Starting phenix.real_space_refine on Fri Jul 26 14:48:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/07_2024/8v89_43031_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/07_2024/8v89_43031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/07_2024/8v89_43031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/07_2024/8v89_43031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/07_2024/8v89_43031_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/07_2024/8v89_43031_trim.cif" } resolution = 2.53 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= 0.097 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 S 115 5.16 5 C 11030 2.51 5 N 2615 2.21 5 O 3105 1.98 5 H 15855 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 70": "OE1" <-> "OE2" Residue "A ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 32725 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "B" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "C" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "D" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "E" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 28.48, per 1000 atoms: 0.87 Number of scatterers: 32725 At special positions: 0 Unit cell: (98.175, 99, 164.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 115 16.00 P 5 15.00 O 3105 8.00 N 2615 7.00 C 11030 6.00 H 15855 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 67 " " NAG B 602 " - " ASN B 67 " " NAG C 602 " - " ASN C 67 " " NAG D 602 " - " ASN D 67 " " NAG E 602 " - " ASN E 67 " " NAG F 1 " - " ASN A 23 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN B 23 " " NAG I 1 " - " ASN B 110 " " NAG J 1 " - " ASN C 23 " " NAG K 1 " - " ASN C 110 " " NAG L 1 " - " ASN D 23 " " NAG M 1 " - " ASN D 110 " " NAG N 1 " - " ASN E 23 " " NAG O 1 " - " ASN E 110 " Time building additional restraints: 26.72 Conformation dependent library (CDL) restraints added in 5.9 seconds 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 45.2% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.595A pdb=" N LYS A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 214 through 227 removed outlier: 3.859A pdb=" N LEU A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.589A pdb=" N SER A 235 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 236' Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.619A pdb=" N LEU A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 409 through 467 removed outlier: 4.078A pdb=" N ALA A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'B' and resid 2 through 12 removed outlier: 3.596A pdb=" N LYS B 12 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.859A pdb=" N LEU B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.588A pdb=" N SER B 235 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY B 236 " --> pdb=" O ALA B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 236' Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.619A pdb=" N LEU B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 409 through 467 removed outlier: 4.077A pdb=" N ALA B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'C' and resid 2 through 12 removed outlier: 3.596A pdb=" N LYS C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.859A pdb=" N LEU C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.589A pdb=" N SER C 235 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY C 236 " --> pdb=" O ALA C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 236' Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.619A pdb=" N LEU C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 409 through 467 removed outlier: 4.077A pdb=" N ALA C 467 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.596A pdb=" N LYS D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 227 removed outlier: 3.860A pdb=" N LEU D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 232 through 236 removed outlier: 3.588A pdb=" N SER D 235 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY D 236 " --> pdb=" O ALA D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 232 through 236' Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.619A pdb=" N LEU D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 409 through 467 removed outlier: 4.077A pdb=" N ALA D 467 " --> pdb=" O ILE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'E' and resid 2 through 12 removed outlier: 3.595A pdb=" N LYS E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 227 removed outlier: 3.859A pdb=" N LEU E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 232 through 236 removed outlier: 3.588A pdb=" N SER E 235 " --> pdb=" O PRO E 232 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY E 236 " --> pdb=" O ALA E 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 232 through 236' Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.619A pdb=" N LEU E 254 " --> pdb=" O THR E 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 409 through 467 removed outlier: 4.078A pdb=" N ALA E 467 " --> pdb=" O ILE E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN A 52 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE A 39 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N TRP A 54 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU A 37 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN A 56 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER A 58 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER A 33 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR A 60 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N TYR A 31 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.928A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR B 60 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N TYR B 31 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.928A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN C 52 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE C 39 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N TRP C 54 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU C 37 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLN C 56 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER C 58 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER C 33 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR C 60 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N TYR C 31 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 6.928A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.164A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.164A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.928A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 6.928A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 931 hydrogen bonds defined for protein. 2733 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: 12.28 Time building geometry restraints manager: 27.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15820 1.04 - 1.24: 2110 1.24 - 1.44: 5321 1.44 - 1.64: 9709 1.64 - 1.84: 170 Bond restraints: 33130 Sorted by residual: bond pdb=" NZ LYS B 303 " pdb=" HZ3 LYS B 303 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS D 412 " pdb=" HZ2 LYS D 412 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS E 45 " pdb=" HZ3 LYS E 45 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS B 5 " pdb=" HZ3 LYS B 5 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS C 5 " pdb=" HZ1 LYS C 5 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 33125 not shown) Histogram of bond angle deviations from ideal: 97.58 - 104.89: 527 104.89 - 112.19: 37269 112.19 - 119.50: 8520 119.50 - 126.80: 12913 126.80 - 134.11: 331 Bond angle restraints: 59560 Sorted by residual: angle pdb=" N ASN D 110 " pdb=" CA ASN D 110 " pdb=" CB ASN D 110 " ideal model delta sigma weight residual 110.51 117.28 -6.77 1.61e+00 3.86e-01 1.77e+01 angle pdb=" N ASN A 110 " pdb=" CA ASN A 110 " pdb=" CB ASN A 110 " ideal model delta sigma weight residual 110.51 117.28 -6.77 1.61e+00 3.86e-01 1.77e+01 angle pdb=" N ASN C 110 " pdb=" CA ASN C 110 " pdb=" CB ASN C 110 " ideal model delta sigma weight residual 110.51 117.26 -6.75 1.61e+00 3.86e-01 1.76e+01 angle pdb=" N ASN B 110 " pdb=" CA ASN B 110 " pdb=" CB ASN B 110 " ideal model delta sigma weight residual 110.51 117.26 -6.75 1.61e+00 3.86e-01 1.76e+01 angle pdb=" N ASN E 110 " pdb=" CA ASN E 110 " pdb=" CB ASN E 110 " ideal model delta sigma weight residual 110.51 117.26 -6.75 1.61e+00 3.86e-01 1.76e+01 ... (remaining 59555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.04: 15705 25.04 - 50.08: 635 50.08 - 75.13: 150 75.13 - 100.17: 35 100.17 - 125.21: 15 Dihedral angle restraints: 16540 sinusoidal: 9345 harmonic: 7195 Sorted by residual: dihedral pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N CYS B 190 " pdb=" CA CYS B 190 " ideal model delta harmonic sigma weight residual 180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual -180.00 -154.49 -25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N CYS A 190 " pdb=" CA CYS A 190 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 16537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2529 0.101 - 0.203: 156 0.203 - 0.304: 5 0.304 - 0.405: 0 0.405 - 0.506: 5 Chirality restraints: 2695 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.51e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.42e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.40e+01 ... (remaining 2692 not shown) Planarity restraints: 4700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.316 2.00e-02 2.50e+03 2.73e-01 9.32e+02 pdb=" C7 NAG L 2 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.031 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.475 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.315 2.00e-02 2.50e+03 2.73e-01 9.32e+02 pdb=" C7 NAG F 2 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.315 2.00e-02 2.50e+03 2.73e-01 9.31e+02 pdb=" C7 NAG H 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.202 2.00e-02 2.50e+03 ... (remaining 4697 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1842 2.20 - 2.80: 65388 2.80 - 3.40: 91293 3.40 - 4.00: 125052 4.00 - 4.60: 187670 Nonbonded interactions: 471245 Sorted by model distance: nonbonded pdb=" OD2 ASP D 81 " pdb=" HD1 HIS D 104 " model vdw 1.604 1.850 nonbonded pdb=" OD2 ASP A 81 " pdb=" HD1 HIS A 104 " model vdw 1.604 1.850 nonbonded pdb=" OD2 ASP E 81 " pdb=" HD1 HIS E 104 " model vdw 1.604 1.850 nonbonded pdb=" OD2 ASP C 81 " pdb=" HD1 HIS C 104 " model vdw 1.604 1.850 nonbonded pdb=" OD2 ASP B 81 " pdb=" HD1 HIS B 104 " model vdw 1.604 1.850 ... (remaining 471240 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' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) selection = (chain 'B' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) selection = (chain 'C' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) selection = (chain 'D' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) selection = (chain 'E' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.410 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: 0.500 Extract box with map and model: 1.280 Check model and map are aligned: 0.230 Set scattering table: 0.320 Process input model: 118.810 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 17270 Z= 0.505 Angle : 0.983 6.870 23510 Z= 0.533 Chirality : 0.056 0.506 2695 Planarity : 0.014 0.273 2825 Dihedral : 15.417 125.211 7155 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.56 % Allowed : 1.68 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.16), residues: 1960 helix: -1.22 (0.15), residues: 790 sheet: -1.05 (0.21), residues: 440 loop : -0.86 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 437 HIS 0.006 0.002 HIS B 296 PHE 0.020 0.003 PHE E 186 TYR 0.017 0.004 TYR B 194 ARG 0.009 0.001 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 377 time to evaluate : 2.491 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 78 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8474 (mpt90) REVERT: B 18 GLU cc_start: 0.8062 (tt0) cc_final: 0.7857 (tt0) REVERT: B 274 PHE cc_start: 0.7351 (m-10) cc_final: 0.7067 (m-10) REVERT: C 249 LEU cc_start: 0.8504 (tp) cc_final: 0.8242 (tm) REVERT: D 160 GLN cc_start: 0.8259 (mt0) cc_final: 0.8046 (mt0) REVERT: D 186 PHE cc_start: 0.7588 (m-80) cc_final: 0.7340 (m-80) REVERT: D 238 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8739 (mtpp) REVERT: E 92 TYR cc_start: 0.8519 (m-10) cc_final: 0.8282 (m-10) REVERT: E 455 PHE cc_start: 0.7557 (t80) cc_final: 0.7146 (t80) outliers start: 10 outliers final: 1 residues processed: 387 average time/residue: 2.0730 time to fit residues: 918.5625 Evaluate side-chains 336 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 333 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain D residue 238 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 47 GLN B 160 GLN B 293 GLN C 47 GLN C 293 GLN D 26 GLN D 47 GLN D 106 ASN E 26 GLN E 47 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17270 Z= 0.218 Angle : 0.639 5.710 23510 Z= 0.334 Chirality : 0.042 0.154 2695 Planarity : 0.005 0.062 2825 Dihedral : 12.207 119.941 3387 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.90 % Allowed : 8.38 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 1960 helix: 0.93 (0.16), residues: 815 sheet: -0.40 (0.21), residues: 445 loop : -0.33 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 437 HIS 0.002 0.001 HIS B 104 PHE 0.019 0.002 PHE A 99 TYR 0.011 0.002 TYR A 117 ARG 0.008 0.001 ARG E 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 359 time to evaluate : 2.668 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: A 216 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7556 (mp) REVERT: A 417 VAL cc_start: 0.7478 (t) cc_final: 0.7277 (t) REVERT: B 216 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7530 (mp) REVERT: B 249 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7865 (tp) REVERT: B 298 ASP cc_start: 0.7861 (t0) cc_final: 0.7575 (t0) REVERT: B 450 MET cc_start: 0.5949 (mmm) cc_final: 0.5593 (mmm) REVERT: C 18 GLU cc_start: 0.8088 (tt0) cc_final: 0.7730 (tt0) REVERT: C 472 GLU cc_start: 0.7431 (tt0) cc_final: 0.7124 (tt0) REVERT: D 186 PHE cc_start: 0.7448 (m-80) cc_final: 0.7243 (m-80) REVERT: D 446 ARG cc_start: 0.7815 (tpp80) cc_final: 0.7585 (tpp80) REVERT: E 212 LEU cc_start: 0.8155 (mt) cc_final: 0.7795 (mm) REVERT: E 216 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7489 (mp) REVERT: E 455 PHE cc_start: 0.7497 (t80) cc_final: 0.7130 (t80) outliers start: 34 outliers final: 17 residues processed: 377 average time/residue: 2.0063 time to fit residues: 873.8609 Evaluate side-chains 358 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 337 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN D 47 GLN E 26 GLN E 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17270 Z= 0.298 Angle : 0.654 10.220 23510 Z= 0.340 Chirality : 0.042 0.161 2695 Planarity : 0.005 0.056 2825 Dihedral : 11.787 112.765 3383 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.29 % Allowed : 8.88 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.46 (0.18), residues: 1960 helix: 1.02 (0.16), residues: 880 sheet: -0.19 (0.22), residues: 425 loop : -0.12 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 148 HIS 0.004 0.001 HIS B 297 PHE 0.015 0.002 PHE D 99 TYR 0.014 0.002 TYR A 419 ARG 0.006 0.001 ARG E 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 335 time to evaluate : 2.583 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 67 ASN cc_start: 0.6652 (t0) cc_final: 0.6373 (m110) REVERT: A 78 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8463 (mpt90) REVERT: A 216 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7697 (mp) REVERT: A 417 VAL cc_start: 0.7488 (t) cc_final: 0.7287 (t) REVERT: B 212 LEU cc_start: 0.8143 (mt) cc_final: 0.7902 (mm) REVERT: B 450 MET cc_start: 0.5968 (mmm) cc_final: 0.5598 (mmm) REVERT: B 472 GLU cc_start: 0.7517 (tt0) cc_final: 0.7205 (tt0) REVERT: C 450 MET cc_start: 0.6993 (ptm) cc_final: 0.6783 (ptt) REVERT: C 472 GLU cc_start: 0.7490 (tt0) cc_final: 0.7102 (tt0) REVERT: D 186 PHE cc_start: 0.7443 (m-80) cc_final: 0.7226 (m-80) REVERT: D 294 TYR cc_start: 0.8623 (m-80) cc_final: 0.8279 (m-80) REVERT: D 446 ARG cc_start: 0.7845 (tpp80) cc_final: 0.7611 (tpp80) REVERT: E 212 LEU cc_start: 0.8237 (mt) cc_final: 0.7896 (mm) REVERT: E 216 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7533 (mp) REVERT: E 278 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.5449 (mpt) REVERT: E 455 PHE cc_start: 0.7535 (t80) cc_final: 0.7131 (t80) REVERT: E 472 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7287 (tt0) outliers start: 38 outliers final: 18 residues processed: 353 average time/residue: 1.9464 time to fit residues: 795.7701 Evaluate side-chains 348 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 325 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 472 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A A 158 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 GLN C 106 ASN C 158 GLN D 47 GLN D 158 GLN E 26 GLN E 47 GLN E 158 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17270 Z= 0.357 Angle : 0.672 7.141 23510 Z= 0.351 Chirality : 0.042 0.145 2695 Planarity : 0.005 0.053 2825 Dihedral : 11.126 104.680 3383 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.68 % Allowed : 9.16 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.18), residues: 1960 helix: 1.32 (0.17), residues: 850 sheet: -0.21 (0.23), residues: 435 loop : -0.08 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 148 HIS 0.004 0.001 HIS B 62 PHE 0.016 0.002 PHE C 470 TYR 0.015 0.003 TYR A 31 ARG 0.006 0.001 ARG E 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 328 time to evaluate : 2.569 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 67 ASN cc_start: 0.6677 (t0) cc_final: 0.6297 (m-40) REVERT: A 278 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6141 (mpt) REVERT: A 417 VAL cc_start: 0.7518 (t) cc_final: 0.7297 (t) REVERT: B 212 LEU cc_start: 0.8179 (mt) cc_final: 0.7933 (mm) REVERT: B 216 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7721 (mp) REVERT: B 278 MET cc_start: 0.6263 (mpt) cc_final: 0.6038 (mpt) REVERT: B 450 MET cc_start: 0.5965 (mmm) cc_final: 0.5558 (mmm) REVERT: B 472 GLU cc_start: 0.7534 (tt0) cc_final: 0.7184 (tt0) REVERT: C 212 LEU cc_start: 0.8296 (mt) cc_final: 0.8034 (mm) REVERT: C 472 GLU cc_start: 0.7546 (tt0) cc_final: 0.7108 (tt0) REVERT: D 294 TYR cc_start: 0.8668 (m-80) cc_final: 0.8301 (m-80) REVERT: D 446 ARG cc_start: 0.7851 (tpp80) cc_final: 0.7609 (tpp80) REVERT: E 212 LEU cc_start: 0.8248 (mt) cc_final: 0.7971 (mm) REVERT: E 216 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7574 (mp) REVERT: E 278 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.5554 (mpt) REVERT: E 455 PHE cc_start: 0.7523 (t80) cc_final: 0.7150 (t80) REVERT: E 472 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7309 (tt0) outliers start: 43 outliers final: 26 residues processed: 342 average time/residue: 1.9279 time to fit residues: 766.3554 Evaluate side-chains 353 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 322 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Chi-restraints excluded: chain E residue 472 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN E 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17270 Z= 0.231 Angle : 0.589 5.864 23510 Z= 0.306 Chirality : 0.040 0.149 2695 Planarity : 0.005 0.058 2825 Dihedral : 10.677 98.784 3383 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.51 % Allowed : 10.11 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 1960 helix: 1.68 (0.17), residues: 845 sheet: -0.12 (0.23), residues: 435 loop : -0.03 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 133 HIS 0.002 0.001 HIS B 297 PHE 0.015 0.002 PHE C 470 TYR 0.010 0.002 TYR A 419 ARG 0.007 0.001 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 327 time to evaluate : 2.799 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 67 ASN cc_start: 0.6722 (t0) cc_final: 0.6337 (m-40) REVERT: A 278 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6090 (mpt) REVERT: A 417 VAL cc_start: 0.7432 (t) cc_final: 0.7212 (t) REVERT: A 436 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6618 (mm-30) REVERT: B 70 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6950 (mt-10) REVERT: B 212 LEU cc_start: 0.8142 (mt) cc_final: 0.7909 (mm) REVERT: B 216 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7675 (mp) REVERT: B 450 MET cc_start: 0.5941 (mmm) cc_final: 0.5518 (mmm) REVERT: B 472 GLU cc_start: 0.7509 (tt0) cc_final: 0.7172 (tt0) REVERT: C 128 TYR cc_start: 0.7309 (t80) cc_final: 0.7005 (t80) REVERT: C 212 LEU cc_start: 0.8255 (mt) cc_final: 0.8021 (mm) REVERT: C 294 TYR cc_start: 0.8661 (m-80) cc_final: 0.8379 (m-80) REVERT: C 472 GLU cc_start: 0.7450 (tt0) cc_final: 0.7091 (tt0) REVERT: D 294 TYR cc_start: 0.8625 (m-80) cc_final: 0.8283 (m-80) REVERT: D 446 ARG cc_start: 0.7831 (tpp80) cc_final: 0.7590 (tpp80) REVERT: E 181 LYS cc_start: 0.7960 (tttt) cc_final: 0.7682 (tmtt) REVERT: E 212 LEU cc_start: 0.8246 (mt) cc_final: 0.7961 (mm) REVERT: E 216 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7577 (mp) REVERT: E 278 MET cc_start: 0.6449 (OUTLIER) cc_final: 0.5530 (mpt) REVERT: E 455 PHE cc_start: 0.7533 (t80) cc_final: 0.7168 (t80) outliers start: 40 outliers final: 25 residues processed: 343 average time/residue: 1.9209 time to fit residues: 763.4639 Evaluate side-chains 351 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 322 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN C 106 ASN D 26 GLN D 47 GLN E 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17270 Z= 0.325 Angle : 0.637 6.031 23510 Z= 0.331 Chirality : 0.041 0.206 2695 Planarity : 0.005 0.060 2825 Dihedral : 10.641 93.227 3383 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.35 % Allowed : 10.73 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 1960 helix: 1.54 (0.17), residues: 850 sheet: -0.10 (0.23), residues: 435 loop : -0.01 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 133 HIS 0.003 0.001 HIS B 297 PHE 0.017 0.002 PHE C 470 TYR 0.014 0.002 TYR A 31 ARG 0.007 0.001 ARG E 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 328 time to evaluate : 2.790 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 67 ASN cc_start: 0.6819 (t0) cc_final: 0.6383 (m-40) REVERT: A 278 MET cc_start: 0.6541 (OUTLIER) cc_final: 0.6127 (mpt) REVERT: A 417 VAL cc_start: 0.7480 (t) cc_final: 0.7248 (t) REVERT: B 70 GLU cc_start: 0.7223 (mt-10) cc_final: 0.7013 (mt-10) REVERT: B 212 LEU cc_start: 0.8160 (mt) cc_final: 0.7938 (mm) REVERT: B 216 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7685 (mp) REVERT: B 294 TYR cc_start: 0.8644 (m-80) cc_final: 0.8342 (m-80) REVERT: B 450 MET cc_start: 0.5982 (mmm) cc_final: 0.5552 (mmm) REVERT: B 472 GLU cc_start: 0.7531 (tt0) cc_final: 0.7187 (tt0) REVERT: C 128 TYR cc_start: 0.7344 (t80) cc_final: 0.7046 (t80) REVERT: C 212 LEU cc_start: 0.8279 (mt) cc_final: 0.8059 (mm) REVERT: C 472 GLU cc_start: 0.7503 (tt0) cc_final: 0.7096 (tt0) REVERT: D 294 TYR cc_start: 0.8652 (m-80) cc_final: 0.8306 (m-80) REVERT: D 446 ARG cc_start: 0.7850 (tpp80) cc_final: 0.7613 (tpp80) REVERT: E 92 TYR cc_start: 0.8506 (m-10) cc_final: 0.8267 (m-10) REVERT: E 212 LEU cc_start: 0.8279 (mt) cc_final: 0.8013 (mm) REVERT: E 216 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7622 (mp) REVERT: E 278 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.5504 (mpt) REVERT: E 455 PHE cc_start: 0.7556 (t80) cc_final: 0.7170 (t80) outliers start: 37 outliers final: 27 residues processed: 345 average time/residue: 1.9971 time to fit residues: 809.9738 Evaluate side-chains 362 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 331 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 187 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 427 GLN D 47 GLN D 106 ASN E 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17270 Z= 0.215 Angle : 0.573 5.962 23510 Z= 0.297 Chirality : 0.040 0.251 2695 Planarity : 0.005 0.059 2825 Dihedral : 10.270 84.887 3383 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.01 % Allowed : 11.06 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1960 helix: 1.84 (0.17), residues: 845 sheet: -0.01 (0.23), residues: 435 loop : 0.04 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 133 HIS 0.002 0.001 HIS B 297 PHE 0.015 0.002 PHE C 470 TYR 0.011 0.002 TYR D 273 ARG 0.008 0.001 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 330 time to evaluate : 2.380 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 67 ASN cc_start: 0.6780 (t0) cc_final: 0.6399 (m-40) REVERT: A 69 SER cc_start: 0.7329 (m) cc_final: 0.7050 (t) REVERT: A 212 LEU cc_start: 0.8083 (mt) cc_final: 0.7739 (mm) REVERT: A 417 VAL cc_start: 0.7424 (t) cc_final: 0.7201 (t) REVERT: B 70 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6989 (mt-10) REVERT: B 212 LEU cc_start: 0.8126 (mt) cc_final: 0.7893 (mm) REVERT: B 294 TYR cc_start: 0.8607 (m-80) cc_final: 0.8396 (m-80) REVERT: B 450 MET cc_start: 0.5912 (mmm) cc_final: 0.5468 (mmm) REVERT: B 472 GLU cc_start: 0.7499 (tt0) cc_final: 0.7166 (tt0) REVERT: C 128 TYR cc_start: 0.7324 (t80) cc_final: 0.7013 (t80) REVERT: C 212 LEU cc_start: 0.8283 (mt) cc_final: 0.8060 (mm) REVERT: C 294 TYR cc_start: 0.8663 (m-80) cc_final: 0.8396 (m-80) REVERT: C 450 MET cc_start: 0.6841 (ptt) cc_final: 0.6605 (ptm) REVERT: C 472 GLU cc_start: 0.7443 (tt0) cc_final: 0.7090 (tt0) REVERT: D 294 TYR cc_start: 0.8614 (m-80) cc_final: 0.8358 (m-80) REVERT: D 446 ARG cc_start: 0.7828 (tpp80) cc_final: 0.7597 (tpp80) REVERT: E 181 LYS cc_start: 0.7937 (tttt) cc_final: 0.7675 (tmtt) REVERT: E 212 LEU cc_start: 0.8215 (mt) cc_final: 0.7956 (mm) REVERT: E 455 PHE cc_start: 0.7539 (t80) cc_final: 0.7185 (t80) outliers start: 31 outliers final: 24 residues processed: 343 average time/residue: 2.0345 time to fit residues: 804.0583 Evaluate side-chains 344 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 320 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 147 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN D 26 GLN D 47 GLN E 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17270 Z= 0.263 Angle : 0.598 7.476 23510 Z= 0.311 Chirality : 0.040 0.207 2695 Planarity : 0.005 0.060 2825 Dihedral : 10.152 74.796 3383 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.90 % Allowed : 11.51 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 1960 helix: 1.73 (0.17), residues: 850 sheet: 0.00 (0.23), residues: 435 loop : 0.11 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 133 HIS 0.002 0.001 HIS B 297 PHE 0.015 0.002 PHE C 470 TYR 0.012 0.002 TYR D 273 ARG 0.008 0.001 ARG C 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 330 time to evaluate : 2.575 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 67 ASN cc_start: 0.6826 (t0) cc_final: 0.6414 (m-40) REVERT: A 69 SER cc_start: 0.7330 (m) cc_final: 0.7035 (t) REVERT: A 212 LEU cc_start: 0.8126 (mt) cc_final: 0.7812 (mm) REVERT: A 417 VAL cc_start: 0.7428 (t) cc_final: 0.7208 (t) REVERT: B 70 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6987 (mt-10) REVERT: B 212 LEU cc_start: 0.8160 (mt) cc_final: 0.7936 (mm) REVERT: B 294 TYR cc_start: 0.8637 (m-80) cc_final: 0.8355 (m-80) REVERT: B 450 MET cc_start: 0.5919 (mmm) cc_final: 0.5480 (mmm) REVERT: B 472 GLU cc_start: 0.7504 (tt0) cc_final: 0.7166 (tt0) REVERT: C 128 TYR cc_start: 0.7313 (t80) cc_final: 0.7008 (t80) REVERT: C 294 TYR cc_start: 0.8685 (m-80) cc_final: 0.8337 (m-80) REVERT: C 472 GLU cc_start: 0.7456 (tt0) cc_final: 0.7071 (tt0) REVERT: D 294 TYR cc_start: 0.8614 (m-80) cc_final: 0.8316 (m-80) REVERT: D 446 ARG cc_start: 0.7837 (tpp80) cc_final: 0.7608 (tpp80) REVERT: E 92 TYR cc_start: 0.8497 (m-10) cc_final: 0.8228 (m-10) REVERT: E 212 LEU cc_start: 0.8273 (mt) cc_final: 0.8010 (mm) REVERT: E 455 PHE cc_start: 0.7517 (t80) cc_final: 0.7178 (t80) outliers start: 29 outliers final: 25 residues processed: 342 average time/residue: 2.0213 time to fit residues: 798.8201 Evaluate side-chains 351 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 326 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 1.9990 chunk 164 optimal weight: 0.0670 chunk 175 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 174 optimal weight: 0.4980 chunk 115 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN D 47 GLN E 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17270 Z= 0.162 Angle : 0.534 8.610 23510 Z= 0.275 Chirality : 0.039 0.203 2695 Planarity : 0.004 0.066 2825 Dihedral : 9.730 69.995 3383 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.40 % Allowed : 12.23 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 1960 helix: 2.09 (0.17), residues: 840 sheet: 0.26 (0.23), residues: 430 loop : 0.18 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 133 HIS 0.002 0.000 HIS B 104 PHE 0.013 0.001 PHE E 470 TYR 0.008 0.001 TYR D 273 ARG 0.011 0.001 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 327 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8039 (mt) cc_final: 0.7754 (mm) REVERT: B 212 LEU cc_start: 0.8071 (mt) cc_final: 0.7854 (mm) REVERT: B 450 MET cc_start: 0.5903 (mmm) cc_final: 0.5462 (mmm) REVERT: B 472 GLU cc_start: 0.7406 (tt0) cc_final: 0.7138 (tt0) REVERT: C 128 TYR cc_start: 0.7304 (t80) cc_final: 0.6985 (t80) REVERT: C 265 ASP cc_start: 0.7320 (t0) cc_final: 0.7116 (t0) REVERT: C 294 TYR cc_start: 0.8645 (m-80) cc_final: 0.8408 (m-80) REVERT: C 472 GLU cc_start: 0.7383 (tt0) cc_final: 0.7125 (tt0) REVERT: D 294 TYR cc_start: 0.8588 (m-80) cc_final: 0.8362 (m-80) REVERT: D 446 ARG cc_start: 0.7810 (tpp80) cc_final: 0.7590 (tpp80) REVERT: E 181 LYS cc_start: 0.7919 (tttt) cc_final: 0.7684 (tmtt) REVERT: E 212 LEU cc_start: 0.8199 (mt) cc_final: 0.7936 (mm) REVERT: E 216 ILE cc_start: 0.7704 (mp) cc_final: 0.7492 (mm) REVERT: E 455 PHE cc_start: 0.7483 (t80) cc_final: 0.7125 (t80) outliers start: 20 outliers final: 19 residues processed: 338 average time/residue: 2.0038 time to fit residues: 783.1991 Evaluate side-chains 337 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 318 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN D 26 GLN D 47 GLN D 106 ASN E 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17270 Z= 0.222 Angle : 0.569 7.330 23510 Z= 0.294 Chirality : 0.040 0.192 2695 Planarity : 0.005 0.064 2825 Dihedral : 9.534 72.933 3383 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.45 % Allowed : 12.18 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.19), residues: 1960 helix: 2.07 (0.17), residues: 840 sheet: 0.15 (0.23), residues: 435 loop : 0.14 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 133 HIS 0.003 0.001 HIS B 297 PHE 0.014 0.002 PHE C 470 TYR 0.010 0.002 TYR D 273 ARG 0.009 0.001 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 319 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8140 (mt) cc_final: 0.7814 (mm) REVERT: B 212 LEU cc_start: 0.8115 (mt) cc_final: 0.7899 (mm) REVERT: B 450 MET cc_start: 0.5913 (mmm) cc_final: 0.5474 (mmm) REVERT: B 472 GLU cc_start: 0.7465 (tt0) cc_final: 0.7150 (tt0) REVERT: C 128 TYR cc_start: 0.7293 (t80) cc_final: 0.6986 (t80) REVERT: C 294 TYR cc_start: 0.8670 (m-80) cc_final: 0.8429 (m-80) REVERT: D 294 TYR cc_start: 0.8605 (m-80) cc_final: 0.8321 (m-80) REVERT: D 446 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7611 (tpp80) REVERT: E 92 TYR cc_start: 0.8501 (m-10) cc_final: 0.8213 (m-10) REVERT: E 181 LYS cc_start: 0.7940 (tttt) cc_final: 0.7700 (tmtt) REVERT: E 212 LEU cc_start: 0.8223 (mt) cc_final: 0.7964 (mm) REVERT: E 216 ILE cc_start: 0.7719 (mp) cc_final: 0.7510 (mm) REVERT: E 455 PHE cc_start: 0.7488 (t80) cc_final: 0.7144 (t80) outliers start: 21 outliers final: 19 residues processed: 331 average time/residue: 1.9875 time to fit residues: 759.8333 Evaluate side-chains 338 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 319 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 475 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.0570 chunk 136 optimal weight: 1.9990 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 47 GLN C 106 ASN D 47 GLN E 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.152182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.132739 restraints weight = 58735.110| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.45 r_work: 0.3252 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17270 Z= 0.256 Angle : 0.594 7.658 23510 Z= 0.308 Chirality : 0.040 0.189 2695 Planarity : 0.005 0.064 2825 Dihedral : 9.476 78.094 3383 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.45 % Allowed : 12.29 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 1960 helix: 1.98 (0.17), residues: 840 sheet: 0.11 (0.23), residues: 435 loop : 0.07 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 66 HIS 0.002 0.001 HIS B 104 PHE 0.017 0.002 PHE C 470 TYR 0.012 0.002 TYR D 273 ARG 0.010 0.001 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12956.65 seconds wall clock time: 223 minutes 51.41 seconds (13431.41 seconds total)