Starting phenix.real_space_refine on Fri Dec 8 09:13:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ewf_28644/12_2023/8ewf_28644_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ewf_28644/12_2023/8ewf_28644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ewf_28644/12_2023/8ewf_28644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ewf_28644/12_2023/8ewf_28644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ewf_28644/12_2023/8ewf_28644_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ewf_28644/12_2023/8ewf_28644_trim.pdb" } resolution = 3.92 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= 0.002 sd= 0.040 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: 5 Type Number sf(0) Gaussians S 220 5.16 5 C 18037 2.51 5 N 4984 2.21 5 O 5424 1.98 5 H 27869 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 188": "OD1" <-> "OD2" Residue "G ASP 311": "OD1" <-> "OD2" Residue "I ASP 43": "OD1" <-> "OD2" Residue "I PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 316": "OE1" <-> "OE2" Residue "I GLU 327": "OE1" <-> "OE2" Residue "I TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 188": "OD1" <-> "OD2" Residue "K ASP 311": "OD1" <-> "OD2" Residue "M ASP 43": "OD1" <-> "OD2" Residue "M PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 139": "OE1" <-> "OE2" Residue "M PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 316": "OE1" <-> "OE2" Residue "M GLU 327": "OE1" <-> "OE2" Residue "M TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 188": "OD1" <-> "OD2" Residue "O ASP 311": "OD1" <-> "OD2" Residue "Q ASP 43": "OD1" <-> "OD2" Residue "Q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 139": "OE1" <-> "OE2" Residue "Q PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 316": "OE1" <-> "OE2" Residue "Q GLU 327": "OE1" <-> "OE2" Residue "Q TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 56534 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6564 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "C" Number of atoms: 6490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6490 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 387} Chain: "E" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4192 Classifications: {'peptide': 265} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 257} Chain: "G" Number of atoms: 6564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6564 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "I" Number of atoms: 6490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6490 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 387} Chain: "K" Number of atoms: 6564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6564 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "M" Number of atoms: 6490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6490 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 387} Chain: "O" Number of atoms: 6564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6564 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "Q" Number of atoms: 6490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6490 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 387} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 17.60, per 1000 atoms: 0.31 Number of scatterers: 56534 At special positions: 0 Unit cell: (194.4, 159.6, 211.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 220 16.00 O 5424 8.00 N 4984 7.00 C 18037 6.00 H 27869 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 125 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 28 " distance=2.03 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 266 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 203 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 396 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 273 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 280 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 125 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 28 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 105 " distance=2.04 Simple disulfide: pdb=" SG CYS I 153 " - pdb=" SG CYS I 266 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 225 " distance=2.03 Simple disulfide: pdb=" SG CYS I 203 " - pdb=" SG CYS I 220 " distance=2.03 Simple disulfide: pdb=" SG CYS I 396 " - pdb=" SG CYS I 417 " distance=2.03 Simple disulfide: pdb=" SG CYS K 49 " - pdb=" SG CYS K 114 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 94 " distance=2.03 Simple disulfide: pdb=" SG CYS K 63 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 68 " - pdb=" SG CYS K 78 " distance=2.03 Simple disulfide: pdb=" SG CYS K 259 " - pdb=" SG CYS K 271 " distance=2.03 Simple disulfide: pdb=" SG CYS K 301 " - pdb=" SG CYS K 376 " distance=2.03 Simple disulfide: pdb=" SG CYS K 306 " - pdb=" SG CYS K 380 " distance=2.03 Simple disulfide: pdb=" SG CYS K 328 " - pdb=" SG CYS K 370 " distance=2.03 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 125 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 28 " distance=2.03 Simple disulfide: pdb=" SG CYS M 91 " - pdb=" SG CYS M 105 " distance=2.04 Simple disulfide: pdb=" SG CYS M 153 " - pdb=" SG CYS M 266 " distance=2.03 Simple disulfide: pdb=" SG CYS M 201 " - pdb=" SG CYS M 225 " distance=2.03 Simple disulfide: pdb=" SG CYS M 203 " - pdb=" SG CYS M 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 396 " - pdb=" SG CYS M 417 " distance=2.03 Simple disulfide: pdb=" SG CYS O 49 " - pdb=" SG CYS O 114 " distance=2.03 Simple disulfide: pdb=" SG CYS O 62 " - pdb=" SG CYS O 94 " distance=2.03 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 68 " - pdb=" SG CYS O 78 " distance=2.03 Simple disulfide: pdb=" SG CYS O 259 " - pdb=" SG CYS O 271 " distance=2.03 Simple disulfide: pdb=" SG CYS O 301 " - pdb=" SG CYS O 376 " distance=2.03 Simple disulfide: pdb=" SG CYS O 306 " - pdb=" SG CYS O 380 " distance=2.03 Simple disulfide: pdb=" SG CYS O 328 " - pdb=" SG CYS O 370 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 125 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 28 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 105 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 153 " - pdb=" SG CYS Q 266 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 201 " - pdb=" SG CYS Q 225 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 203 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 396 " - pdb=" SG CYS Q 417 " distance=2.03 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 NAG-ASN " NAG A 501 " - " ASN A 141 " " NAG G 501 " - " ASN G 141 " " NAG K 501 " - " ASN K 141 " " NAG O 501 " - " ASN O 141 " Time building additional restraints: 32.63 Conformation dependent library (CDL) restraints added in 4.4 seconds 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6932 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 88 sheets defined 12.6% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.598A pdb=" N TYR A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 259 removed outlier: 4.277A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 259' Processing helix chain 'A' and resid 404 through 414 removed outlier: 3.955A pdb=" N SER A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 434 Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.671A pdb=" N CYS C 225 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.917A pdb=" N TYR C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 401 Proline residue: C 399 - end of helix Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.729A pdb=" N VAL E 59 " --> pdb=" O PRO E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 119 Processing helix chain 'E' and resid 129 through 133 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.909A pdb=" N ALA E 163 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.875A pdb=" N ARG E 243 " --> pdb=" O PHE E 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 239 through 243' Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.599A pdb=" N TYR G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS G 245 " --> pdb=" O LYS G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 256 through 259 removed outlier: 4.278A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 256 through 259' Processing helix chain 'G' and resid 404 through 414 removed outlier: 3.956A pdb=" N SER G 408 " --> pdb=" O THR G 404 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP G 409 " --> pdb=" O THR G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 434 Processing helix chain 'I' and resid 221 through 225 removed outlier: 3.670A pdb=" N CYS I 225 " --> pdb=" O ILE I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 362 removed outlier: 3.917A pdb=" N TYR I 358 " --> pdb=" O GLU I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 401 Proline residue: I 399 - end of helix Processing helix chain 'I' and resid 411 through 416 Processing helix chain 'K' and resid 112 through 116 Processing helix chain 'K' and resid 238 through 246 removed outlier: 3.599A pdb=" N TYR K 242 " --> pdb=" O SER K 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS K 245 " --> pdb=" O LYS K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 255 Processing helix chain 'K' and resid 256 through 259 removed outlier: 4.278A pdb=" N CYS K 259 " --> pdb=" O PRO K 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 256 through 259' Processing helix chain 'K' and resid 404 through 414 removed outlier: 3.955A pdb=" N SER K 408 " --> pdb=" O THR K 404 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP K 409 " --> pdb=" O THR K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 434 Processing helix chain 'M' and resid 221 through 225 removed outlier: 3.670A pdb=" N CYS M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 362 removed outlier: 3.916A pdb=" N TYR M 358 " --> pdb=" O GLU M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 401 Proline residue: M 399 - end of helix Processing helix chain 'M' and resid 411 through 416 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'O' and resid 238 through 246 removed outlier: 3.598A pdb=" N TYR O 242 " --> pdb=" O SER O 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS O 245 " --> pdb=" O LYS O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 255 Processing helix chain 'O' and resid 256 through 259 removed outlier: 4.277A pdb=" N CYS O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 259' Processing helix chain 'O' and resid 404 through 414 removed outlier: 3.954A pdb=" N SER O 408 " --> pdb=" O THR O 404 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP O 409 " --> pdb=" O THR O 405 " (cutoff:3.500A) Processing helix chain 'O' and resid 417 through 434 Processing helix chain 'Q' and resid 221 through 225 removed outlier: 3.670A pdb=" N CYS Q 225 " --> pdb=" O ILE Q 222 " (cutoff:3.500A) Processing helix chain 'Q' and resid 354 through 362 removed outlier: 3.917A pdb=" N TYR Q 358 " --> pdb=" O GLU Q 354 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 401 Proline residue: Q 399 - end of helix Processing helix chain 'Q' and resid 411 through 416 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.593A pdb=" N MET A 31 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU A 136 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 134 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 35 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 48 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA7, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA8, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AA9, first strand: chain 'A' and resid 220 through 221 removed outlier: 3.620A pdb=" N VAL A 220 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 305 removed outlier: 4.109A pdb=" N MET A 299 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 319 " --> pdb=" O MET A 299 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS A 301 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 317 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL A 303 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL A 315 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB3, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 18 Processing sheet with id=AB5, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AB6, first strand: chain 'C' and resid 66 through 71 Processing sheet with id=AB7, first strand: chain 'C' and resid 84 through 86 Processing sheet with id=AB8, first strand: chain 'C' and resid 149 through 156 Processing sheet with id=AB9, first strand: chain 'C' and resid 236 through 237 Processing sheet with id=AC1, first strand: chain 'C' and resid 183 through 184 Processing sheet with id=AC2, first strand: chain 'C' and resid 208 through 211 removed outlier: 3.638A pdb=" N LYS C 200 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS C 226 " --> pdb=" O LYS C 200 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 275 through 279 Processing sheet with id=AC4, first strand: chain 'E' and resid 34 through 44 removed outlier: 4.835A pdb=" N LEU E 35 " --> pdb=" O ARG E 285 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N VAL E 287 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER E 37 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N HIS E 289 " --> pdb=" O SER E 37 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER E 39 " --> pdb=" O HIS E 289 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLN E 291 " --> pdb=" O SER E 39 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL E 41 " --> pdb=" O GLN E 291 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N THR E 293 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU E 43 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG E 210 " --> pdb=" O ARG E 222 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG E 222 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 49 through 51 Processing sheet with id=AC6, first strand: chain 'E' and resid 99 through 100 removed outlier: 6.969A pdb=" N TRP E 74 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP E 91 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL E 72 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR E 93 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG E 70 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA E 173 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AC9, first strand: chain 'G' and resid 15 through 19 removed outlier: 6.592A pdb=" N MET G 31 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG G 134 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER G 35 " --> pdb=" O LYS G 132 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 15 through 19 Processing sheet with id=AD2, first strand: chain 'G' and resid 44 through 48 Processing sheet with id=AD3, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AD4, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AD5, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AD6, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AD7, first strand: chain 'G' and resid 220 through 221 removed outlier: 3.619A pdb=" N VAL G 220 " --> pdb=" O SER G 234 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 296 through 305 removed outlier: 4.108A pdb=" N MET G 299 " --> pdb=" O LYS G 319 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS G 319 " --> pdb=" O MET G 299 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS G 301 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE G 317 " --> pdb=" O CYS G 301 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL G 303 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL G 315 " --> pdb=" O VAL G 303 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AE1, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AE2, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AE3, first strand: chain 'I' and resid 37 through 38 Processing sheet with id=AE4, first strand: chain 'I' and resid 66 through 71 Processing sheet with id=AE5, first strand: chain 'I' and resid 84 through 86 Processing sheet with id=AE6, first strand: chain 'I' and resid 149 through 156 Processing sheet with id=AE7, first strand: chain 'I' and resid 236 through 237 Processing sheet with id=AE8, first strand: chain 'I' and resid 183 through 184 Processing sheet with id=AE9, first strand: chain 'I' and resid 208 through 211 removed outlier: 3.638A pdb=" N LYS I 200 " --> pdb=" O HIS I 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS I 226 " --> pdb=" O LYS I 200 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 275 through 279 Processing sheet with id=AF2, first strand: chain 'K' and resid 2 through 8 Processing sheet with id=AF3, first strand: chain 'K' and resid 15 through 19 removed outlier: 6.593A pdb=" N MET K 31 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU K 136 " --> pdb=" O MET K 31 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU K 33 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG K 134 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER K 35 " --> pdb=" O LYS K 132 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 15 through 19 Processing sheet with id=AF5, first strand: chain 'K' and resid 44 through 48 Processing sheet with id=AF6, first strand: chain 'K' and resid 51 through 54 Processing sheet with id=AF7, first strand: chain 'K' and resid 51 through 54 Processing sheet with id=AF8, first strand: chain 'K' and resid 87 through 88 Processing sheet with id=AF9, first strand: chain 'K' and resid 203 through 205 Processing sheet with id=AG1, first strand: chain 'K' and resid 220 through 221 removed outlier: 3.619A pdb=" N VAL K 220 " --> pdb=" O SER K 234 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 296 through 305 removed outlier: 4.108A pdb=" N MET K 299 " --> pdb=" O LYS K 319 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS K 319 " --> pdb=" O MET K 299 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS K 301 " --> pdb=" O ILE K 317 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE K 317 " --> pdb=" O CYS K 301 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL K 303 " --> pdb=" O VAL K 315 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL K 315 " --> pdb=" O VAL K 303 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 343 through 346 Processing sheet with id=AG4, first strand: chain 'K' and resid 387 through 388 Processing sheet with id=AG5, first strand: chain 'M' and resid 17 through 18 Processing sheet with id=AG6, first strand: chain 'M' and resid 37 through 38 Processing sheet with id=AG7, first strand: chain 'M' and resid 66 through 71 Processing sheet with id=AG8, first strand: chain 'M' and resid 84 through 86 Processing sheet with id=AG9, first strand: chain 'M' and resid 149 through 156 Processing sheet with id=AH1, first strand: chain 'M' and resid 236 through 237 Processing sheet with id=AH2, first strand: chain 'M' and resid 183 through 184 Processing sheet with id=AH3, first strand: chain 'M' and resid 208 through 211 removed outlier: 3.638A pdb=" N LYS M 200 " --> pdb=" O HIS M 226 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS M 226 " --> pdb=" O LYS M 200 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 275 through 279 Processing sheet with id=AH5, first strand: chain 'O' and resid 2 through 8 Processing sheet with id=AH6, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.592A pdb=" N MET O 31 " --> pdb=" O LEU O 136 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU O 136 " --> pdb=" O MET O 31 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU O 33 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG O 134 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER O 35 " --> pdb=" O LYS O 132 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 15 through 19 Processing sheet with id=AH8, first strand: chain 'O' and resid 44 through 48 Processing sheet with id=AH9, first strand: chain 'O' and resid 51 through 54 Processing sheet with id=AI1, first strand: chain 'O' and resid 51 through 54 Processing sheet with id=AI2, first strand: chain 'O' and resid 87 through 88 Processing sheet with id=AI3, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AI4, first strand: chain 'O' and resid 220 through 221 removed outlier: 3.620A pdb=" N VAL O 220 " --> pdb=" O SER O 234 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'O' and resid 296 through 305 removed outlier: 4.109A pdb=" N MET O 299 " --> pdb=" O LYS O 319 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS O 319 " --> pdb=" O MET O 299 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS O 301 " --> pdb=" O ILE O 317 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE O 317 " --> pdb=" O CYS O 301 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL O 303 " --> pdb=" O VAL O 315 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL O 315 " --> pdb=" O VAL O 303 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'O' and resid 343 through 346 Processing sheet with id=AI7, first strand: chain 'O' and resid 387 through 388 Processing sheet with id=AI8, first strand: chain 'Q' and resid 17 through 18 Processing sheet with id=AI9, first strand: chain 'Q' and resid 37 through 38 Processing sheet with id=AJ1, first strand: chain 'Q' and resid 66 through 71 Processing sheet with id=AJ2, first strand: chain 'Q' and resid 84 through 86 Processing sheet with id=AJ3, first strand: chain 'Q' and resid 149 through 156 Processing sheet with id=AJ4, first strand: chain 'Q' and resid 236 through 237 Processing sheet with id=AJ5, first strand: chain 'Q' and resid 183 through 184 Processing sheet with id=AJ6, first strand: chain 'Q' and resid 208 through 211 removed outlier: 3.638A pdb=" N LYS Q 200 " --> pdb=" O HIS Q 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS Q 226 " --> pdb=" O LYS Q 200 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Q' and resid 275 through 279 1026 hydrogen bonds defined for protein. 2574 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: 20.87 Time building geometry restraints manager: 34.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 27852 1.04 - 1.24: 3984 1.24 - 1.45: 8754 1.45 - 1.65: 16374 1.65 - 1.86: 297 Bond restraints: 57261 Sorted by residual: bond pdb=" N SER E 32 " pdb=" H2 SER E 32 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" N TYR O 1 " pdb=" H3 TYR O 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N TYR G 1 " pdb=" H2 TYR G 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N TYR K 1 " pdb=" H3 TYR K 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N TYR A 1 " pdb=" H3 TYR A 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 57256 not shown) Histogram of bond angle deviations from ideal: 56.30 - 72.34: 1 72.34 - 88.38: 0 88.38 - 104.43: 603 104.43 - 120.47: 85937 120.47 - 136.51: 16913 Bond angle restraints: 103454 Sorted by residual: angle pdb=" H1 SER E 32 " pdb=" N SER E 32 " pdb=" H2 SER E 32 " ideal model delta sigma weight residual 109.47 56.30 53.17 3.00e+00 1.11e-01 3.14e+02 angle pdb=" H1 SER E 32 " pdb=" N SER E 32 " pdb=" H3 SER E 32 " ideal model delta sigma weight residual 109.47 136.51 -27.04 3.00e+00 1.11e-01 8.13e+01 angle pdb=" N GLY E 96 " pdb=" CA GLY E 96 " pdb=" C GLY E 96 " ideal model delta sigma weight residual 110.69 118.73 -8.04 2.05e+00 2.38e-01 1.54e+01 angle pdb=" H1 TYR G 1 " pdb=" N TYR G 1 " pdb=" H2 TYR G 1 " ideal model delta sigma weight residual 109.47 97.73 11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" H1 TYR K 1 " pdb=" N TYR K 1 " pdb=" H2 TYR K 1 " ideal model delta sigma weight residual 109.47 97.77 11.70 3.00e+00 1.11e-01 1.52e+01 ... (remaining 103449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 23527 17.80 - 35.61: 2648 35.61 - 53.41: 675 53.41 - 71.21: 122 71.21 - 89.01: 72 Dihedral angle restraints: 27044 sinusoidal: 14410 harmonic: 12634 Sorted by residual: dihedral pdb=" CB CYS I 153 " pdb=" SG CYS I 153 " pdb=" SG CYS I 266 " pdb=" CB CYS I 266 " ideal model delta sinusoidal sigma weight residual -86.00 -164.48 78.48 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS C 153 " pdb=" SG CYS C 153 " pdb=" SG CYS C 266 " pdb=" CB CYS C 266 " ideal model delta sinusoidal sigma weight residual -86.00 -164.47 78.47 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS M 153 " pdb=" SG CYS M 153 " pdb=" SG CYS M 266 " pdb=" CB CYS M 266 " ideal model delta sinusoidal sigma weight residual -86.00 -164.46 78.46 1 1.00e+01 1.00e-02 7.68e+01 ... (remaining 27041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2736 0.030 - 0.061: 1164 0.061 - 0.091: 349 0.091 - 0.121: 303 0.121 - 0.152: 22 Chirality restraints: 4574 Sorted by residual: chirality pdb=" CA ILE E 153 " pdb=" N ILE E 153 " pdb=" C ILE E 153 " pdb=" CB ILE E 153 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CB THR M 403 " pdb=" CA THR M 403 " pdb=" OG1 THR M 403 " pdb=" CG2 THR M 403 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CB THR Q 403 " pdb=" CA THR Q 403 " pdb=" OG1 THR Q 403 " pdb=" CG2 THR Q 403 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 4571 not shown) Planarity restraints: 8618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 141 " -0.030 2.00e-02 2.50e+03 3.28e-02 1.35e+01 pdb=" CG ASN K 141 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN K 141 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN K 141 " 0.052 2.00e-02 2.50e+03 pdb=" C1 NAG K 501 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 339 " -0.021 2.00e-02 2.50e+03 1.12e-02 5.03e+00 pdb=" CG TRP C 339 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP C 339 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 339 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP C 339 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 339 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 339 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 339 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 339 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 339 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP C 339 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP C 339 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP C 339 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 339 " 0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 339 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP C 339 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 339 " 0.020 2.00e-02 2.50e+03 1.12e-02 5.02e+00 pdb=" CG TRP Q 339 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 339 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 339 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 339 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 339 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 339 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 339 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 339 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 339 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP Q 339 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP Q 339 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP Q 339 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP Q 339 " -0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP Q 339 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP Q 339 " -0.001 2.00e-02 2.50e+03 ... (remaining 8615 not shown) Histogram of nonbonded interaction distances: 1.34 - 1.99: 788 1.99 - 2.64: 79593 2.64 - 3.29: 170334 3.29 - 3.95: 215546 3.95 - 4.60: 316706 Nonbonded interactions: 782967 Sorted by model distance: nonbonded pdb=" O PRO C 20 " pdb="HH12 ARG I 144 " model vdw 1.337 1.850 nonbonded pdb=" O PRO I 20 " pdb="HH12 ARG M 144 " model vdw 1.386 1.850 nonbonded pdb=" O TYR K 390 " pdb=" HE1 TRP M 339 " model vdw 1.441 1.850 nonbonded pdb=" HZ1 LYS C 120 " pdb=" OD1 ASP E 97 " model vdw 1.485 1.850 nonbonded pdb="HH12 ARG C 144 " pdb=" O PRO M 20 " model vdw 1.502 1.850 ... (remaining 782962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = (chain 'C' and resid 5 through 423) selection = chain 'I' selection = (chain 'M' and resid 5 through 423) selection = (chain 'Q' and resid 5 through 423) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.850 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: 0.630 Extract box with map and model: 6.430 Check model and map are aligned: 0.630 Set scattering table: 0.360 Process input model: 130.940 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 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 : 0.004 0.048 29392 Z= 0.255 Angle : 0.684 8.863 40098 Z= 0.359 Chirality : 0.043 0.152 4574 Planarity : 0.005 0.058 5165 Dihedral : 16.919 89.015 10772 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.88 % Allowed : 35.98 % Favored : 63.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3679 helix: -1.58 (0.26), residues: 330 sheet: -0.26 (0.15), residues: 1193 loop : -1.03 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP Q 339 HIS 0.009 0.001 HIS Q 142 PHE 0.026 0.002 PHE A 161 TYR 0.020 0.002 TYR M 237 ARG 0.012 0.001 ARG M 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 884 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 28 outliers final: 18 residues processed: 899 average time/residue: 0.7767 time to fit residues: 1074.9018 Evaluate side-chains 717 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 699 time to evaluate : 3.295 Switching outliers to nearest non-outliers 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 outliers start: 18 outliers final: 10 residues processed: 18 average time/residue: 0.6765 time to fit residues: 24.1749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 0.0060 chunk 274 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 211 optimal weight: 0.8980 chunk 328 optimal weight: 2.9990 overall best weight: 2.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN A 270 ASN C 130 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN E 189 ASN E 191 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS G 264 ASN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 ASN I 234 ASN ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 ASN K 138 GLN ** K 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 HIS M 142 HIS ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 273 ASN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN O 264 ASN O 270 ASN ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 273 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29392 Z= 0.257 Angle : 0.643 7.963 40098 Z= 0.334 Chirality : 0.044 0.176 4574 Planarity : 0.004 0.060 5165 Dihedral : 6.396 59.278 4202 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.72 % Allowed : 33.30 % Favored : 62.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -1.24 (0.14), residues: 3679 helix: -1.19 (0.26), residues: 340 sheet: -0.28 (0.15), residues: 1213 loop : -1.07 (0.14), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 339 HIS 0.020 0.001 HIS I 130 PHE 0.025 0.002 PHE Q 376 TYR 0.021 0.002 TYR I 237 ARG 0.008 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 700 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 84 residues processed: 774 average time/residue: 0.7484 time to fit residues: 901.4748 Evaluate side-chains 737 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 653 time to evaluate : 3.273 Switching outliers to nearest non-outliers 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 outliers start: 84 outliers final: 9 residues processed: 84 average time/residue: 0.5172 time to fit residues: 81.4202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 182 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 273 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 329 optimal weight: 7.9990 chunk 355 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 chunk 326 optimal weight: 0.0270 chunk 112 optimal weight: 7.9990 chunk 264 optimal weight: 6.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 GLN ** I 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** M 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 29392 Z= 0.303 Angle : 0.642 6.578 40098 Z= 0.336 Chirality : 0.043 0.144 4574 Planarity : 0.005 0.068 5165 Dihedral : 6.333 59.836 4202 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.44 % Allowed : 32.07 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.38 (0.14), residues: 3679 helix: -0.88 (0.27), residues: 340 sheet: -0.33 (0.14), residues: 1205 loop : -1.27 (0.14), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 339 HIS 0.010 0.002 HIS I 130 PHE 0.031 0.002 PHE Q 376 TYR 0.023 0.002 TYR I 237 ARG 0.006 0.001 ARG I 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 663 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 109 outliers final: 76 residues processed: 741 average time/residue: 0.7576 time to fit residues: 893.5907 Evaluate side-chains 708 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 632 time to evaluate : 3.291 Switching outliers to nearest non-outliers 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 outliers start: 76 outliers final: 11 residues processed: 76 average time/residue: 0.5485 time to fit residues: 79.5381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 325 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 330 optimal weight: 3.9990 chunk 349 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 ASN ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 216 ASN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 29392 Z= 0.253 Angle : 0.632 19.529 40098 Z= 0.326 Chirality : 0.044 0.146 4574 Planarity : 0.004 0.059 5165 Dihedral : 6.232 58.570 4202 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.87 % Allowed : 31.41 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -1.34 (0.14), residues: 3679 helix: -0.61 (0.28), residues: 340 sheet: -0.37 (0.15), residues: 1213 loop : -1.25 (0.14), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 339 HIS 0.011 0.001 HIS I 130 PHE 0.029 0.002 PHE Q 376 TYR 0.021 0.001 TYR C 237 ARG 0.005 0.000 ARG G 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 647 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 91 outliers final: 69 residues processed: 709 average time/residue: 0.7895 time to fit residues: 883.1461 Evaluate side-chains 698 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 629 time to evaluate : 3.241 Switching outliers to nearest non-outliers 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 outliers start: 69 outliers final: 12 residues processed: 69 average time/residue: 0.5814 time to fit residues: 74.9146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 298 optimal weight: 8.9990 chunk 241 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 178 optimal weight: 2.9990 chunk 314 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 389 ASN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 299 ASN ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 ASN M 224 GLN ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 299 ASN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 29392 Z= 0.415 Angle : 0.699 9.232 40098 Z= 0.371 Chirality : 0.044 0.157 4574 Planarity : 0.005 0.073 5165 Dihedral : 6.579 59.714 4202 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 26.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 3.91 % Allowed : 30.31 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3679 helix: -0.58 (0.27), residues: 340 sheet: -0.73 (0.14), residues: 1282 loop : -1.60 (0.14), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 339 HIS 0.009 0.002 HIS G 230 PHE 0.039 0.002 PHE Q 376 TYR 0.026 0.002 TYR M 237 ARG 0.007 0.001 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 625 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 88 residues processed: 711 average time/residue: 0.7739 time to fit residues: 872.1849 Evaluate side-chains 698 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 610 time to evaluate : 3.263 Switching outliers to nearest non-outliers 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 outliers start: 88 outliers final: 12 residues processed: 88 average time/residue: 0.5495 time to fit residues: 91.2177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 117 optimal weight: 4.9990 chunk 315 optimal weight: 0.0010 chunk 69 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 350 optimal weight: 3.9990 chunk 290 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29392 Z= 0.203 Angle : 0.636 14.212 40098 Z= 0.326 Chirality : 0.045 0.173 4574 Planarity : 0.004 0.056 5165 Dihedral : 6.138 56.602 4202 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.67 % Allowed : 30.62 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -1.43 (0.14), residues: 3679 helix: -0.33 (0.29), residues: 340 sheet: -0.54 (0.14), residues: 1241 loop : -1.30 (0.14), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 339 HIS 0.010 0.001 HIS M 170 PHE 0.030 0.002 PHE M 115 TYR 0.016 0.001 TYR C 15 ARG 0.005 0.000 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 654 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 45 residues processed: 684 average time/residue: 0.7498 time to fit residues: 806.2139 Evaluate side-chains 668 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 623 time to evaluate : 3.260 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 13 residues processed: 45 average time/residue: 0.5803 time to fit residues: 49.6032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 337 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 294 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 348 optimal weight: 0.9990 chunk 218 optimal weight: 0.4980 chunk 212 optimal weight: 5.9990 chunk 161 optimal weight: 0.2980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 HIS ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29392 Z= 0.188 Angle : 0.629 16.992 40098 Z= 0.319 Chirality : 0.045 0.197 4574 Planarity : 0.004 0.056 5165 Dihedral : 5.990 56.197 4202 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.10 % Allowed : 32.17 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -1.27 (0.14), residues: 3679 helix: -0.36 (0.29), residues: 340 sheet: -0.43 (0.15), residues: 1221 loop : -1.17 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 339 HIS 0.008 0.001 HIS M 170 PHE 0.037 0.001 PHE Q 376 TYR 0.016 0.001 TYR C 15 ARG 0.004 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 657 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 25 residues processed: 679 average time/residue: 0.7538 time to fit residues: 801.3205 Evaluate side-chains 650 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 625 time to evaluate : 3.282 Switching outliers to nearest non-outliers 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 outliers start: 25 outliers final: 11 residues processed: 25 average time/residue: 0.5650 time to fit residues: 28.4799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 215 optimal weight: 3.9990 chunk 139 optimal weight: 0.0270 chunk 208 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 221 optimal weight: 0.9980 chunk 237 optimal weight: 0.6980 chunk 172 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 overall best weight: 2.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 ASN K 204 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 400 GLN ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29392 Z= 0.216 Angle : 0.624 16.082 40098 Z= 0.318 Chirality : 0.044 0.197 4574 Planarity : 0.004 0.057 5165 Dihedral : 5.998 57.309 4202 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.36 % Allowed : 32.45 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -1.30 (0.14), residues: 3679 helix: -0.14 (0.29), residues: 328 sheet: -0.53 (0.14), residues: 1261 loop : -1.17 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 339 HIS 0.008 0.001 HIS M 170 PHE 0.032 0.002 PHE C 376 TYR 0.017 0.001 TYR C 237 ARG 0.008 0.000 ARG O 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 641 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 43 outliers final: 36 residues processed: 662 average time/residue: 0.7825 time to fit residues: 820.5266 Evaluate side-chains 661 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 625 time to evaluate : 3.316 Switching outliers to nearest non-outliers 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 outliers start: 36 outliers final: 11 residues processed: 36 average time/residue: 0.5990 time to fit residues: 41.9263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 317 optimal weight: 4.9990 chunk 334 optimal weight: 8.9990 chunk 304 optimal weight: 2.9990 chunk 325 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 255 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 293 optimal weight: 7.9990 chunk 307 optimal weight: 0.6980 chunk 324 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29392 Z= 0.220 Angle : 0.628 15.937 40098 Z= 0.320 Chirality : 0.044 0.181 4574 Planarity : 0.004 0.057 5165 Dihedral : 5.977 56.786 4202 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.79 % Allowed : 32.48 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3679 helix: -0.20 (0.29), residues: 332 sheet: -0.48 (0.14), residues: 1245 loop : -1.14 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 89 HIS 0.017 0.001 HIS C 130 PHE 0.050 0.002 PHE M 115 TYR 0.019 0.001 TYR C 237 ARG 0.005 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 627 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 25 outliers final: 20 residues processed: 646 average time/residue: 0.7524 time to fit residues: 762.5589 Evaluate side-chains 632 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 612 time to evaluate : 3.301 Switching outliers to nearest non-outliers 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 outliers start: 20 outliers final: 11 residues processed: 20 average time/residue: 0.6016 time to fit residues: 24.7345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 213 optimal weight: 0.9990 chunk 343 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 163 optimal weight: 0.0770 chunk 239 optimal weight: 2.9990 chunk 360 optimal weight: 7.9990 chunk 331 optimal weight: 0.7980 chunk 287 optimal weight: 9.9990 chunk 29 optimal weight: 0.0370 chunk 221 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 245 ASN ** O 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29392 Z= 0.190 Angle : 0.631 15.845 40098 Z= 0.320 Chirality : 0.045 0.185 4574 Planarity : 0.004 0.054 5165 Dihedral : 5.880 55.686 4202 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.66 % Allowed : 33.14 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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 (0.14), residues: 3679 helix: -0.20 (0.29), residues: 332 sheet: -0.30 (0.15), residues: 1133 loop : -1.07 (0.14), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 89 HIS 0.010 0.001 HIS C 130 PHE 0.046 0.002 PHE M 115 TYR 0.015 0.001 TYR C 15 ARG 0.009 0.000 ARG O 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 648 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 662 average time/residue: 0.7681 time to fit residues: 794.8356 Evaluate side-chains 652 residues out of total 3171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 634 time to evaluate : 3.299 Switching outliers to nearest non-outliers 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 outliers start: 18 outliers final: 11 residues processed: 18 average time/residue: 0.6079 time to fit residues: 22.7521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 228 optimal weight: 7.9990 chunk 305 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 264 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 287 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 295 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 GLN ** K 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.080566 restraints weight = 243606.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.084499 restraints weight = 91764.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.086833 restraints weight = 46477.381| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29392 Z= 0.196 Angle : 0.636 15.716 40098 Z= 0.322 Chirality : 0.045 0.259 4574 Planarity : 0.004 0.062 5165 Dihedral : 5.873 56.258 4202 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.88 % Allowed : 33.40 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -1.09 (0.14), residues: 3679 helix: -0.17 (0.29), residues: 332 sheet: -0.28 (0.15), residues: 1128 loop : -1.05 (0.13), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 89 HIS 0.009 0.001 HIS C 130 PHE 0.040 0.001 PHE M 115 TYR 0.017 0.001 TYR C 237 ARG 0.011 0.000 ARG K 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13445.79 seconds wall clock time: 233 minutes 29.94 seconds (14009.94 seconds total)