Starting phenix.real_space_refine on Wed Feb 21 04:28:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8s_22729/02_2024/7k8s_22729_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8s_22729/02_2024/7k8s_22729.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/7k8s_22729/02_2024/7k8s_22729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8s_22729/02_2024/7k8s_22729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8s_22729/02_2024/7k8s_22729_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8s_22729/02_2024/7k8s_22729_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 123 5.16 5 C 18837 2.51 5 N 4875 2.21 5 O 5814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 820": "OD1" <-> "OD2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 808": "OD1" <-> "OD2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 72": "OD1" <-> "OD2" Residue "M ARG 83": "NH1" <-> "NH2" Residue "M PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 70": "OD1" <-> "OD2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 83": "NH1" <-> "NH2" Residue "P ASP 17": "OD1" <-> "OD2" Residue "P ASP 70": "OD1" <-> "OD2" Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29649 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7845 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 7 Chain: "B" Number of atoms: 7845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7845 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 7 Chain: "C" Number of atoms: 7845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7845 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 7 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "O" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "P" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.47, per 1000 atoms: 0.49 Number of scatterers: 29649 At special positions: 0 Unit cell: (137.104, 139.612, 205.656, 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 123 16.00 O 5814 8.00 N 4875 7.00 C 18837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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=2.04 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 234 " " NAG K 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 12.38 Conformation dependent library (CDL) restraints added in 5.3 seconds 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 56 sheets defined 22.5% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.791A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.909A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.581A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.582A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.546A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.575A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.677A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.379A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.602A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.596A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.742A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.801A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.808A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.979A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.516A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.893A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.556A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.145A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.598A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.508A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.502A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.377A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.629A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.600A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.805A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.095A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 3.793A pdb=" N VAL B1128 " --> pdb=" O ASN B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.113A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.895A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.939A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.771A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.976A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.361A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.774A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.506A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.595A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.574A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.542A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.627A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.560A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.795A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.055A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 4.289A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.047A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.933A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.887A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.164A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 4.379A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.101A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.333A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.681A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.936A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.757A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.861A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.227A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.227A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.027A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.868A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.951A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.164A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.666A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.639A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.664A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 448 through 452 removed outlier: 5.795A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.328A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.624A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.021A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.651A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.725A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.518A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 52 removed outlier: 3.993A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.688A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.023A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.239A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.610A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 540 removed outlier: 4.992A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.040A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.919A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.647A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.253A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.609A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.857A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.577A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.809A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.682A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) 1155 hydrogen bonds defined for protein. 3126 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: 13.96 Time building geometry restraints manager: 13.04 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: 9273 1.34 - 1.46: 7817 1.46 - 1.59: 13051 1.59 - 1.72: 0 1.72 - 1.85: 153 Bond restraints: 30294 Sorted by residual: bond pdb=" C ALA B 67 " pdb=" N ILE B 68 " ideal model delta sigma weight residual 1.331 1.424 -0.092 1.20e-02 6.94e+03 5.91e+01 bond pdb=" N ILE A 472 " pdb=" CA ILE A 472 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.25e-02 6.40e+03 1.54e+01 bond pdb=" N ILE C 472 " pdb=" CA ILE C 472 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" N VAL C 445 " pdb=" CA VAL C 445 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.20e+01 bond pdb=" N ILE B 68 " pdb=" CA ILE B 68 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.18e-02 7.18e+03 1.10e+01 ... (remaining 30289 not shown) Histogram of bond angle deviations from ideal: 97.19 - 104.59: 498 104.59 - 111.98: 15105 111.98 - 119.38: 9588 119.38 - 126.78: 15678 126.78 - 134.18: 324 Bond angle restraints: 41193 Sorted by residual: angle pdb=" CA GLY C 548 " pdb=" C GLY C 548 " pdb=" O GLY C 548 " ideal model delta sigma weight residual 122.23 118.28 3.95 6.90e-01 2.10e+00 3.28e+01 angle pdb=" CA GLU A 471 " pdb=" C GLU A 471 " pdb=" O GLU A 471 " ideal model delta sigma weight residual 120.82 114.96 5.86 1.05e+00 9.07e-01 3.11e+01 angle pdb=" CA GLY B 548 " pdb=" C GLY B 548 " pdb=" O GLY B 548 " ideal model delta sigma weight residual 122.37 118.34 4.03 7.30e-01 1.88e+00 3.04e+01 angle pdb=" CA GLY A 548 " pdb=" C GLY A 548 " pdb=" O GLY A 548 " ideal model delta sigma weight residual 122.37 118.42 3.95 7.30e-01 1.88e+00 2.93e+01 angle pdb=" CA LYS C 444 " pdb=" C LYS C 444 " pdb=" O LYS C 444 " ideal model delta sigma weight residual 120.82 115.39 5.43 1.05e+00 9.07e-01 2.67e+01 ... (remaining 41188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 17140 17.97 - 35.93: 1270 35.93 - 53.90: 248 53.90 - 71.87: 64 71.87 - 89.84: 28 Dihedral angle restraints: 18750 sinusoidal: 7989 harmonic: 10761 Sorted by residual: dihedral pdb=" CA ILE H 100A" pdb=" C ILE H 100A" pdb=" N VAL H 100B" pdb=" CA VAL H 100B" ideal model delta harmonic sigma weight residual 180.00 128.27 51.73 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA ILE M 100A" pdb=" C ILE M 100A" pdb=" N VAL M 100B" pdb=" CA VAL M 100B" ideal model delta harmonic sigma weight residual 180.00 131.83 48.17 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.83 -86.83 1 1.00e+01 1.00e-02 9.07e+01 ... (remaining 18747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 4723 0.126 - 0.252: 102 0.252 - 0.379: 5 0.379 - 0.505: 4 0.505 - 0.631: 2 Chirality restraints: 4836 Sorted by residual: chirality pdb=" CB VAL C 445 " pdb=" CA VAL C 445 " pdb=" CG1 VAL C 445 " pdb=" CG2 VAL C 445 " both_signs ideal model delta sigma weight residual False -2.63 -2.00 -0.63 2.00e-01 2.50e+01 9.95e+00 chirality pdb=" CB VAL A 445 " pdb=" CA VAL A 445 " pdb=" CG1 VAL A 445 " pdb=" CG2 VAL A 445 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" CA THR C 547 " pdb=" N THR C 547 " pdb=" C THR C 547 " pdb=" CB THR C 547 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 6.01e+00 ... (remaining 4833 not shown) Planarity restraints: 5286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " -0.009 2.00e-02 2.50e+03 5.17e-02 3.34e+01 pdb=" CG ASN B 234 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 478 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO C 479 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO C 479 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 479 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 442 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C ASP B 442 " 0.062 2.00e-02 2.50e+03 pdb=" O ASP B 442 " -0.024 2.00e-02 2.50e+03 pdb=" N SER B 443 " -0.020 2.00e-02 2.50e+03 ... (remaining 5283 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 188 2.45 - 3.06: 21498 3.06 - 3.68: 44042 3.68 - 4.29: 65411 4.29 - 4.90: 107136 Nonbonded interactions: 238275 Sorted by model distance: nonbonded pdb=" CB HIS C 66 " pdb=" CE2 PHE C 79 " model vdw 1.841 3.740 nonbonded pdb=" NE2 GLN B 804 " pdb=" OE1 GLN B 935 " model vdw 1.970 2.520 nonbonded pdb=" OD1 ASP C 389 " pdb=" NZ LYS C 528 " model vdw 2.010 2.520 nonbonded pdb=" OE1 GLU A 406 " pdb=" NE2 GLN A 409 " model vdw 2.013 2.520 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.022 2.440 ... (remaining 238270 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 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } 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: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.170 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 78.930 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 30294 Z= 0.564 Angle : 0.898 9.658 41193 Z= 0.512 Chirality : 0.056 0.631 4836 Planarity : 0.005 0.109 5244 Dihedral : 13.330 89.836 11721 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.69 % Favored : 93.01 % Rotamer: Outliers : 0.34 % Allowed : 0.68 % Favored : 98.97 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 3648 helix: 0.14 (0.19), residues: 665 sheet: -0.50 (0.16), residues: 903 loop : -1.46 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 64 HIS 0.009 0.001 HIS C 66 PHE 0.043 0.003 PHE A 906 TYR 0.029 0.002 TYR C 904 ARG 0.015 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 349 time to evaluate : 3.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8973 (p90) cc_final: 0.8662 (p90) REVERT: A 895 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7247 (pp30) REVERT: B 197 ILE cc_start: 0.9092 (tp) cc_final: 0.8890 (tp) REVERT: B 198 ASP cc_start: 0.8210 (p0) cc_final: 0.7878 (p0) REVERT: B 342 PHE cc_start: 0.8871 (m-80) cc_final: 0.8431 (m-80) REVERT: B 740 MET cc_start: 0.8372 (tpp) cc_final: 0.8083 (tpp) REVERT: B 1092 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7989 (mm-30) REVERT: C 242 LEU cc_start: 0.8723 (mm) cc_final: 0.8419 (mm) REVERT: C 406 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8944 (mp0) REVERT: C 529 LYS cc_start: 0.8929 (pptt) cc_final: 0.8587 (mmmt) REVERT: C 1072 GLU cc_start: 0.9095 (pm20) cc_final: 0.8756 (pm20) REVERT: C 1094 VAL cc_start: 0.8986 (t) cc_final: 0.8764 (m) REVERT: H 36 TRP cc_start: 0.7203 (m100) cc_final: 0.6896 (m100) REVERT: L 3 GLN cc_start: 0.8963 (mm110) cc_final: 0.8388 (mp10) REVERT: L 35 TRP cc_start: 0.9052 (m100) cc_final: 0.8497 (m100) REVERT: L 75 ILE cc_start: 0.8862 (mm) cc_final: 0.8113 (tp) REVERT: L 82 ASP cc_start: 0.7819 (m-30) cc_final: 0.7437 (m-30) REVERT: L 85 THR cc_start: 0.8823 (m) cc_final: 0.8549 (t) REVERT: L 96 ARG cc_start: 0.6090 (ptp-110) cc_final: 0.5811 (mmt90) REVERT: L 103 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8617 (mtmm) REVERT: M 67 PHE cc_start: 0.8806 (m-10) cc_final: 0.8372 (m-10) REVERT: M 79 TYR cc_start: 0.7995 (m-80) cc_final: 0.7461 (m-80) REVERT: N 62 PHE cc_start: 0.8941 (m-80) cc_final: 0.8726 (m-80) REVERT: O 80 LEU cc_start: 0.4348 (tp) cc_final: 0.4139 (tp) REVERT: O 82 MET cc_start: 0.5950 (mpp) cc_final: 0.4949 (mpp) REVERT: O 100 PHE cc_start: 0.5527 (m-10) cc_final: 0.5228 (m-80) REVERT: P 35 TRP cc_start: 0.1662 (m100) cc_final: 0.1383 (m100) REVERT: P 97 THR cc_start: 0.5068 (m) cc_final: 0.4785 (p) outliers start: 11 outliers final: 1 residues processed: 359 average time/residue: 0.4369 time to fit residues: 242.8742 Evaluate side-chains 211 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 895 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 20.0000 chunk 277 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 286 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 332 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 498 GLN A 751 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN A1064 HIS A1106 GLN B 69 HIS ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 955 ASN C1005 GLN H 76 ASN M 39 GLN N 37 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30294 Z= 0.234 Angle : 0.686 8.775 41193 Z= 0.364 Chirality : 0.047 0.229 4836 Planarity : 0.005 0.069 5244 Dihedral : 7.761 59.178 5183 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.70 % Favored : 94.19 % Rotamer: Outliers : 1.03 % Allowed : 7.08 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 3648 helix: 1.62 (0.19), residues: 629 sheet: -0.33 (0.16), residues: 928 loop : -1.34 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 103 HIS 0.007 0.001 HIS B 69 PHE 0.022 0.002 PHE A 906 TYR 0.022 0.002 TYR O 102 ARG 0.013 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 302 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8814 (t80) cc_final: 0.8612 (t80) REVERT: A 104 TRP cc_start: 0.8609 (m-90) cc_final: 0.8166 (m-90) REVERT: A 135 PHE cc_start: 0.6698 (m-80) cc_final: 0.6245 (m-80) REVERT: A 265 TYR cc_start: 0.8513 (p90) cc_final: 0.8263 (p90) REVERT: A 740 MET cc_start: 0.8411 (ttm) cc_final: 0.8198 (ttt) REVERT: A 950 ASP cc_start: 0.8944 (t70) cc_final: 0.8564 (t0) REVERT: B 101 ILE cc_start: 0.9022 (mt) cc_final: 0.8793 (tp) REVERT: B 197 ILE cc_start: 0.9291 (tp) cc_final: 0.9045 (tp) REVERT: B 342 PHE cc_start: 0.8933 (m-80) cc_final: 0.8447 (m-80) REVERT: B 568 ASP cc_start: 0.8587 (t0) cc_final: 0.8160 (t0) REVERT: B 855 PHE cc_start: 0.7038 (m-80) cc_final: 0.6713 (m-80) REVERT: B 1029 MET cc_start: 0.8975 (tpp) cc_final: 0.8365 (tpt) REVERT: C 406 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8852 (mp0) REVERT: C 529 LYS cc_start: 0.8948 (pptt) cc_final: 0.8593 (mmmt) REVERT: C 1072 GLU cc_start: 0.8895 (pm20) cc_final: 0.8674 (pm20) REVERT: H 66 ARG cc_start: 0.7934 (ptp-110) cc_final: 0.7330 (ptt180) REVERT: H 67 PHE cc_start: 0.6783 (m-10) cc_final: 0.6058 (m-80) REVERT: H 82 MET cc_start: 0.8426 (mtm) cc_final: 0.7451 (ptp) REVERT: H 94 LYS cc_start: 0.8741 (tttm) cc_final: 0.8408 (tttm) REVERT: H 100 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8380 (tt) REVERT: L 3 GLN cc_start: 0.8932 (mm110) cc_final: 0.8557 (mp10) REVERT: L 35 TRP cc_start: 0.9232 (m100) cc_final: 0.8535 (m100) REVERT: L 70 ASP cc_start: 0.9317 (p0) cc_final: 0.8911 (m-30) REVERT: L 75 ILE cc_start: 0.8778 (mm) cc_final: 0.7930 (tp) REVERT: M 67 PHE cc_start: 0.8625 (m-10) cc_final: 0.8419 (m-10) REVERT: N 73 LEU cc_start: 0.8809 (tt) cc_final: 0.8286 (mt) REVERT: N 75 ILE cc_start: 0.8054 (mp) cc_final: 0.7850 (mp) REVERT: N 103 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8261 (tppt) REVERT: O 38 ARG cc_start: 0.7095 (ptm160) cc_final: 0.6511 (ttt90) REVERT: O 80 LEU cc_start: 0.3799 (tp) cc_final: 0.3581 (tp) REVERT: O 82 MET cc_start: 0.5342 (mpp) cc_final: 0.4625 (mpp) REVERT: O 100 PHE cc_start: 0.5555 (m-10) cc_final: 0.5213 (m-80) REVERT: P 97 THR cc_start: 0.4950 (m) cc_final: 0.4714 (p) outliers start: 33 outliers final: 20 residues processed: 322 average time/residue: 0.4601 time to fit residues: 236.5881 Evaluate side-chains 260 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 239 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain P residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 226 optimal weight: 0.0470 chunk 91 optimal weight: 2.9990 chunk 332 optimal weight: 0.8980 chunk 359 optimal weight: 30.0000 chunk 296 optimal weight: 2.9990 chunk 330 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 267 optimal weight: 0.0470 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 913 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30294 Z= 0.216 Angle : 0.620 8.228 41193 Z= 0.327 Chirality : 0.045 0.202 4836 Planarity : 0.004 0.047 5244 Dihedral : 7.016 59.733 5178 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 1.74 % Allowed : 9.85 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3648 helix: 1.96 (0.20), residues: 634 sheet: -0.29 (0.16), residues: 976 loop : -1.25 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 36 HIS 0.007 0.001 HIS B 69 PHE 0.017 0.001 PHE A 400 TYR 0.024 0.001 TYR H 102 ARG 0.009 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 280 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8816 (t80) cc_final: 0.8458 (t80) REVERT: A 104 TRP cc_start: 0.8593 (m-90) cc_final: 0.8069 (m-90) REVERT: A 265 TYR cc_start: 0.8515 (p90) cc_final: 0.8258 (p90) REVERT: A 740 MET cc_start: 0.8348 (ttm) cc_final: 0.8120 (ttt) REVERT: A 950 ASP cc_start: 0.8937 (t70) cc_final: 0.8563 (t0) REVERT: B 69 HIS cc_start: 0.5933 (OUTLIER) cc_final: 0.4389 (m-70) REVERT: B 101 ILE cc_start: 0.9026 (mt) cc_final: 0.8780 (tp) REVERT: B 342 PHE cc_start: 0.8941 (m-80) cc_final: 0.8406 (m-80) REVERT: B 360 ASN cc_start: 0.9225 (t0) cc_final: 0.8978 (p0) REVERT: B 568 ASP cc_start: 0.8541 (t0) cc_final: 0.8140 (t0) REVERT: B 1017 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8668 (tm-30) REVERT: C 406 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8803 (mp0) REVERT: C 529 LYS cc_start: 0.8985 (pptt) cc_final: 0.8651 (mmmt) REVERT: C 740 MET cc_start: 0.8549 (mtt) cc_final: 0.8331 (mtt) REVERT: C 995 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8028 (mpp80) REVERT: C 1072 GLU cc_start: 0.8954 (pm20) cc_final: 0.8747 (pm20) REVERT: H 66 ARG cc_start: 0.7985 (ptp-110) cc_final: 0.7271 (ptt180) REVERT: H 67 PHE cc_start: 0.6490 (m-10) cc_final: 0.6002 (m-80) REVERT: H 82 MET cc_start: 0.8169 (mtm) cc_final: 0.6943 (ptp) REVERT: L 3 GLN cc_start: 0.8933 (mm110) cc_final: 0.8567 (mp10) REVERT: L 35 TRP cc_start: 0.9185 (m100) cc_final: 0.8387 (m100) REVERT: L 70 ASP cc_start: 0.9322 (p0) cc_final: 0.8933 (m-30) REVERT: L 73 LEU cc_start: 0.8781 (tp) cc_final: 0.8499 (mt) REVERT: L 75 ILE cc_start: 0.8762 (mm) cc_final: 0.7900 (tp) REVERT: M 67 PHE cc_start: 0.8721 (m-10) cc_final: 0.8501 (m-10) REVERT: N 62 PHE cc_start: 0.8512 (m-80) cc_final: 0.8168 (m-80) REVERT: N 73 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8359 (mt) REVERT: O 38 ARG cc_start: 0.7298 (ptm160) cc_final: 0.7074 (ttm-80) REVERT: O 82 MET cc_start: 0.5435 (mpp) cc_final: 0.5048 (mpp) REVERT: O 100 PHE cc_start: 0.5655 (m-10) cc_final: 0.5267 (m-80) REVERT: P 97 THR cc_start: 0.4696 (m) cc_final: 0.4479 (p) outliers start: 56 outliers final: 24 residues processed: 317 average time/residue: 0.4491 time to fit residues: 224.5366 Evaluate side-chains 266 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 0.0070 chunk 250 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 334 optimal weight: 2.9990 chunk 353 optimal weight: 6.9990 chunk 174 optimal weight: 0.0980 chunk 316 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 105 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30294 Z= 0.208 Angle : 0.599 8.314 41193 Z= 0.314 Chirality : 0.044 0.304 4836 Planarity : 0.004 0.088 5244 Dihedral : 6.558 57.335 5178 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.33 % Favored : 93.59 % Rotamer: Outliers : 1.58 % Allowed : 11.87 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3648 helix: 2.14 (0.20), residues: 632 sheet: -0.31 (0.16), residues: 998 loop : -1.16 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.011 0.001 HIS B 69 PHE 0.018 0.001 PHE B 392 TYR 0.022 0.001 TYR H 102 ARG 0.014 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 272 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8800 (t80) cc_final: 0.8388 (t80) REVERT: A 104 TRP cc_start: 0.8575 (m-90) cc_final: 0.8082 (m-90) REVERT: A 265 TYR cc_start: 0.8474 (p90) cc_final: 0.8199 (p90) REVERT: A 740 MET cc_start: 0.8347 (ttm) cc_final: 0.8128 (ttt) REVERT: A 950 ASP cc_start: 0.8917 (t70) cc_final: 0.8529 (t0) REVERT: B 101 ILE cc_start: 0.9010 (mt) cc_final: 0.8750 (tp) REVERT: B 342 PHE cc_start: 0.8957 (m-80) cc_final: 0.8414 (m-80) REVERT: B 568 ASP cc_start: 0.8573 (t0) cc_final: 0.8261 (t0) REVERT: B 661 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 786 LYS cc_start: 0.8886 (pttm) cc_final: 0.8595 (pttm) REVERT: B 1017 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8608 (tm-30) REVERT: C 212 LEU cc_start: 0.8946 (tp) cc_final: 0.8701 (tt) REVERT: C 406 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8808 (mp0) REVERT: C 529 LYS cc_start: 0.8979 (pptt) cc_final: 0.8592 (mmmt) REVERT: C 957 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8163 (tm-30) REVERT: C 995 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8020 (mpp80) REVERT: H 66 ARG cc_start: 0.8530 (ptp-110) cc_final: 0.8297 (ptt180) REVERT: H 67 PHE cc_start: 0.6451 (m-10) cc_final: 0.5964 (m-80) REVERT: H 82 MET cc_start: 0.8304 (mtm) cc_final: 0.6954 (ptp) REVERT: H 94 LYS cc_start: 0.8331 (tttm) cc_final: 0.7860 (tttp) REVERT: L 3 GLN cc_start: 0.8986 (mm110) cc_final: 0.8617 (mp10) REVERT: L 35 TRP cc_start: 0.9177 (m100) cc_final: 0.8470 (m100) REVERT: L 75 ILE cc_start: 0.8781 (mm) cc_final: 0.7958 (tp) REVERT: M 67 PHE cc_start: 0.8773 (m-10) cc_final: 0.8542 (m-10) REVERT: N 62 PHE cc_start: 0.8485 (m-80) cc_final: 0.8053 (m-80) REVERT: N 73 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8421 (mt) REVERT: O 38 ARG cc_start: 0.7445 (ptm160) cc_final: 0.6898 (ttt180) REVERT: O 100 PHE cc_start: 0.5605 (m-10) cc_final: 0.5172 (m-80) outliers start: 51 outliers final: 30 residues processed: 307 average time/residue: 0.4414 time to fit residues: 215.3785 Evaluate side-chains 276 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 244 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain P residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 263 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 301 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 317 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN N 38 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30294 Z= 0.319 Angle : 0.626 9.866 41193 Z= 0.326 Chirality : 0.045 0.281 4836 Planarity : 0.004 0.047 5244 Dihedral : 6.398 58.006 5178 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 2.49 % Allowed : 12.86 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3648 helix: 2.11 (0.20), residues: 638 sheet: -0.39 (0.16), residues: 1022 loop : -1.13 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 103 HIS 0.009 0.001 HIS B 69 PHE 0.012 0.001 PHE C 906 TYR 0.023 0.002 TYR H 102 ARG 0.007 0.001 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 246 time to evaluate : 3.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8777 (t80) cc_final: 0.8329 (t80) REVERT: A 104 TRP cc_start: 0.8611 (m-90) cc_final: 0.8131 (m-90) REVERT: A 265 TYR cc_start: 0.8550 (p90) cc_final: 0.8289 (p90) REVERT: A 370 ASN cc_start: 0.8981 (m110) cc_final: 0.8532 (m110) REVERT: A 740 MET cc_start: 0.8392 (ttm) cc_final: 0.8174 (ttt) REVERT: A 950 ASP cc_start: 0.8952 (t70) cc_final: 0.8568 (t0) REVERT: B 101 ILE cc_start: 0.9014 (mt) cc_final: 0.8756 (tp) REVERT: B 342 PHE cc_start: 0.8918 (m-80) cc_final: 0.8453 (m-80) REVERT: B 495 TYR cc_start: 0.6192 (m-10) cc_final: 0.5832 (m-80) REVERT: B 568 ASP cc_start: 0.8517 (t0) cc_final: 0.8204 (t0) REVERT: B 661 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 935 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8808 (tt0) REVERT: B 1017 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8679 (tm-30) REVERT: C 212 LEU cc_start: 0.8960 (tp) cc_final: 0.8727 (tt) REVERT: C 370 ASN cc_start: 0.8584 (m-40) cc_final: 0.8350 (m110) REVERT: C 406 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8861 (mp0) REVERT: C 493 GLN cc_start: 0.7956 (mm110) cc_final: 0.7689 (mm110) REVERT: C 957 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8162 (tm-30) REVERT: C 995 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8067 (mpp80) REVERT: H 66 ARG cc_start: 0.8595 (ptp-110) cc_final: 0.8264 (ptt180) REVERT: H 75 LYS cc_start: 0.9151 (tppt) cc_final: 0.8933 (tptp) REVERT: H 85 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: H 94 LYS cc_start: 0.8329 (tttm) cc_final: 0.7964 (tttp) REVERT: L 3 GLN cc_start: 0.8925 (mm110) cc_final: 0.8406 (mp10) REVERT: L 35 TRP cc_start: 0.9144 (m100) cc_final: 0.8302 (m100) REVERT: L 75 ILE cc_start: 0.8738 (mm) cc_final: 0.7954 (tp) REVERT: M 67 PHE cc_start: 0.8882 (m-10) cc_final: 0.8628 (m-10) REVERT: M 82 LEU cc_start: 0.9171 (tp) cc_final: 0.8844 (pp) REVERT: N 24 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8451 (ttp-110) REVERT: N 62 PHE cc_start: 0.8481 (m-80) cc_final: 0.8029 (m-80) REVERT: N 73 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8440 (mt) REVERT: O 38 ARG cc_start: 0.7362 (ptm160) cc_final: 0.7070 (ttm-80) REVERT: O 100 PHE cc_start: 0.5683 (m-10) cc_final: 0.5132 (m-80) outliers start: 80 outliers final: 48 residues processed: 307 average time/residue: 0.4267 time to fit residues: 210.0122 Evaluate side-chains 277 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 225 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 354 optimal weight: 0.0470 chunk 293 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN P 55 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 30294 Z= 0.273 Angle : 0.611 9.267 41193 Z= 0.318 Chirality : 0.045 0.316 4836 Planarity : 0.004 0.047 5244 Dihedral : 6.101 57.366 5178 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.14 % Allowed : 13.86 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3648 helix: 2.22 (0.20), residues: 637 sheet: -0.48 (0.15), residues: 1057 loop : -1.08 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 103 HIS 0.005 0.001 HIS B 69 PHE 0.028 0.001 PHE L 98 TYR 0.023 0.001 TYR H 102 ARG 0.010 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 239 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8585 (m-90) cc_final: 0.8108 (m-90) REVERT: A 265 TYR cc_start: 0.8490 (p90) cc_final: 0.8277 (p90) REVERT: A 370 ASN cc_start: 0.9078 (m110) cc_final: 0.8631 (m110) REVERT: A 740 MET cc_start: 0.8364 (ttm) cc_final: 0.8129 (ttt) REVERT: A 950 ASP cc_start: 0.8921 (t70) cc_final: 0.8538 (t0) REVERT: B 342 PHE cc_start: 0.8919 (m-80) cc_final: 0.8515 (m-80) REVERT: B 495 TYR cc_start: 0.6150 (m-10) cc_final: 0.5777 (m-80) REVERT: B 568 ASP cc_start: 0.8531 (t0) cc_final: 0.8160 (t0) REVERT: B 661 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7753 (tm-30) REVERT: C 212 LEU cc_start: 0.8987 (tp) cc_final: 0.8768 (tt) REVERT: C 369 TYR cc_start: 0.7854 (p90) cc_final: 0.7622 (p90) REVERT: C 406 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8892 (mp0) REVERT: C 957 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7985 (tm-30) REVERT: H 66 ARG cc_start: 0.8526 (ptp-110) cc_final: 0.8255 (ptt180) REVERT: H 67 PHE cc_start: 0.5450 (m-80) cc_final: 0.5169 (m-80) REVERT: H 75 LYS cc_start: 0.9165 (tppt) cc_final: 0.8913 (tptp) REVERT: H 78 LEU cc_start: 0.7687 (tp) cc_final: 0.7439 (tp) REVERT: H 79 TYR cc_start: 0.8950 (m-10) cc_final: 0.8586 (m-10) REVERT: H 94 LYS cc_start: 0.8317 (tttm) cc_final: 0.7961 (tttp) REVERT: L 3 GLN cc_start: 0.8910 (mm110) cc_final: 0.8506 (mp10) REVERT: L 35 TRP cc_start: 0.9191 (m100) cc_final: 0.8296 (m100) REVERT: L 45 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8176 (mtmm) REVERT: L 55 GLN cc_start: 0.8632 (tp40) cc_final: 0.8332 (tm-30) REVERT: L 75 ILE cc_start: 0.8772 (mm) cc_final: 0.7895 (tp) REVERT: M 67 PHE cc_start: 0.8856 (m-10) cc_final: 0.8458 (m-10) REVERT: N 62 PHE cc_start: 0.8476 (m-80) cc_final: 0.8036 (m-80) REVERT: N 73 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8428 (mt) REVERT: O 38 ARG cc_start: 0.7430 (ptm160) cc_final: 0.7130 (ttm-80) REVERT: O 100 PHE cc_start: 0.5723 (m-10) cc_final: 0.5184 (m-80) outliers start: 69 outliers final: 51 residues processed: 289 average time/residue: 0.4204 time to fit residues: 193.0089 Evaluate side-chains 279 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 227 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 258 optimal weight: 0.3980 chunk 200 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 352 optimal weight: 20.0000 chunk 220 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30294 Z= 0.314 Angle : 0.628 11.332 41193 Z= 0.325 Chirality : 0.045 0.245 4836 Planarity : 0.004 0.049 5244 Dihedral : 5.895 57.087 5178 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 2.27 % Allowed : 14.88 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3648 helix: 2.22 (0.20), residues: 635 sheet: -0.54 (0.15), residues: 1069 loop : -1.06 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 103 HIS 0.005 0.001 HIS O 35 PHE 0.021 0.001 PHE L 98 TYR 0.026 0.002 TYR B 421 ARG 0.012 0.001 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 245 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8598 (p90) cc_final: 0.8386 (p90) REVERT: A 370 ASN cc_start: 0.9071 (m110) cc_final: 0.8649 (m110) REVERT: A 740 MET cc_start: 0.8371 (ttm) cc_final: 0.8150 (ttt) REVERT: A 950 ASP cc_start: 0.8926 (t70) cc_final: 0.8533 (t0) REVERT: B 342 PHE cc_start: 0.8881 (m-80) cc_final: 0.8487 (m-80) REVERT: B 495 TYR cc_start: 0.6159 (m-10) cc_final: 0.5502 (m-80) REVERT: B 661 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7763 (tm-30) REVERT: C 212 LEU cc_start: 0.9047 (tp) cc_final: 0.8840 (tt) REVERT: C 369 TYR cc_start: 0.8030 (p90) cc_final: 0.7735 (p90) REVERT: C 370 ASN cc_start: 0.8641 (m-40) cc_final: 0.8333 (m110) REVERT: C 406 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8906 (mp0) REVERT: C 957 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7964 (tm-30) REVERT: H 66 ARG cc_start: 0.8666 (ptp-110) cc_final: 0.8442 (ptt180) REVERT: H 75 LYS cc_start: 0.9133 (tppt) cc_final: 0.8893 (tptp) REVERT: H 85 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: L 3 GLN cc_start: 0.8930 (mm110) cc_final: 0.8380 (mp10) REVERT: L 35 TRP cc_start: 0.9104 (m100) cc_final: 0.8088 (m100) REVERT: L 55 GLN cc_start: 0.8699 (tp40) cc_final: 0.8410 (tm-30) REVERT: L 75 ILE cc_start: 0.8776 (mm) cc_final: 0.8035 (tp) REVERT: M 75 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8683 (tptp) REVERT: N 62 PHE cc_start: 0.8494 (m-80) cc_final: 0.8034 (m-80) REVERT: N 73 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8469 (mt) REVERT: N 92 TYR cc_start: 0.7372 (t80) cc_final: 0.7153 (t80) REVERT: O 38 ARG cc_start: 0.7439 (ptm160) cc_final: 0.7089 (ttm-80) REVERT: O 100 PHE cc_start: 0.5755 (m-10) cc_final: 0.5256 (m-80) outliers start: 73 outliers final: 57 residues processed: 301 average time/residue: 0.4295 time to fit residues: 206.5487 Evaluate side-chains 288 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 229 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain P residue 22 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 1.9990 chunk 140 optimal weight: 40.0000 chunk 210 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 240 optimal weight: 0.5980 chunk 174 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 277 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 564 GLN L 34 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30294 Z= 0.178 Angle : 0.595 8.821 41193 Z= 0.305 Chirality : 0.044 0.228 4836 Planarity : 0.004 0.049 5244 Dihedral : 5.530 57.097 5178 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 2.17 % Allowed : 15.75 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3648 helix: 2.38 (0.20), residues: 642 sheet: -0.52 (0.16), residues: 1069 loop : -1.02 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP M 36 HIS 0.005 0.001 HIS O 35 PHE 0.028 0.001 PHE A 92 TYR 0.035 0.001 TYR B 904 ARG 0.010 0.001 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 259 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.9048 (p) REVERT: A 740 MET cc_start: 0.8321 (ttm) cc_final: 0.8100 (ttt) REVERT: A 950 ASP cc_start: 0.8866 (t70) cc_final: 0.8447 (t0) REVERT: B 342 PHE cc_start: 0.8845 (m-80) cc_final: 0.8441 (m-80) REVERT: B 495 TYR cc_start: 0.6241 (m-10) cc_final: 0.5481 (m-80) REVERT: B 568 ASP cc_start: 0.8507 (t0) cc_final: 0.8134 (t0) REVERT: B 661 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7749 (tm-30) REVERT: C 369 TYR cc_start: 0.8058 (p90) cc_final: 0.7754 (p90) REVERT: C 370 ASN cc_start: 0.8744 (m-40) cc_final: 0.8467 (m110) REVERT: C 406 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8892 (mp0) REVERT: C 957 GLN cc_start: 0.8250 (tm-30) cc_final: 0.8036 (tm-30) REVERT: C 995 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8040 (mpp80) REVERT: C 1111 GLU cc_start: 0.8780 (pt0) cc_final: 0.8578 (pt0) REVERT: H 34 MET cc_start: 0.9291 (mmm) cc_final: 0.8910 (mmm) REVERT: H 66 ARG cc_start: 0.8821 (ptp-110) cc_final: 0.8605 (ptt180) REVERT: H 75 LYS cc_start: 0.9132 (tppt) cc_final: 0.8853 (tptp) REVERT: H 79 TYR cc_start: 0.8722 (m-10) cc_final: 0.8470 (m-10) REVERT: H 83 ARG cc_start: 0.7738 (ptp90) cc_final: 0.7518 (ptp-170) REVERT: H 85 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7442 (pm20) REVERT: H 94 LYS cc_start: 0.8242 (tttm) cc_final: 0.7848 (tttp) REVERT: L 3 GLN cc_start: 0.8927 (mm110) cc_final: 0.8467 (mp10) REVERT: L 27 GLN cc_start: 0.8540 (pm20) cc_final: 0.8254 (pm20) REVERT: L 35 TRP cc_start: 0.9062 (m100) cc_final: 0.7994 (m100) REVERT: L 45 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8226 (mtmm) REVERT: L 55 GLN cc_start: 0.8685 (tp40) cc_final: 0.8449 (tm-30) REVERT: L 75 ILE cc_start: 0.8821 (mm) cc_final: 0.7967 (tp) REVERT: L 98 PHE cc_start: 0.7629 (m-80) cc_final: 0.7369 (m-80) REVERT: M 67 PHE cc_start: 0.8099 (m-10) cc_final: 0.6893 (m-80) REVERT: M 75 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8709 (tptp) REVERT: N 62 PHE cc_start: 0.8494 (m-80) cc_final: 0.8038 (m-80) REVERT: N 73 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8471 (mt) REVERT: O 38 ARG cc_start: 0.7426 (ptm160) cc_final: 0.7187 (ttm-80) REVERT: O 100 PHE cc_start: 0.5890 (m-10) cc_final: 0.5406 (m-80) outliers start: 70 outliers final: 44 residues processed: 314 average time/residue: 0.4760 time to fit residues: 243.9917 Evaluate side-chains 293 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 245 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 8.9990 chunk 337 optimal weight: 20.0000 chunk 308 optimal weight: 6.9990 chunk 328 optimal weight: 8.9990 chunk 197 optimal weight: 0.0970 chunk 143 optimal weight: 10.0000 chunk 258 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 297 optimal weight: 0.0270 chunk 310 optimal weight: 8.9990 chunk 327 optimal weight: 8.9990 overall best weight: 3.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 532 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 30294 Z= 0.459 Angle : 0.701 10.741 41193 Z= 0.362 Chirality : 0.046 0.217 4836 Planarity : 0.004 0.049 5244 Dihedral : 5.861 56.769 5178 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.24 % Favored : 92.68 % Rotamer: Outliers : 2.33 % Allowed : 16.34 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3648 helix: 2.09 (0.20), residues: 635 sheet: -0.57 (0.15), residues: 1133 loop : -1.15 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 104 HIS 0.005 0.001 HIS O 35 PHE 0.025 0.002 PHE H 67 TYR 0.031 0.002 TYR A 904 ARG 0.008 0.001 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 229 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8123 (m110) cc_final: 0.7705 (p0) REVERT: A 370 ASN cc_start: 0.9108 (m110) cc_final: 0.8693 (m110) REVERT: A 740 MET cc_start: 0.8420 (ttm) cc_final: 0.8203 (ttt) REVERT: A 950 ASP cc_start: 0.8950 (t70) cc_final: 0.8549 (t0) REVERT: B 408 ARG cc_start: 0.9113 (tmm160) cc_final: 0.8898 (ttp80) REVERT: B 495 TYR cc_start: 0.6353 (m-10) cc_final: 0.5441 (m-80) REVERT: B 661 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7861 (tm-30) REVERT: B 740 MET cc_start: 0.8553 (mmm) cc_final: 0.8310 (mmt) REVERT: C 369 TYR cc_start: 0.8076 (p90) cc_final: 0.7790 (p90) REVERT: C 370 ASN cc_start: 0.8711 (m-40) cc_final: 0.8432 (m110) REVERT: C 406 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8916 (mp0) REVERT: C 957 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8024 (tm-30) REVERT: H 66 ARG cc_start: 0.8765 (ptp-110) cc_final: 0.8541 (ptt180) REVERT: H 75 LYS cc_start: 0.9182 (tppt) cc_final: 0.8906 (tptp) REVERT: H 94 LYS cc_start: 0.8379 (tttm) cc_final: 0.8028 (tttp) REVERT: L 3 GLN cc_start: 0.8932 (mm110) cc_final: 0.8363 (mp10) REVERT: L 35 TRP cc_start: 0.9103 (m100) cc_final: 0.8040 (m100) REVERT: L 45 LYS cc_start: 0.8707 (mtmm) cc_final: 0.8284 (mtmm) REVERT: L 55 GLN cc_start: 0.8754 (tp40) cc_final: 0.8492 (tm-30) REVERT: L 75 ILE cc_start: 0.8822 (mm) cc_final: 0.7943 (tp) REVERT: L 98 PHE cc_start: 0.7760 (m-80) cc_final: 0.7522 (m-80) REVERT: M 75 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8671 (tptp) REVERT: M 99 SER cc_start: 0.8100 (m) cc_final: 0.7858 (p) REVERT: N 62 PHE cc_start: 0.8492 (m-80) cc_final: 0.8033 (m-80) REVERT: N 73 LEU cc_start: 0.8863 (tt) cc_final: 0.8541 (mt) REVERT: O 38 ARG cc_start: 0.7336 (ptm160) cc_final: 0.7069 (ttm-80) REVERT: O 100 PHE cc_start: 0.5822 (m-10) cc_final: 0.5361 (m-80) outliers start: 75 outliers final: 60 residues processed: 289 average time/residue: 0.4186 time to fit residues: 195.6853 Evaluate side-chains 286 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 226 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain P residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 2.9990 chunk 347 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 241 optimal weight: 4.9990 chunk 364 optimal weight: 50.0000 chunk 335 optimal weight: 7.9990 chunk 290 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 224 optimal weight: 0.0370 chunk 178 optimal weight: 0.8980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30294 Z= 0.179 Angle : 0.610 10.227 41193 Z= 0.313 Chirality : 0.045 0.226 4836 Planarity : 0.004 0.050 5244 Dihedral : 5.519 57.157 5178 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.24 % Rotamer: Outliers : 1.68 % Allowed : 17.05 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3648 helix: 2.39 (0.20), residues: 642 sheet: -0.49 (0.15), residues: 1110 loop : -1.12 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP O 103 HIS 0.004 0.001 HIS B1048 PHE 0.024 0.001 PHE H 67 TYR 0.029 0.001 TYR B 421 ARG 0.008 0.000 ARG B 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 247 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.9052 (p) REVERT: A 370 ASN cc_start: 0.9090 (m110) cc_final: 0.8646 (m110) REVERT: A 740 MET cc_start: 0.8350 (ttm) cc_final: 0.8128 (ttt) REVERT: A 950 ASP cc_start: 0.8856 (t70) cc_final: 0.8461 (t0) REVERT: B 342 PHE cc_start: 0.8828 (m-80) cc_final: 0.8458 (m-80) REVERT: B 408 ARG cc_start: 0.9070 (tmm160) cc_final: 0.8843 (ttp80) REVERT: B 568 ASP cc_start: 0.8602 (t0) cc_final: 0.8200 (t0) REVERT: B 661 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 369 TYR cc_start: 0.8039 (p90) cc_final: 0.7733 (p90) REVERT: C 370 ASN cc_start: 0.8763 (m-40) cc_final: 0.8498 (m110) REVERT: C 406 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8887 (mp0) REVERT: C 957 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7848 (tm-30) REVERT: H 34 MET cc_start: 0.9218 (mmm) cc_final: 0.8769 (mmm) REVERT: H 75 LYS cc_start: 0.9162 (tppt) cc_final: 0.8843 (tptp) REVERT: H 79 TYR cc_start: 0.8792 (m-10) cc_final: 0.8568 (m-10) REVERT: H 83 ARG cc_start: 0.7658 (ptp90) cc_final: 0.7353 (ptp-170) REVERT: H 94 LYS cc_start: 0.8287 (tttm) cc_final: 0.7890 (tttp) REVERT: L 3 GLN cc_start: 0.8940 (mm110) cc_final: 0.8469 (mp10) REVERT: L 27 GLN cc_start: 0.8550 (pm20) cc_final: 0.8290 (pm20) REVERT: L 35 TRP cc_start: 0.9082 (m100) cc_final: 0.8023 (m100) REVERT: L 45 LYS cc_start: 0.8730 (mtmm) cc_final: 0.8297 (mtmm) REVERT: L 55 GLN cc_start: 0.8742 (tp40) cc_final: 0.8538 (tm-30) REVERT: L 75 ILE cc_start: 0.8780 (mm) cc_final: 0.7983 (tp) REVERT: L 98 PHE cc_start: 0.7659 (m-80) cc_final: 0.7443 (m-80) REVERT: M 75 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8697 (tptp) REVERT: M 82 MET cc_start: 0.7305 (mmt) cc_final: 0.6961 (mmp) REVERT: M 82 LEU cc_start: 0.8809 (tp) cc_final: 0.8536 (pp) REVERT: N 62 PHE cc_start: 0.8539 (m-80) cc_final: 0.8084 (m-80) REVERT: N 73 LEU cc_start: 0.8845 (tt) cc_final: 0.8515 (mt) REVERT: O 38 ARG cc_start: 0.7323 (ptm160) cc_final: 0.7071 (ttm-80) REVERT: O 100 PHE cc_start: 0.5959 (m-10) cc_final: 0.5682 (m-80) outliers start: 54 outliers final: 45 residues processed: 289 average time/residue: 0.4279 time to fit residues: 197.9973 Evaluate side-chains 284 residues out of total 3219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 238 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 0.7980 chunk 309 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 267 optimal weight: 0.0980 chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 290 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 298 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.108651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.065879 restraints weight = 72402.819| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 4.16 r_work: 0.2870 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30294 Z= 0.173 Angle : 0.591 9.514 41193 Z= 0.303 Chirality : 0.044 0.254 4836 Planarity : 0.004 0.050 5244 Dihedral : 5.220 57.216 5178 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % Rotamer: Outliers : 1.52 % Allowed : 17.27 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3648 helix: 2.49 (0.20), residues: 644 sheet: -0.45 (0.15), residues: 1108 loop : -1.06 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.004 0.001 HIS O 35 PHE 0.026 0.001 PHE H 67 TYR 0.029 0.001 TYR B 421 ARG 0.009 0.000 ARG O 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6358.12 seconds wall clock time: 117 minutes 9.35 seconds (7029.35 seconds total)