Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 19:24:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugq_26496/04_2023/7ugq_26496.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugq_26496/04_2023/7ugq_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_26496/04_2023/7ugq_26496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugq_26496/04_2023/7ugq_26496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugq_26496/04_2023/7ugq_26496.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugq_26496/04_2023/7ugq_26496.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 13.40, per 1000 atoms: 0.51 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: 12.99 Conformation dependent library (CDL) restraints added in 3.9 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: 1.83 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: 9.77 Time building geometry restraints manager: 13.77 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 - 17.83: 12976 17.83 - 35.66: 1426 35.66 - 53.49: 369 53.49 - 71.33: 58 71.33 - 89.16: 21 Dihedral angle restraints: 14850 sinusoidal: 5844 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 14847 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 12.090 Check model and map are aligned: 0.440 Set scattering table: 0.250 Process input model: 69.870 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.520 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.190 ------------------------------------------------------------------------------- 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 : 15.747 89.157 8931 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 % 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 *********************** 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 : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 195 outliers final: 119 residues processed: 600 average time/residue: 0.4079 time to fit residues: 374.4426 Evaluate side-chains 439 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 320 time to evaluate : 2.818 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 119 outliers final: 1 residues processed: 119 average time/residue: 0.2310 time to fit residues: 55.8234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 0.1980 chunk 237 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 275 optimal weight: 4.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 169 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN D 652 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN E 650 GLN ** 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 K 54 ASN 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: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 26644 Z= 0.188 Angle : 0.705 15.947 36210 Z= 0.325 Chirality : 0.048 0.320 4429 Planarity : 0.005 0.053 4446 Dihedral : 4.708 24.226 3390 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 2.88 % 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: -3.75 (0.13), residues: 3078 helix: -1.82 (0.21), residues: 423 sheet: -2.06 (0.17), residues: 822 loop : -2.98 (0.12), residues: 1833 *********************** 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 429 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 352 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 39 residues processed: 411 average time/residue: 0.4111 time to fit residues: 261.3887 Evaluate side-chains 348 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 309 time to evaluate : 2.979 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2369 time to fit residues: 21.3990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 229 optimal weight: 0.0670 chunk 187 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 275 optimal weight: 10.0000 chunk 297 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN ** 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 543 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS J 54 ASN K 41 HIS L 41 HIS N 39 GLN Q 66CASN ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 26644 Z= 0.264 Angle : 0.711 15.823 36210 Z= 0.329 Chirality : 0.049 0.434 4429 Planarity : 0.004 0.043 4446 Dihedral : 4.617 27.906 3390 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 3.40 % 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: -3.28 (0.13), residues: 3078 helix: -1.03 (0.24), residues: 429 sheet: -1.88 (0.17), residues: 825 loop : -2.72 (0.12), residues: 1824 *********************** 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 407 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 316 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 48 residues processed: 387 average time/residue: 0.4229 time to fit residues: 253.5409 Evaluate side-chains 350 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 302 time to evaluate : 3.207 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.2387 time to fit residues: 25.6916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 292 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 262 optimal weight: 30.0000 chunk 78 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS A 195 ASN A 374 HIS B 374 HIS C 195 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.098 26644 Z= 0.636 Angle : 0.939 15.761 36210 Z= 0.445 Chirality : 0.057 0.411 4429 Planarity : 0.006 0.056 4446 Dihedral : 5.465 27.982 3390 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.10 % Favored : 90.81 % Rotamer Outliers : 4.90 % 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: -3.41 (0.13), residues: 3078 helix: -1.14 (0.24), residues: 411 sheet: -1.95 (0.17), residues: 852 loop : -2.79 (0.12), residues: 1815 *********************** 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 474 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 343 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 73 residues processed: 450 average time/residue: 0.4199 time to fit residues: 290.1351 Evaluate side-chains 385 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 312 time to evaluate : 2.902 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.2528 time to fit residues: 37.8616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 4 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 249 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 chunk 262 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 173 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 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** O 39 GLN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 26644 Z= 0.214 Angle : 0.728 15.097 36210 Z= 0.335 Chirality : 0.050 0.360 4429 Planarity : 0.004 0.050 4446 Dihedral : 4.957 26.615 3390 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 2.36 % 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: -3.05 (0.14), residues: 3078 helix: -0.50 (0.26), residues: 402 sheet: -1.84 (0.17), residues: 840 loop : -2.57 (0.12), residues: 1836 *********************** 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 397 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 334 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 27 residues processed: 386 average time/residue: 0.4291 time to fit residues: 252.1522 Evaluate side-chains 341 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 314 time to evaluate : 3.083 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2624 time to fit residues: 17.1999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 4.9990 chunk 263 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 293 optimal weight: 30.0000 chunk 243 optimal weight: 5.9990 chunk 135 optimal weight: 0.4980 chunk 24 optimal weight: 0.3980 chunk 96 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS A 362 ASN B 173 HIS ** 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** D 650 GLN ** E 540 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 26644 Z= 0.263 Angle : 0.724 14.822 36210 Z= 0.332 Chirality : 0.049 0.361 4429 Planarity : 0.004 0.044 4446 Dihedral : 4.773 25.125 3390 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer Outliers : 2.62 % 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: -2.87 (0.14), residues: 3078 helix: -0.38 (0.26), residues: 405 sheet: -1.72 (0.17), residues: 828 loop : -2.45 (0.13), residues: 1845 *********************** 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 394 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 324 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 42 residues processed: 375 average time/residue: 0.4138 time to fit residues: 241.4441 Evaluate side-chains 351 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 309 time to evaluate : 2.944 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2522 time to fit residues: 23.3851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 214 optimal weight: 0.9990 chunk 165 optimal weight: 0.0980 chunk 246 optimal weight: 0.0980 chunk 163 optimal weight: 0.6980 chunk 292 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- 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 173 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 39 GLN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 26644 Z= 0.174 Angle : 0.683 14.131 36210 Z= 0.312 Chirality : 0.049 0.354 4429 Planarity : 0.004 0.046 4446 Dihedral : 4.591 24.038 3390 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer Outliers : 1.57 % 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: -2.66 (0.14), residues: 3078 helix: -0.36 (0.26), residues: 420 sheet: -1.56 (0.17), residues: 825 loop : -2.29 (0.13), residues: 1833 *********************** 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 353 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 311 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 344 average time/residue: 0.4154 time to fit residues: 221.6194 Evaluate side-chains 319 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 300 time to evaluate : 2.997 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2724 time to fit residues: 13.1525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 174 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 185 optimal weight: 0.0050 chunk 198 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 229 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS B 173 HIS ** 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** ** 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** P 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 26644 Z= 0.183 Angle : 0.678 13.536 36210 Z= 0.308 Chirality : 0.048 0.361 4429 Planarity : 0.003 0.041 4446 Dihedral : 4.477 23.717 3390 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 1.35 % 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: -2.53 (0.14), residues: 3078 helix: -0.25 (0.26), residues: 420 sheet: -1.45 (0.17), residues: 825 loop : -2.22 (0.13), residues: 1833 *********************** 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 341 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 305 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 331 average time/residue: 0.4270 time to fit residues: 217.2630 Evaluate side-chains 312 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 291 time to evaluate : 3.032 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2507 time to fit residues: 13.7813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 8.9990 chunk 279 optimal weight: 20.0000 chunk 255 optimal weight: 8.9990 chunk 272 optimal weight: 0.4980 chunk 163 optimal weight: 0.0770 chunk 118 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 257 optimal weight: 0.6980 chunk 271 optimal weight: 0.8980 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 173 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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** M 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 26644 Z= 0.181 Angle : 0.677 12.839 36210 Z= 0.308 Chirality : 0.048 0.367 4429 Planarity : 0.004 0.091 4446 Dihedral : 4.445 23.293 3390 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 0.90 % 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: -2.43 (0.14), residues: 3078 helix: -0.32 (0.26), residues: 429 sheet: -1.46 (0.18), residues: 804 loop : -2.07 (0.13), residues: 1845 *********************** 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 331 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 307 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 323 average time/residue: 0.4389 time to fit residues: 216.6190 Evaluate side-chains 303 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 294 time to evaluate : 2.948 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2416 time to fit residues: 7.9542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 301 optimal weight: 8.9990 chunk 277 optimal weight: 6.9990 chunk 240 optimal weight: 40.0000 chunk 24 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS B 173 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 650 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 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** Q 26 GLN ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 26644 Z= 0.380 Angle : 0.773 12.792 36210 Z= 0.359 Chirality : 0.052 0.387 4429 Planarity : 0.004 0.070 4446 Dihedral : 4.791 25.631 3390 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer Outliers : 0.67 % 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: -2.62 (0.14), residues: 3078 helix: -0.44 (0.26), residues: 423 sheet: -1.49 (0.17), residues: 831 loop : -2.26 (0.13), residues: 1824 ********************** 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 314 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 296 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 309 average time/residue: 0.4394 time to fit residues: 208.6672 Evaluate side-chains 303 residues out of total 2697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 294 time to evaluate : 2.949 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2486 time to fit residues: 8.1110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 2.9990 chunk 256 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 240 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 247 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 173 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 650 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.158276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136530 restraints weight = 35979.013| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.93 r_work: 0.3285 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 26644 Z= 0.279 Angle : 0.728 12.216 36210 Z= 0.335 Chirality : 0.050 0.366 4429 Planarity : 0.004 0.064 4446 Dihedral : 4.735 25.095 3390 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer Outliers : 0.79 % 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: -2.57 (0.14), residues: 3078 helix: -0.36 (0.26), residues: 423 sheet: -1.47 (0.17), residues: 831 loop : -2.22 (0.13), residues: 1824 =============================================================================== Job complete usr+sys time: 5925.53 seconds wall clock time: 108 minutes 27.74 seconds (6507.74 seconds total)