Starting phenix.real_space_refine on Mon Feb 19 23:36:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugq_26496/02_2024/7ugq_26496.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugq_26496/02_2024/7ugq_26496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugq_26496/02_2024/7ugq_26496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugq_26496/02_2024/7ugq_26496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugq_26496/02_2024/7ugq_26496.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugq_26496/02_2024/7ugq_26496.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 16269 2.51 5 N 4374 2.21 5 O 5320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 57": "OD1" <-> "OD2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B ASP 457": "OD1" <-> "OD2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 460": "OD1" <-> "OD2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D ASP 624": "OD1" <-> "OD2" Residue "D GLU 647": "OE1" <-> "OE2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "E ASP 624": "OD1" <-> "OD2" Residue "E GLU 648": "OE1" <-> "OE2" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F ASP 632": "OD1" <-> "OD2" Residue "F GLU 648": "OE1" <-> "OE2" Residue "G ARG 8": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "H ARG 8": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 66": "NH1" <-> "NH2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "J TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 27": "OD1" <-> "OD2" Residue "M GLU 55": "OE1" <-> "OE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 16": "OE1" <-> "OE2" Residue "N ASP 27": "OD1" <-> "OD2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 16": "OE1" <-> "OE2" Residue "O GLU 55": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "P ARG 9": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 70": "NH1" <-> "NH2" Residue "P GLU 79": "OE1" <-> "OE2" Residue "P ASP 85": "OD1" <-> "OD2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "Q ARG 9": "NH1" <-> "NH2" Residue "Q ARG 20": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q ARG 94": "NH1" <-> "NH2" Residue "R ARG 9": "NH1" <-> "NH2" Residue "R ARG 20": "NH1" <-> "NH2" Residue "R ASP 53": "OD1" <-> "OD2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ASP 85": "OD1" <-> "OD2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "R ARG 94": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26113 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3498 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 3 Chain: "B" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3498 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 3 Chain: "C" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3498 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 3 Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 119} Chain: "H" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 119} Chain: "I" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 758 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "K" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 758 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 758 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "N" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "O" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "Q" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "1" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.13, per 1000 atoms: 0.54 Number of scatterers: 26113 At special positions: 0 Unit cell: (152.075, 158.158, 150.337, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 5320 8.00 N 4374 7.00 C 16269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 385 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.05 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 385 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.05 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 385 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 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 Links applied ALPHA1-2 " MAN 1 4 " - " MAN 1 5 " " MAN 1 5 " - " MAN 1 6 " " MAN d 4 " - " MAN d 5 " " MAN d 5 " - " MAN d 6 " " MAN p 4 " - " MAN p 5 " " MAN p 5 " - " MAN p 6 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " MAN 1 7 " - " MAN 1 8 " " BMA W 3 " - " MAN W 4 " " BMA d 3 " - " MAN d 4 " " MAN d 7 " - " MAN d 8 " " BMA i 3 " - " MAN i 4 " " BMA p 3 " - " MAN p 4 " " MAN p 7 " - " MAN p 8 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 7 " " MAN 1 7 " - " MAN 1 9 " " BMA W 3 " - " MAN W 5 " " BMA d 3 " - " MAN d 7 " " MAN d 7 " - " MAN d 9 " " BMA i 3 " - " MAN i 5 " " BMA p 3 " - " MAN p 7 " " BMA u 3 " - " MAN u 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN C 465 " " NAG 1 1 " - " ASN C 332 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 241 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 354 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 448 " " NAG A 607 " - " ASN A 461 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 241 " " NAG B 603 " - " ASN B 301 " " NAG B 604 " - " ASN B 354 " " NAG B 605 " - " ASN B 392 " " NAG B 606 " - " ASN B 461 " " NAG B 607 " - " ASN B 448 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 354 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 461 " " NAG C 607 " - " ASN C 448 " " NAG D 701 " - " ASN D 637 " " NAG E 701 " - " ASN E 637 " " NAG F 701 " - " ASN F 637 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 160 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN A 234 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 295 " " NAG Y 1 " - " ASN A 276 " " NAG Z 1 " - " ASN A 340 " " NAG a 1 " - " ASN A 289 " " NAG b 1 " - " ASN A 386 " " NAG c 1 " - " ASN A 465 " " NAG d 1 " - " ASN A 332 " " NAG e 1 " - " ASN B 156 " " NAG f 1 " - " ASN B 160 " " NAG g 1 " - " ASN B 197 " " NAG h 1 " - " ASN B 234 " " NAG i 1 " - " ASN B 262 " " NAG j 1 " - " ASN B 295 " " NAG k 1 " - " ASN B 276 " " NAG l 1 " - " ASN B 340 " " NAG m 1 " - " ASN B 289 " " NAG n 1 " - " ASN B 386 " " NAG o 1 " - " ASN B 465 " " NAG p 1 " - " ASN B 332 " " NAG q 1 " - " ASN C 156 " " NAG r 1 " - " ASN C 160 " " NAG s 1 " - " ASN C 197 " " NAG t 1 " - " ASN C 234 " " NAG u 1 " - " ASN C 262 " " NAG v 1 " - " ASN C 295 " " NAG w 1 " - " ASN C 276 " " NAG x 1 " - " ASN C 340 " " NAG y 1 " - " ASN C 289 " " NAG z 1 " - " ASN C 386 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.75 Conformation dependent library (CDL) restraints added in 4.3 seconds 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 75 sheets defined 12.7% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.819A pdb=" N SER A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 354 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.532A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.723A pdb=" N SER B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 334 through 354 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.536A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.806A pdb=" N SER C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.536A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 535 through 537 No H-bonds generated for 'chain 'D' and resid 535 through 537' Processing helix chain 'D' and resid 541 through 545 removed outlier: 3.731A pdb=" N LEU D 544 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU D 545 " --> pdb=" O ARG D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 541 through 545' Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 664 removed outlier: 4.114A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 535 through 537 No H-bonds generated for 'chain 'E' and resid 535 through 537' Processing helix chain 'E' and resid 573 through 595 Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 535 through 537 No H-bonds generated for 'chain 'F' and resid 535 through 537' Processing helix chain 'F' and resid 541 through 545 removed outlier: 3.738A pdb=" N LEU F 544 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU F 545 " --> pdb=" O ARG F 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 541 through 545' Processing helix chain 'F' and resid 573 through 595 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 removed outlier: 4.180A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.638A pdb=" N ASP G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.594A pdb=" N ASP H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.828A pdb=" N GLN I 64 " --> pdb=" O GLN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.617A pdb=" N ASP I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'N' and resid 61 through 64 removed outlier: 3.983A pdb=" N ASN N 64 " --> pdb=" O PRO N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 3.531A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 37 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 499 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A 35 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.826A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.958A pdb=" N HIS A 66 " --> pdb=" O THR A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.604A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.571A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AB1, first strand: chain 'A' and resid 330 through 333 removed outlier: 3.828A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS A 385 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 393 through 396 removed outlier: 6.889A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB4, first strand: chain 'B' and resid 494 through 495 removed outlier: 5.232A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB6, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.819A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 66 through 67 removed outlier: 7.303A pdb=" N HIS B 66 " --> pdb=" O THR B 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.585A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 154 through 162 Processing sheet with id=AC1, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AC2, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.650A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.952A pdb=" N THR B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE B 468 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 304 through 306 Processing sheet with id=AC5, first strand: chain 'B' and resid 330 through 333 removed outlier: 3.804A pdb=" N ARG B 419 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 381 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS B 385 " --> pdb=" O HIS B 374 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 423 through 425 Processing sheet with id=AC7, first strand: chain 'C' and resid 494 through 495 Processing sheet with id=AC8, first strand: chain 'C' and resid 494 through 495 removed outlier: 5.054A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AD1, first strand: chain 'C' and resid 75 through 76 removed outlier: 7.448A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 66 through 67 removed outlier: 7.039A pdb=" N HIS C 66 " --> pdb=" O THR C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.585A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AD5, first strand: chain 'C' and resid 182 through 183 Processing sheet with id=AD6, first strand: chain 'C' and resid 259 through 261 removed outlier: 5.520A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.880A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 304 through 306 Processing sheet with id=AD9, first strand: chain 'C' and resid 329 through 333 removed outlier: 4.155A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 419 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS C 385 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 423 through 425 Processing sheet with id=AE2, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AE3, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AE4, first strand: chain 'G' and resid 56 through 59 removed outlier: 3.549A pdb=" N GLY G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP G 50 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 56 through 59 removed outlier: 3.549A pdb=" N GLY G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP G 50 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AE7, first strand: chain 'H' and resid 22 through 23 Processing sheet with id=AE8, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.514A pdb=" N GLY H 56 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP H 50 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.514A pdb=" N GLY H 56 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP H 50 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 18 through 19 Processing sheet with id=AF2, first strand: chain 'I' and resid 22 through 23 Processing sheet with id=AF3, first strand: chain 'I' and resid 56 through 59 removed outlier: 3.590A pdb=" N GLY I 56 " --> pdb=" O ASN I 52 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP I 50 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 56 through 59 removed outlier: 3.590A pdb=" N GLY I 56 " --> pdb=" O ASN I 52 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP I 50 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.068A pdb=" N VAL J 10 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA J 86 " --> pdb=" O LEU J 102 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 18 through 22 Processing sheet with id=AF7, first strand: chain 'J' and resid 47 through 49 removed outlier: 4.202A pdb=" N TRP J 37 " --> pdb=" O ILE J 49 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.597A pdb=" N THR K 103 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA K 86 " --> pdb=" O LEU K 102 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 18 through 22 Processing sheet with id=AG1, first strand: chain 'K' and resid 47 through 49 removed outlier: 4.232A pdb=" N TRP K 37 " --> pdb=" O ILE K 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.101A pdb=" N VAL L 10 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA L 86 " --> pdb=" O LEU L 102 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AG4, first strand: chain 'L' and resid 47 through 49 removed outlier: 4.184A pdb=" N TRP L 37 " --> pdb=" O ILE L 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.692A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP M 72 " --> pdb=" O GLN M 77 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.693A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR M 58 " --> pdb=" O TYR M 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 97 through 100A Processing sheet with id=AG8, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.568A pdb=" N GLN N 77 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP N 72 " --> pdb=" O GLN N 77 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AH1, first strand: chain 'N' and resid 58 through 59 removed outlier: 3.964A pdb=" N THR N 58 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 97 through 100A Processing sheet with id=AH3, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.620A pdb=" N GLN O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP O 72 " --> pdb=" O GLN O 77 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.509A pdb=" N TYR O 33 " --> pdb=" O ALA O 95 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR O 58 " --> pdb=" O TYR O 50 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 97 through 100A Processing sheet with id=AH6, first strand: chain 'P' and resid 11 through 14 removed outlier: 5.625A pdb=" N LEU P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU P 107 " --> pdb=" O LEU P 11 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL P 13 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 19 through 22 Processing sheet with id=AH8, first strand: chain 'Q' and resid 12 through 14 removed outlier: 6.670A pdb=" N VAL Q 13 " --> pdb=" O LEU Q 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id=AI1, first strand: chain 'Q' and resid 44 through 48 removed outlier: 6.693A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.943A pdb=" N LEU R 11 " --> pdb=" O ARG R 103 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 19 through 22 754 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.57 Time building geometry restraints manager: 12.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7895 1.34 - 1.47: 7159 1.47 - 1.60: 11377 1.60 - 1.73: 3 1.73 - 1.86: 210 Bond restraints: 26644 Sorted by residual: bond pdb=" C1 NAG c 1 " pdb=" C2 NAG c 1 " ideal model delta sigma weight residual 1.532 1.636 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C1 NAG o 1 " pdb=" C2 NAG o 1 " ideal model delta sigma weight residual 1.532 1.635 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C1 NAG 0 1 " pdb=" C2 NAG 0 1 " ideal model delta sigma weight residual 1.532 1.632 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C1 MAN 1 7 " pdb=" O5 MAN 1 7 " ideal model delta sigma weight residual 1.399 1.486 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C1 MAN d 7 " pdb=" O5 MAN d 7 " ideal model delta sigma weight residual 1.399 1.482 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 26639 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.83: 927 106.83 - 114.09: 15706 114.09 - 121.35: 11978 121.35 - 128.60: 7328 128.60 - 135.86: 271 Bond angle restraints: 36210 Sorted by residual: angle pdb=" C ARG R 54 " pdb=" N PRO R 55 " pdb=" CA PRO R 55 " ideal model delta sigma weight residual 119.85 127.66 -7.81 1.01e+00 9.80e-01 5.98e+01 angle pdb=" C ASP C 460 " pdb=" N ASN C 461 " pdb=" CA ASN C 461 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" C ILE E 642 " pdb=" CA ILE E 642 " pdb=" CB ILE E 642 " ideal model delta sigma weight residual 111.97 105.08 6.89 1.28e+00 6.10e-01 2.90e+01 angle pdb=" C ILE Q 66B" pdb=" N ASN Q 66C" pdb=" CA ASN Q 66C" ideal model delta sigma weight residual 120.79 127.65 -6.86 1.39e+00 5.18e-01 2.43e+01 angle pdb=" N ILE A 68 " pdb=" CA ILE A 68 " pdb=" C ILE A 68 " ideal model delta sigma weight residual 110.05 104.83 5.22 1.09e+00 8.42e-01 2.29e+01 ... (remaining 36205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 15804 21.79 - 43.58: 1301 43.58 - 65.38: 311 65.38 - 87.17: 111 87.17 - 108.96: 61 Dihedral angle restraints: 17588 sinusoidal: 8582 harmonic: 9006 Sorted by residual: dihedral pdb=" CB CYS Q 23 " pdb=" SG CYS Q 23 " pdb=" SG CYS Q 88 " pdb=" CB CYS Q 88 " ideal model delta sinusoidal sigma weight residual -86.00 -3.02 -82.98 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -166.77 80.77 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 88 " pdb=" CB CYS R 88 " ideal model delta sinusoidal sigma weight residual -86.00 -5.49 -80.51 1 1.00e+01 1.00e-02 8.02e+01 ... (remaining 17585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.495: 4421 0.495 - 0.990: 5 0.990 - 1.486: 0 1.486 - 1.981: 0 1.981 - 2.476: 3 Chirality restraints: 4429 Sorted by residual: chirality pdb=" C1 BMA 0 3 " pdb=" O4 NAG 0 2 " pdb=" C2 BMA 0 3 " pdb=" O5 BMA 0 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.59e+02 chirality pdb=" C1 NAG 0 1 " pdb=" ND2 ASN C 465 " pdb=" C2 NAG 0 1 " pdb=" O5 NAG 0 1 " both_signs ideal model delta sigma weight residual False -2.40 0.08 -2.48 2.00e-01 2.50e+01 1.53e+02 chirality pdb=" C1 NAG o 1 " pdb=" ND2 ASN B 465 " pdb=" C2 NAG o 1 " pdb=" O5 NAG o 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.05 -2.35 2.00e-01 2.50e+01 1.38e+02 ... (remaining 4426 not shown) Planarity restraints: 4506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " -0.289 2.00e-02 2.50e+03 2.43e-01 7.39e+02 pdb=" C7 NAG c 2 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " 0.415 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 1 " 0.225 2.00e-02 2.50e+03 1.97e-01 4.85e+02 pdb=" C7 NAG c 1 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG c 1 " -0.011 2.00e-02 2.50e+03 pdb=" N2 NAG c 1 " -0.335 2.00e-02 2.50e+03 pdb=" O7 NAG c 1 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG o 1 " -0.203 2.00e-02 2.50e+03 1.74e-01 3.76e+02 pdb=" C7 NAG o 1 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG o 1 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG o 1 " 0.286 2.00e-02 2.50e+03 pdb=" O7 NAG o 1 " -0.158 2.00e-02 2.50e+03 ... (remaining 4503 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.71: 4 1.71 - 2.51: 185 2.51 - 3.31: 25664 3.31 - 4.10: 64273 4.10 - 4.90: 114338 Warning: very small nonbonded interaction distances. Nonbonded interactions: 204464 Sorted by model distance: nonbonded pdb=" CG1 ILE E 595 " pdb=" OE2 GLU E 647 " model vdw 0.915 3.440 nonbonded pdb=" CB ILE E 595 " pdb=" OE2 GLU E 647 " model vdw 1.293 3.470 nonbonded pdb=" CB SER B 463 " pdb=" C8 NAG o 1 " model vdw 1.482 3.860 nonbonded pdb=" CD1 ILE E 595 " pdb=" OE1 GLU E 647 " model vdw 1.572 3.460 nonbonded pdb=" CG1 ILE E 595 " pdb=" CD GLU E 647 " model vdw 1.716 3.670 ... (remaining 204459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain 'S' selection = chain 'V' selection = chain 'c' selection = chain 'e' selection = chain 'h' selection = chain 'o' selection = chain 'q' selection = chain 't' } ncs_group { reference = (chain '1' and (resid 2 or resid 5 through 9)) selection = (chain 'd' and (resid 2 or resid 5 through 9)) selection = (chain 'p' and (resid 1 or resid 4 through 8)) } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'f' selection = chain 'g' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'r' selection = chain 's' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'W' selection = chain 'i' selection = chain 'u' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 11.800 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 71.150 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.610 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 26644 Z= 0.436 Angle : 1.075 11.301 36210 Z= 0.546 Chirality : 0.096 2.476 4429 Planarity : 0.010 0.243 4446 Dihedral : 18.240 108.960 11669 Min Nonbonded Distance : 0.915 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 7.30 % Allowed : 17.70 % Favored : 75.01 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.27 % 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: -4.58 (0.12), residues: 3078 helix: -3.58 (0.15), residues: 411 sheet: -2.53 (0.15), residues: 855 loop : -3.29 (0.11), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 50 HIS 0.007 0.001 HIS H 35 PHE 0.019 0.002 PHE A 53 TYR 0.019 0.002 TYR L 51 ARG 0.004 0.000 ARG I 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 431 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7351 (tm-30) REVERT: B 114 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7270 (tm-30) REVERT: B 169 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8625 (mt0) REVERT: B 192 MET cc_start: 0.8202 (ptt) cc_final: 0.7995 (ptt) REVERT: C 169 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7874 (mt0) REVERT: D 651 ASN cc_start: 0.4831 (OUTLIER) cc_final: 0.4532 (t0) REVERT: D 655 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7558 (mptt) REVERT: E 650 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7240 (mm110) REVERT: E 655 LYS cc_start: 0.7893 (mmtp) cc_final: 0.7682 (mmtp) REVERT: H 18 VAL cc_start: 0.7875 (OUTLIER) cc_final: 0.7608 (p) REVERT: I 18 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7504 (p) REVERT: M 100 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8345 (m) outliers start: 195 outliers final: 119 residues processed: 600 average time/residue: 0.3997 time to fit residues: 368.5472 Evaluate side-chains 449 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 323 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 169 GLN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 PHE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 54 ASN Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 107 THR Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 9.9990 chunk 229 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 0.1980 chunk 237 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 275 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 105 HIS A 130 GLN A 258 GLN A 408 ASN B 105 HIS B 130 GLN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN C 67 ASN C 80 ASN C 105 HIS C 130 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN D 651 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN G 43 GLN H 43 GLN H 82AASN I 43 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82AASN J 16 GLN J 41 HIS K 16 GLN K 41 HIS L 16 GLN L 41 HIS L 54 ASN M 39 GLN N 30 ASN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 GLN O 39 GLN Q 51 ASN Q 66CASN R 50 ASN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26644 Z= 0.195 Angle : 0.707 15.499 36210 Z= 0.325 Chirality : 0.050 0.349 4429 Planarity : 0.005 0.054 4446 Dihedral : 13.950 84.667 6313 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.31 % Allowed : 20.31 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -3.77 (0.13), residues: 3078 helix: -1.89 (0.21), residues: 429 sheet: -2.07 (0.17), residues: 822 loop : -2.99 (0.12), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 623 HIS 0.004 0.001 HIS C 72 PHE 0.010 0.001 PHE A 159 TYR 0.015 0.001 TYR K 51 ARG 0.006 0.000 ARG G 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 346 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7432 (tm-30) REVERT: B 114 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7402 (tm-30) REVERT: B 169 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8460 (mt0) REVERT: C 80 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.6801 (p0) REVERT: C 492 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6973 (mm-30) REVERT: E 643 TYR cc_start: 0.7839 (m-10) cc_final: 0.7417 (m-10) REVERT: J 94 GLU cc_start: 0.8561 (pm20) cc_final: 0.8148 (pm20) REVERT: R 54 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.7551 (ptp-170) outliers start: 142 outliers final: 95 residues processed: 459 average time/residue: 0.3856 time to fit residues: 275.8491 Evaluate side-chains 406 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 309 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 229 optimal weight: 1.9990 chunk 187 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 275 optimal weight: 6.9990 chunk 297 optimal weight: 0.7980 chunk 245 optimal weight: 1.9990 chunk 273 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS K 41 HIS L 41 HIS ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN Q 66CASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26644 Z= 0.234 Angle : 0.692 15.807 36210 Z= 0.318 Chirality : 0.049 0.385 4429 Planarity : 0.004 0.047 4446 Dihedral : 11.885 87.449 6228 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 6.06 % Allowed : 20.73 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -3.31 (0.13), residues: 3078 helix: -1.03 (0.24), residues: 429 sheet: -1.89 (0.17), residues: 834 loop : -2.75 (0.12), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 35 HIS 0.005 0.001 HIS C 72 PHE 0.009 0.001 PHE C 53 TYR 0.022 0.001 TYR M 50 ARG 0.004 0.000 ARG R 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 313 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7354 (tt0) REVERT: A 341 MET cc_start: 0.8614 (tmm) cc_final: 0.8354 (tmm) REVERT: A 398 MET cc_start: 0.6426 (ppp) cc_final: 0.5222 (ptm) REVERT: A 452 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8724 (mt) REVERT: B 114 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7369 (tm-30) REVERT: B 452 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8469 (mt) REVERT: C 229 ARG cc_start: 0.7581 (mtp85) cc_final: 0.7015 (mtt180) REVERT: E 643 TYR cc_start: 0.7989 (m-10) cc_final: 0.7692 (m-10) REVERT: I 71 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8519 (pmt-80) REVERT: N 34 TRP cc_start: 0.7250 (m100) cc_final: 0.6986 (m100) REVERT: N 100 MET cc_start: 0.7476 (mpp) cc_final: 0.6954 (mtm) REVERT: O 100 MET cc_start: 0.7388 (mpp) cc_final: 0.7069 (mtm) REVERT: P 47 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8082 (mt) REVERT: R 54 ARG cc_start: 0.7813 (ptp-170) cc_final: 0.7538 (ptp-170) outliers start: 162 outliers final: 114 residues processed: 445 average time/residue: 0.3732 time to fit residues: 260.5189 Evaluate side-chains 418 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 300 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 65 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 276 optimal weight: 0.9980 chunk 292 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 262 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 ASN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 26644 Z= 0.409 Angle : 0.793 15.876 36210 Z= 0.370 Chirality : 0.052 0.394 4429 Planarity : 0.005 0.059 4446 Dihedral : 10.838 80.735 6217 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 7.30 % Allowed : 20.69 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -3.19 (0.13), residues: 3078 helix: -0.95 (0.24), residues: 429 sheet: -1.81 (0.17), residues: 828 loop : -2.67 (0.12), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 35 HIS 0.004 0.001 HIS B 173 PHE 0.017 0.002 PHE B 361 TYR 0.024 0.002 TYR M 50 ARG 0.005 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 337 time to evaluate : 2.699 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: A 114 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7526 (tt0) REVERT: A 135 LYS cc_start: 0.7930 (tppt) cc_final: 0.7429 (tmtt) REVERT: A 169 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: A 184 ILE cc_start: 0.8703 (tt) cc_final: 0.8405 (tt) REVERT: A 398 MET cc_start: 0.6702 (ppp) cc_final: 0.5838 (ptt) REVERT: A 452 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8688 (mt) REVERT: A 492 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6865 (mm-30) REVERT: B 114 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7509 (tm-30) REVERT: B 135 LYS cc_start: 0.7910 (tppt) cc_final: 0.7422 (tmtt) REVERT: B 169 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8604 (mt0) REVERT: B 398 MET cc_start: 0.6396 (ppp) cc_final: 0.5508 (ptt) REVERT: B 452 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8487 (mt) REVERT: C 135 LYS cc_start: 0.7809 (tppt) cc_final: 0.7380 (tmtt) REVERT: C 169 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8407 (mt0) REVERT: E 643 TYR cc_start: 0.8144 (m-10) cc_final: 0.7942 (m-10) REVERT: F 633 LYS cc_start: 0.7552 (mmtm) cc_final: 0.7336 (mmtp) REVERT: F 646 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7857 (tp) REVERT: H 71 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7359 (pmt-80) REVERT: I 71 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8366 (pmt-80) REVERT: N 100 MET cc_start: 0.7620 (mpp) cc_final: 0.7200 (mtm) REVERT: O 100 MET cc_start: 0.7521 (mpp) cc_final: 0.7092 (mtm) REVERT: P 47 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8231 (mt) REVERT: R 54 ARG cc_start: 0.7843 (ptp-170) cc_final: 0.7511 (ptp-170) outliers start: 195 outliers final: 141 residues processed: 491 average time/residue: 0.3885 time to fit residues: 296.2255 Evaluate side-chains 460 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 310 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 169 GLN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 23 THR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 249 optimal weight: 6.9990 chunk 202 optimal weight: 0.0270 chunk 0 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 262 optimal weight: 20.0000 chunk 73 optimal weight: 0.6980 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN P 34 GLN R 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26644 Z= 0.223 Angle : 0.696 15.683 36210 Z= 0.318 Chirality : 0.049 0.389 4429 Planarity : 0.004 0.051 4446 Dihedral : 9.885 76.902 6212 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 5.61 % Allowed : 22.41 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.96 (0.14), residues: 3078 helix: -0.66 (0.25), residues: 429 sheet: -1.71 (0.17), residues: 828 loop : -2.51 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 35 HIS 0.004 0.001 HIS C 374 PHE 0.023 0.001 PHE F 522 TYR 0.024 0.001 TYR M 50 ARG 0.005 0.000 ARG A 321B *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 332 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7490 (tt0) REVERT: A 135 LYS cc_start: 0.7946 (tppt) cc_final: 0.7466 (tmtt) REVERT: A 321 ARG cc_start: 0.7122 (ttt-90) cc_final: 0.6715 (ttm-80) REVERT: A 398 MET cc_start: 0.6706 (ppp) cc_final: 0.5883 (ptt) REVERT: A 452 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8677 (mt) REVERT: B 114 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7373 (tt0) REVERT: B 135 LYS cc_start: 0.7922 (tppt) cc_final: 0.7451 (tmtt) REVERT: B 398 MET cc_start: 0.6376 (ppp) cc_final: 0.5556 (ptt) REVERT: B 452 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8433 (mt) REVERT: C 229 ARG cc_start: 0.7520 (mtp85) cc_final: 0.6935 (mtt180) REVERT: D 540 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7616 (mp-120) REVERT: G 71 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8105 (pmt-80) REVERT: L 64 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.5867 (p90) REVERT: N 100 MET cc_start: 0.7678 (mpp) cc_final: 0.7188 (mtm) REVERT: N 105 LYS cc_start: 0.5736 (OUTLIER) cc_final: 0.5360 (mtmm) REVERT: O 100 MET cc_start: 0.7455 (mpp) cc_final: 0.7006 (mtm) REVERT: R 54 ARG cc_start: 0.7818 (ptp-170) cc_final: 0.7449 (ptp-170) outliers start: 150 outliers final: 113 residues processed: 452 average time/residue: 0.3899 time to fit residues: 274.4364 Evaluate side-chains 433 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 314 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 6.9990 chunk 263 optimal weight: 20.0000 chunk 57 optimal weight: 0.5980 chunk 171 optimal weight: 5.9990 chunk 72 optimal weight: 0.3980 chunk 293 optimal weight: 20.0000 chunk 243 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 0.0060 chunk 153 optimal weight: 6.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 61 GLN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN M 39 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26644 Z= 0.262 Angle : 0.699 15.746 36210 Z= 0.321 Chirality : 0.049 0.357 4429 Planarity : 0.004 0.051 4446 Dihedral : 9.444 78.232 6207 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 6.36 % Allowed : 22.52 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.84 (0.14), residues: 3078 helix: -0.58 (0.25), residues: 429 sheet: -1.63 (0.17), residues: 828 loop : -2.42 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 35 HIS 0.004 0.001 HIS C 72 PHE 0.023 0.001 PHE R 62 TYR 0.021 0.001 TYR M 50 ARG 0.008 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 320 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7506 (tt0) REVERT: A 135 LYS cc_start: 0.7951 (tppt) cc_final: 0.7458 (tmtt) REVERT: A 184 ILE cc_start: 0.8675 (tt) cc_final: 0.8388 (tt) REVERT: A 398 MET cc_start: 0.6729 (ppp) cc_final: 0.5929 (ptt) REVERT: A 452 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8664 (mt) REVERT: A 492 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6592 (mm-30) REVERT: B 114 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7397 (tt0) REVERT: B 135 LYS cc_start: 0.7941 (tppt) cc_final: 0.7458 (tmtt) REVERT: B 398 MET cc_start: 0.6404 (ppp) cc_final: 0.5595 (ptt) REVERT: B 452 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8423 (mt) REVERT: C 135 LYS cc_start: 0.7819 (tppt) cc_final: 0.7406 (tmtt) REVERT: C 229 ARG cc_start: 0.7544 (mtp85) cc_final: 0.6958 (mtt180) REVERT: D 540 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7630 (mp-120) REVERT: E 655 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7637 (mmtm) REVERT: G 71 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8184 (pmt-80) REVERT: H 71 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7034 (pmt-80) REVERT: L 64 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.5782 (p90) REVERT: N 100 MET cc_start: 0.7597 (mpp) cc_final: 0.7075 (mtm) REVERT: N 105 LYS cc_start: 0.5777 (OUTLIER) cc_final: 0.5402 (mtmm) REVERT: R 54 ARG cc_start: 0.7774 (ptp-170) cc_final: 0.7420 (ptp-170) outliers start: 170 outliers final: 137 residues processed: 458 average time/residue: 0.3908 time to fit residues: 280.0601 Evaluate side-chains 456 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 312 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 23 THR Chi-restraints excluded: chain K residue 54 ASN Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 94 ARG Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 94 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 246 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 292 optimal weight: 0.0040 chunk 182 optimal weight: 0.9980 chunk 178 optimal weight: 0.0270 chunk 134 optimal weight: 4.9990 overall best weight: 0.4652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 650 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26644 Z= 0.157 Angle : 0.655 15.740 36210 Z= 0.297 Chirality : 0.048 0.320 4429 Planarity : 0.004 0.047 4446 Dihedral : 8.761 77.421 6204 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.31 % Allowed : 23.79 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.63 (0.14), residues: 3078 helix: -0.45 (0.26), residues: 435 sheet: -1.52 (0.17), residues: 798 loop : -2.25 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 34 HIS 0.004 0.001 HIS C 72 PHE 0.020 0.001 PHE Q 62 TYR 0.026 0.001 TYR M 50 ARG 0.006 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 303 time to evaluate : 2.907 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: A 114 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7444 (tt0) REVERT: A 169 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7903 (mt0) REVERT: A 184 ILE cc_start: 0.8608 (tt) cc_final: 0.8336 (tt) REVERT: A 398 MET cc_start: 0.6559 (ppp) cc_final: 0.5787 (ptt) REVERT: B 114 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7371 (tt0) REVERT: B 398 MET cc_start: 0.6326 (ppp) cc_final: 0.5526 (ptt) REVERT: C 229 ARG cc_start: 0.7527 (mtp85) cc_final: 0.6982 (mtt180) REVERT: H 108 MET cc_start: 0.7788 (tmm) cc_final: 0.7570 (tmm) REVERT: K 64 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.6482 (p90) REVERT: N 105 LYS cc_start: 0.5667 (OUTLIER) cc_final: 0.5256 (mtmm) REVERT: O 100 MET cc_start: 0.7561 (mpp) cc_final: 0.6942 (mtm) REVERT: R 54 ARG cc_start: 0.7753 (ptp-170) cc_final: 0.7371 (ptp-170) outliers start: 142 outliers final: 111 residues processed: 421 average time/residue: 0.3807 time to fit residues: 250.3160 Evaluate side-chains 409 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 295 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 94 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 174 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 144 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 229 optimal weight: 0.0030 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26644 Z= 0.146 Angle : 0.643 15.791 36210 Z= 0.291 Chirality : 0.047 0.447 4429 Planarity : 0.003 0.042 4446 Dihedral : 8.383 78.610 6200 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.60 % Allowed : 24.35 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.44 (0.14), residues: 3078 helix: -0.31 (0.26), residues: 435 sheet: -1.35 (0.18), residues: 798 loop : -2.15 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 35 HIS 0.005 0.001 HIS C 72 PHE 0.019 0.001 PHE R 62 TYR 0.024 0.001 TYR M 50 ARG 0.008 0.000 ARG R 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 308 time to evaluate : 2.600 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: A 114 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7418 (tt0) REVERT: A 169 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: A 398 MET cc_start: 0.6452 (ppp) cc_final: 0.5645 (ptt) REVERT: A 452 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8595 (mt) REVERT: B 114 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7424 (tt0) REVERT: B 398 MET cc_start: 0.6294 (ppp) cc_final: 0.5326 (ptm) REVERT: C 114 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7286 (tt0) REVERT: C 229 ARG cc_start: 0.7505 (mtp85) cc_final: 0.6964 (mtt180) REVERT: E 655 LYS cc_start: 0.8196 (mmtp) cc_final: 0.7756 (mmtm) REVERT: J 77 ILE cc_start: 0.6587 (OUTLIER) cc_final: 0.6329 (tp) REVERT: K 64 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.6692 (p90) REVERT: N 100 MET cc_start: 0.7740 (mpp) cc_final: 0.7123 (mtm) REVERT: N 105 LYS cc_start: 0.5556 (OUTLIER) cc_final: 0.5138 (mtmm) REVERT: R 54 ARG cc_start: 0.7759 (ptp-170) cc_final: 0.7367 (ptp-170) outliers start: 123 outliers final: 100 residues processed: 413 average time/residue: 0.3684 time to fit residues: 238.7283 Evaluate side-chains 398 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 293 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 54 ASN Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 5.9990 chunk 279 optimal weight: 9.9990 chunk 255 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 163 optimal weight: 0.0050 chunk 118 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 257 optimal weight: 0.5980 chunk 271 optimal weight: 1.9990 overall best weight: 2.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN A 374 HIS B 195 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 HIS M 39 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 26644 Z= 0.432 Angle : 0.792 15.435 36210 Z= 0.369 Chirality : 0.052 0.403 4429 Planarity : 0.005 0.076 4446 Dihedral : 8.840 81.661 6190 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 5.50 % Allowed : 23.34 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.63 (0.14), residues: 3078 helix: -0.53 (0.25), residues: 429 sheet: -1.47 (0.17), residues: 804 loop : -2.26 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 338 HIS 0.005 0.001 HIS C 173 PHE 0.022 0.002 PHE F 522 TYR 0.020 0.002 TYR M 50 ARG 0.013 0.001 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 294 time to evaluate : 2.987 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: A 114 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7598 (tt0) REVERT: A 135 LYS cc_start: 0.7982 (tppt) cc_final: 0.7454 (tmtt) REVERT: A 169 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: A 184 ILE cc_start: 0.8746 (tt) cc_final: 0.8465 (tt) REVERT: A 398 MET cc_start: 0.6569 (ppp) cc_final: 0.5780 (ptt) REVERT: A 452 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8649 (mt) REVERT: B 114 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7462 (tt0) REVERT: B 135 LYS cc_start: 0.8050 (tppt) cc_final: 0.7526 (tmtt) REVERT: B 398 MET cc_start: 0.6500 (ppp) cc_final: 0.5604 (ptt) REVERT: C 135 LYS cc_start: 0.7909 (tppt) cc_final: 0.7450 (tmtt) REVERT: C 352 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8765 (mp) REVERT: G 71 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8185 (pmt-80) REVERT: H 71 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.6622 (pmt-80) REVERT: N 100 MET cc_start: 0.7809 (mpp) cc_final: 0.7346 (mtm) REVERT: N 105 LYS cc_start: 0.5794 (OUTLIER) cc_final: 0.5347 (mtmm) REVERT: O 100 MET cc_start: 0.7689 (mpp) cc_final: 0.7078 (mtm) REVERT: R 54 ARG cc_start: 0.7749 (ptp-170) cc_final: 0.7300 (ptp-170) outliers start: 147 outliers final: 124 residues processed: 422 average time/residue: 0.3825 time to fit residues: 252.5266 Evaluate side-chains 418 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 288 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 301 optimal weight: 1.9990 chunk 277 optimal weight: 0.9980 chunk 240 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN L 41 HIS ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26644 Z= 0.202 Angle : 0.686 15.354 36210 Z= 0.314 Chirality : 0.049 0.345 4429 Planarity : 0.004 0.047 4446 Dihedral : 8.414 78.745 6188 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.38 % Allowed : 24.39 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.48 (0.14), residues: 3078 helix: -0.31 (0.26), residues: 429 sheet: -1.39 (0.18), residues: 792 loop : -2.17 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 34 HIS 0.004 0.001 HIS B 374 PHE 0.018 0.001 PHE R 62 TYR 0.022 0.001 TYR M 50 ARG 0.008 0.000 ARG N 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 299 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7503 (tt0) REVERT: A 135 LYS cc_start: 0.7979 (tppt) cc_final: 0.7456 (tmtt) REVERT: A 169 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: A 184 ILE cc_start: 0.8675 (tt) cc_final: 0.8420 (tt) REVERT: A 398 MET cc_start: 0.6501 (ppp) cc_final: 0.5750 (ptt) REVERT: B 114 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7376 (tt0) REVERT: B 135 LYS cc_start: 0.7994 (tppt) cc_final: 0.7479 (tmtt) REVERT: B 398 MET cc_start: 0.6406 (ppp) cc_final: 0.5545 (ptt) REVERT: I 76 ASP cc_start: 0.8094 (m-30) cc_final: 0.7875 (m-30) REVERT: L 102 LEU cc_start: 0.6143 (tp) cc_final: 0.5835 (tp) REVERT: M 54 ARG cc_start: 0.7087 (mmm160) cc_final: 0.6779 (mmm-85) REVERT: N 100 MET cc_start: 0.7816 (mpp) cc_final: 0.7237 (mtm) REVERT: N 105 LYS cc_start: 0.5689 (OUTLIER) cc_final: 0.5239 (mtmm) REVERT: O 100 MET cc_start: 0.7740 (mpp) cc_final: 0.7084 (mtm) REVERT: R 54 ARG cc_start: 0.7717 (ptp-170) cc_final: 0.7313 (ptp-170) outliers start: 117 outliers final: 108 residues processed: 397 average time/residue: 0.3786 time to fit residues: 235.4053 Evaluate side-chains 407 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 297 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 101 ASP Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 0.0980 chunk 256 optimal weight: 30.0000 chunk 73 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 240 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.160448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.134897 restraints weight = 35942.832| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.88 r_work: 0.3292 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26644 Z= 0.185 Angle : 0.669 15.350 36210 Z= 0.305 Chirality : 0.048 0.330 4429 Planarity : 0.004 0.043 4446 Dihedral : 8.154 79.494 6188 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.45 % Allowed : 24.43 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.37 (0.14), residues: 3078 helix: -0.28 (0.26), residues: 435 sheet: -1.33 (0.18), residues: 798 loop : -2.07 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 96 HIS 0.004 0.001 HIS C 72 PHE 0.018 0.001 PHE R 62 TYR 0.023 0.001 TYR M 50 ARG 0.009 0.000 ARG N 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6082.21 seconds wall clock time: 114 minutes 22.13 seconds (6862.13 seconds total)