 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 526 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 87007 Z= 0.161 Angle : 0.599 14.876 126130 Z= 0.308 Chirality : 0.038 0.293 15698 Planarity : 0.004 0.073 9479 Dihedral : 22.679 179.628 33499 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.75 % Favored : 94.23 % Rotamer: Outliers : 3.04 % Allowed : 20.78 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 (0.11), residues: 5532 helix: 0.91 (0.12), residues: 1797 sheet: -0.45 (0.17), residues: 919 loop : -1.37 (0.11), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 53 HIS 0.042 0.001 HIS N 93 PHE 0.030 0.001 PHE A 107 TYR 0.038 0.001 TYR C 14 ARG 0.011 0.000 ARG z 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 590 time to evaluate : 5.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 3 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7500 (mpp-170) REVERT: a 12 TYR cc_start: 0.8080 (t80) cc_final: 0.7169 (t80) REVERT: E 104 GLN cc_start: 0.6287 (tp-100) cc_final: 0.6059 (tp40) REVERT: F 46 PHE cc_start: 0.5942 (OUTLIER) cc_final: 0.5180 (t80) REVERT: H 76 GLU cc_start: 0.4579 (tm-30) cc_final: 0.4143 (tm-30) REVERT: y 188 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7245 (mtm) REVERT: y 207 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7102 (ttpp) outliers start: 143 outliers final: 75 residues processed: 677 average time/residue: 1.6401 time to fit residues: 1486.3127 Evaluate side-chains 634 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 555 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain V residue 105 ASP Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 3 ARG Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain a residue 5 LYS Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 42 GLU Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain e residue 27 SER Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 54 SER Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 41 THR Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain E residue 28 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain N residue 119 ARG Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain y residue 188 MET Chi-restraints excluded: chain y residue 196 THR Chi-restraints excluded: chain y residue 207 LYS Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 189 GLU Chi-restraints excluded: chain x residue 275 ILE Chi-restraints excluded: chain x residue 277 VAL Chi-restraints excluded: chain x residue 310 VAL Chi-restraints excluded: chain x residue 408 GLN Chi-restraints excluded: chain x residue 435 PHE Chi-restraints excluded: chain x residue 520 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 675 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 399 optimal weight: 2.9990 chunk 511 optimal weight: 7.9990 chunk 396 optimal weight: 5.9990 chunk 589 optimal weight: 0.7980 chunk 391 optimal weight: 0.9990 chunk 697 optimal weight: 6.9990 chunk 436 optimal weight: 5.9990 chunk 425 optimal weight: 0.0020 chunk 322 optimal weight: 6.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 211 HIS S 67 GLN S 259 GLN U 110 GLN V 111 GLN V 159 GLN d 34 ASN d 107 GLN e 69 ASN A 67 ASN A 74 GLN B 35 GLN C 28 ASN H 104 ASN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN L 82 HIS ** y 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 526 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 87007 Z= 0.153 Angle : 0.575 13.923 126130 Z= 0.295 Chirality : 0.037 0.286 15698 Planarity : 0.004 0.069 9479 Dihedral : 22.552 179.289 33499 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.95 % Favored : 94.03 % Rotamer: Outliers : 2.70 % Allowed : 21.78 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.11), residues: 5532 helix: 1.04 (0.12), residues: 1790 sheet: -0.35 (0.17), residues: 929 loop : -1.28 (0.11), residues: 2813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 53 HIS 0.013 0.001 HIS I 78 PHE 0.016 0.001 PHE x 447 TYR 0.027 0.001 TYR z 172 ARG 0.013 0.000 ARG Z 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 606 time to evaluate : 5.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 3 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7490 (mpp-170) REVERT: a 44 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6831 (mmt-90) REVERT: F 46 PHE cc_start: 0.5713 (OUTLIER) cc_final: 0.4844 (t80) REVERT: N 119 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.6198 (ptp-170) REVERT: N 136 LYS cc_start: 0.5865 (mmpt) cc_final: 0.5543 (mppt) REVERT: O 102 ARG cc_start: 0.6376 (mtp-110) cc_final: 0.6132 (mtp-110) outliers start: 127 outliers final: 78 residues processed: 685 average time/residue: 1.6404 time to fit residues: 1513.7199 Evaluate side-chains 653 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 571 time to evaluate : 5.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 50 ASP Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 105 ASP Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 3 ARG Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 79 ASN Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 42 GLU Chi-restraints excluded: chain e residue 27 SER Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 54 SER Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 41 THR Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain E residue 28 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain N residue 119 ARG Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 233 THR Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain z residue 210 GLU Chi-restraints excluded: chain y residue 196 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 180 ILE Chi-restraints excluded: chain x residue 189 GLU Chi-restraints excluded: chain x residue 275 ILE Chi-restraints excluded: chain x residue 277 VAL Chi-restraints excluded: chain x residue 310 VAL Chi-restraints excluded: chain x residue 408 GLN Chi-restraints excluded: chain x residue 489 TYR Chi-restraints excluded: chain x residue 520 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 431 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 chunk 416 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 443 optimal weight: 2.9990 chunk 475 optimal weight: 1.9990 chunk 345 optimal weight: 0.9980 chunk 65 optimal weight: 40.0000 chunk 548 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 21 ASN ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN S 259 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 81 ASN d 15 ASN ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 107 GLN e 69 ASN g 51 ASN E 15 HIS A 67 ASN A 74 GLN B 35 GLN C 13 GLN C 28 ASN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** K 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS N 93 HIS N 145 HIS ** y 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 526 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 87007 Z= 0.317 Angle : 0.651 13.714 126130 Z= 0.333 Chirality : 0.042 0.385 15698 Planarity : 0.005 0.077 9479 Dihedral : 22.558 179.513 33499 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.42 % Favored : 93.56 % Rotamer: Outliers : 2.98 % Allowed : 22.42 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -0.58 (0.11), residues: 5532 helix: 1.00 (0.12), residues: 1789 sheet: -0.43 (0.17), residues: 932 loop : -1.29 (0.11), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 150 HIS 0.007 0.001 HIS N 93 PHE 0.046 0.002 PHE x 447 TYR 0.033 0.002 TYR C 14 ARG 0.013 0.001 ARG z 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 575 time to evaluate : 5.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 3 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7494 (mpp-170) REVERT: a 44 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6818 (mmt-90) REVERT: b 117 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7235 (mpp80) REVERT: F 46 PHE cc_start: 0.5998 (OUTLIER) cc_final: 0.5024 (t80) REVERT: O 292 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7708 (pp) REVERT: y 188 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7332 (mtm) outliers start: 140 outliers final: 96 residues processed: 669 average time/residue: 1.6386 time to fit residues: 1467.8636 Evaluate side-chains 667 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 565 time to evaluate : 5.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain T residue 170 THR Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 50 ASP Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 105 ASP Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 3 ARG Chi-restraints excluded: chain Z residue 26 THR Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain b residue 117 ARG Chi-restraints excluded: chain c residue 79 ASN Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 42 GLU Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain e residue 27 SER Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 23 THR Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 25 GLU Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 41 THR Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain N residue 93 HIS Chi-restraints excluded: chain N residue 119 ARG Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 233 THR Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain y residue 188 MET Chi-restraints excluded: chain y residue 196 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 180 ILE Chi-restraints excluded: chain x residue 189 GLU Chi-restraints excluded: chain x residue 275 ILE Chi-restraints excluded: chain x residue 277 VAL Chi-restraints excluded: chain x residue 310 VAL Chi-restraints excluded: chain x residue 408 GLN Chi-restraints excluded: chain x residue 435 PHE Chi-restraints excluded: chain x residue 476 VAL Chi-restraints excluded: chain x residue 489 TYR Chi-restraints excluded: chain x residue 520 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 634 optimal weight: 3.9990 chunk 668 optimal weight: 0.3980 chunk 609 optimal weight: 0.0570 chunk 650 optimal weight: 10.0000 chunk 391 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 510 optimal weight: 10.0000 chunk 199 optimal weight: 30.0000 chunk 587 optimal weight: 1.9990 chunk 615 optimal weight: 10.0000 chunk 648 optimal weight: 6.9990 overall best weight: 1.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 21 ASN ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 259 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 159 GLN a 81 ASN d 34 ASN e 69 ASN E 15 HIS A 67 ASN A 74 GLN B 35 GLN C 13 GLN C 28 ASN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** K 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS y 213 GLN x 526 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 87007 Z= 0.191 Angle : 0.612 13.760 126130 Z= 0.314 Chirality : 0.038 0.327 15698 Planarity : 0.004 0.074 9479 Dihedral : 22.556 179.593 33499 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.25 % Favored : 93.73 % Rotamer: Outliers : 2.51 % Allowed : 23.10 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -0.53 (0.11), residues: 5532 helix: 1.04 (0.12), residues: 1789 sheet: -0.40 (0.17), residues: 934 loop : -1.27 (0.11), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 129 HIS 0.039 0.001 HIS N 93 PHE 0.059 0.001 PHE x 447 TYR 0.028 0.001 TYR L 101 ARG 0.015 0.000 ARG O 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 579 time to evaluate : 5.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 3 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7482 (mpp-170) REVERT: a 44 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6777 (mmt-90) REVERT: A 218 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5218 (pt) REVERT: F 46 PHE cc_start: 0.5863 (OUTLIER) cc_final: 0.5011 (t80) REVERT: I 73 MET cc_start: 0.4585 (mtt) cc_final: 0.4325 (mtt) REVERT: K 70 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7939 (t) REVERT: O 102 ARG cc_start: 0.6504 (mtp-110) cc_final: 0.6190 (mtp-110) REVERT: y 164 MET cc_start: 0.6715 (mmp) cc_final: 0.6454 (mmm) REVERT: y 188 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7305 (mtm) outliers start: 118 outliers final: 84 residues processed: 656 average time/residue: 1.6605 time to fit residues: 1461.7410 Evaluate side-chains 650 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 560 time to evaluate : 5.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 105 ASP Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 3 ARG Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Z residue 26 THR Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain c residue 79 ASN Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 42 GLU Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain e residue 27 SER Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 25 GLU Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 41 THR Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 233 THR Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain y residue 188 MET Chi-restraints excluded: chain y residue 196 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 180 ILE Chi-restraints excluded: chain x residue 189 GLU Chi-restraints excluded: chain x residue 275 ILE Chi-restraints excluded: chain x residue 277 VAL Chi-restraints excluded: chain x residue 310 VAL Chi-restraints excluded: chain x residue 451 VAL Chi-restraints excluded: chain x residue 476 VAL Chi-restraints excluded: chain x residue 489 TYR Chi-restraints excluded: chain x residue 520 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 427 optimal weight: 5.9990 chunk 687 optimal weight: 9.9990 chunk 419 optimal weight: 9.9990 chunk 326 optimal weight: 0.9990 chunk 478 optimal weight: 10.0000 chunk 721 optimal weight: 2.9990 chunk 663 optimal weight: 2.9990 chunk 574 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 443 optimal weight: 3.9990 chunk 352 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 21 ASN ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 259 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 116 HIS V 159 GLN e 69 ASN E 15 HIS A 74 GLN B 35 GLN C 28 ASN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** K 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS y 213 GLN x 408 GLN x 526 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 87007 Z= 0.253 Angle : 0.633 13.743 126130 Z= 0.324 Chirality : 0.040 0.356 15698 Planarity : 0.005 0.076 9479 Dihedral : 22.527 179.802 33499 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.67 % Favored : 93.31 % Rotamer: Outliers : 2.28 % Allowed : 23.46 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -0.56 (0.11), residues: 5532 helix: 1.00 (0.12), residues: 1789 sheet: -0.40 (0.17), residues: 941 loop : -1.28 (0.11), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 150 HIS 0.006 0.001 HIS N 95 PHE 0.061 0.002 PHE x 447 TYR 0.031 0.002 TYR O 250 ARG 0.015 0.001 ARG z 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11064 Ramachandran restraints generated. 5532 Oldfield, 0 Emsley, 5532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 571 time to evaluate : 8.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 3 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7476 (mpp-170) REVERT: a 44 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6844 (mmt-90) REVERT: C 74 GLU cc_start: 0.5841 (mm-30) cc_final: 0.5613 (mm-30) REVERT: F 46 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.5053 (t80) REVERT: I 73 MET cc_start: 0.4522 (mtt) cc_final: 0.4318 (mtt) REVERT: L 94 LYS cc_start: 0.6273 (tppt) cc_final: 0.5969 (tptt) REVERT: O 102 ARG cc_start: 0.6547 (mtp-110) cc_final: 0.6241 (mtp-110) REVERT: y 188 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7302 (mtm) outliers start: 107 outliers final: 90 residues processed: 646 average time/residue: 1.6984 time to fit residues: 1479.6919 Evaluate side-chains 660 residues out of total 4785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 566 time to evaluate : 5.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 50 ASP Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 105 ASP Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 3 ARG Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Z residue 26 THR Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain c residue 79 ASN Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 42 GLU Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain e residue 27 SER Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 25 GLU Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 41 THR Chi-restraints excluded: chain g residue 47 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain J residue 8 ASP Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain y residue 188 MET Chi-restraints excluded: chain y residue 196 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 180 ILE Chi-restraints excluded: chain x residue 189 GLU Chi-restraints excluded: chain x residue 275 ILE Chi-restraints excluded: chain x residue 277 VAL Chi-restraints excluded: chain x residue 310 VAL Chi-restraints excluded: chain x residue 331 THR Chi-restraints excluded: chain x residue 451 VAL Chi-restraints excluded: chain x residue 476 VAL Chi-restraints excluded: chain x residue 489 TYR Chi-restraints excluded: chain x residue 520 THR Chi-restraints excluded: chain x residue 571 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 456 optimal weight: 10.0000 chunk 611 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 529 optimal weight: 0.0370 chunk 84 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 575 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 590 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 overall best weight: 3.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 21 ASN ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 259 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 159 GLN a 81 ASN d 34 ASN e 69 ASN E 15 HIS A 67 ASN A 74 GLN B 35 GLN ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** K 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS ** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 526 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.054201 restraints weight = 226542.329| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.47 r_work: 0.2704 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 87007 Z= 0.312 Angle : 0.664 13.768 126130 Z= 0.340 Chirality : 0.042 0.384 15698 Planarity : 0.005 0.077 9479 Dihedral : 22.556 179.938 33499 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.69 % Favored : 93.29 % Rotamer: Outliers : 2.34 % Allowed : 23.50 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -0.63 (0.11), residues: 5532 helix: 0.93 (0.12), residues: 1791 sheet: -0.44 (0.16), residues: 957 loop : -1.32 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 150 HIS 0.009 0.001 HIS x 550 PHE 0.060 0.002 PHE x 447 TYR 0.028 0.002 TYR L 101 ARG 0.016 0.001 ARG y 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23901.79 seconds wall clock time: 421 minutes 23.68 seconds (25283.68 seconds total)