Starting phenix.real_space_refine on Sat Mar 16 02:32:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkf_9403/03_2024/5bkf_9403.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkf_9403/03_2024/5bkf_9403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkf_9403/03_2024/5bkf_9403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkf_9403/03_2024/5bkf_9403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkf_9403/03_2024/5bkf_9403.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bkf_9403/03_2024/5bkf_9403.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 8785 2.51 5 N 2125 2.21 5 O 2473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 19": "OD1" <-> "OD2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D ASP 22": "OD1" <-> "OD2" Residue "D TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 87": "OD1" <-> "OD2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 291": "OD1" <-> "OD2" Residue "D PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 104": "OD1" <-> "OD2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 133": "OD1" <-> "OD2" Residue "E PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E ASP 188": "OD1" <-> "OD2" Residue "E ASP 215": "OD1" <-> "OD2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13470 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2667 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2667 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 2661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2661 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2660 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "E" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2664 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 18, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 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: 7.37, per 1000 atoms: 0.55 Number of scatterers: 13470 At special positions: 0 Unit cell: (92.96, 91.3, 130.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2473 8.00 N 2125 7.00 C 8785 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 205 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " distance=2.02 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 45 " " NAG A 502 " - " ASN A 76 " " NAG B 501 " - " ASN B 45 " " NAG B 502 " - " ASN B 76 " " NAG C 501 " - " ASN C 45 " " NAG C 502 " - " ASN C 76 " " NAG D 501 " - " ASN D 45 " " NAG D 502 " - " ASN D 76 " " NAG E 501 " - " ASN E 220 " Time building additional restraints: 4.91 Conformation dependent library (CDL) restraints added in 2.3 seconds 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 21 sheets defined 38.4% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 16 through 25 Processing helix chain 'A' and resid 78 through 81 removed outlier: 3.505A pdb=" N ALA A 81 " --> pdb=" O SER A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 93 through 100 removed outlier: 3.953A pdb=" N ASP A 98 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 248 removed outlier: 5.007A pdb=" N ILE A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Proline residue: A 237 - end of helix Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.681A pdb=" N ARG A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 316 removed outlier: 3.551A pdb=" N ARG A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 416 Proline residue: A 400 - end of helix Processing helix chain 'B' and resid 16 through 25 Processing helix chain 'B' and resid 78 through 81 removed outlier: 3.747A pdb=" N ALA B 81 " --> pdb=" O SER B 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 78 through 81' Processing helix chain 'B' and resid 93 through 100 removed outlier: 4.061A pdb=" N ASP B 98 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 248 removed outlier: 5.173A pdb=" N ILE B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Proline residue: B 237 - end of helix Processing helix chain 'B' and resid 255 through 280 removed outlier: 3.813A pdb=" N ARG B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 316 Processing helix chain 'B' and resid 384 through 416 Proline residue: B 400 - end of helix Processing helix chain 'C' and resid 16 through 25 Processing helix chain 'C' and resid 93 through 100 removed outlier: 4.027A pdb=" N ASP C 98 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 100 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 248 removed outlier: 5.050A pdb=" N ILE C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Proline residue: C 237 - end of helix Processing helix chain 'C' and resid 255 through 280 Processing helix chain 'C' and resid 288 through 315 Processing helix chain 'C' and resid 384 through 414 Proline residue: C 400 - end of helix Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 26 through 30 removed outlier: 3.883A pdb=" N GLY D 30 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 81 Processing helix chain 'D' and resid 93 through 100 removed outlier: 4.186A pdb=" N ASP D 98 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 99 " --> pdb=" O MET D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 235 Processing helix chain 'D' and resid 235 through 248 Processing helix chain 'D' and resid 255 through 280 Processing helix chain 'D' and resid 288 through 316 removed outlier: 3.698A pdb=" N ARG D 316 " --> pdb=" O ASN D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 416 Proline residue: D 400 - end of helix removed outlier: 3.538A pdb=" N ILE D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 39 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'E' and resid 251 through 268 removed outlier: 3.732A pdb=" N THR E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 298 removed outlier: 3.921A pdb=" N GLY E 280 " --> pdb=" O ARG E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 333 removed outlier: 3.552A pdb=" N ASN E 333 " --> pdb=" O GLN E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 474 Proline residue: E 460 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 removed outlier: 4.047A pdb=" N PHE A 51 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 removed outlier: 4.047A pdb=" N PHE A 51 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N GLN A 184 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 50 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 59 removed outlier: 4.292A pdb=" N VAL A 58 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP A 64 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 112 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N SER A 144 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU A 110 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.664A pdb=" N GLU A 224 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 91 removed outlier: 6.785A pdb=" N ASP B 64 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL B 58 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 54 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE B 70 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 52 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG B 72 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE B 50 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLN B 74 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N CYS B 48 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ASN B 76 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL B 46 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 114 removed outlier: 6.178A pdb=" N GLU B 110 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER B 144 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY B 112 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP B 64 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL B 58 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 54 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE B 70 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 52 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG B 72 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE B 50 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLN B 74 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N CYS B 48 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ASN B 76 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL B 46 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N GLN B 184 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE B 50 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 106 through 107 removed outlier: 3.809A pdb=" N GLU B 224 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AB1, first strand: chain 'C' and resid 174 through 177 removed outlier: 6.498A pdb=" N ASN C 45 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASN C 76 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 51 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN C 68 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE C 55 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ARG C 66 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER C 57 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASP C 64 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY C 112 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N SER C 144 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLU C 110 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 59 Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AB4, first strand: chain 'C' and resid 106 through 107 removed outlier: 3.706A pdb=" N GLU C 224 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.607A pdb=" N LEU D 125 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP D 64 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 58 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER D 54 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N PHE D 70 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE D 52 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG D 72 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE D 50 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN D 74 " --> pdb=" O CYS D 48 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N CYS D 48 " --> pdb=" O GLN D 74 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ASN D 76 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL D 46 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL D 44 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLU D 176 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL D 46 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 110 through 114 removed outlier: 6.083A pdb=" N GLU D 110 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N SER D 144 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY D 112 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP D 64 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 58 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER D 54 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N PHE D 70 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE D 52 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG D 72 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE D 50 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN D 74 " --> pdb=" O CYS D 48 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N CYS D 48 " --> pdb=" O GLN D 74 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ASN D 76 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL D 46 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 106 through 107 removed outlier: 3.522A pdb=" N GLU D 201 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS D 222 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU D 199 " --> pdb=" O HIS D 222 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLU D 224 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LYS D 197 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 66 through 70 removed outlier: 6.488A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN E 130 " --> pdb=" O SER E 156 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER E 128 " --> pdb=" O THR E 158 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER E 160 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU E 126 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 105 through 107 removed outlier: 6.017A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 122 through 123 Processing sheet with id=AC3, first strand: chain 'E' and resid 224 through 225 removed outlier: 3.553A pdb=" N TYR E 225 " --> pdb=" O GLY E 229 " (cutoff:3.500A) 751 hydrogen bonds defined for protein. 2127 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: 3.99 Time building geometry restraints manager: 5.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4139 1.34 - 1.46: 3544 1.46 - 1.58: 5979 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 13804 Sorted by residual: bond pdb=" N TYR D 235 " pdb=" CA TYR D 235 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.27e-02 6.20e+03 6.70e+00 bond pdb=" N GLN C 157 " pdb=" CA GLN C 157 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.57e+00 bond pdb=" N TYR C 235 " pdb=" CA TYR C 235 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.30e-02 5.92e+03 6.30e+00 bond pdb=" N LYS D 213 " pdb=" CA LYS D 213 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.23e-02 6.61e+03 6.16e+00 bond pdb=" N THR D 211 " pdb=" CA THR D 211 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.72e+00 ... (remaining 13799 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.33: 391 106.33 - 113.26: 7537 113.26 - 120.19: 4767 120.19 - 127.11: 5942 127.11 - 134.04: 162 Bond angle restraints: 18799 Sorted by residual: angle pdb=" CA GLY D 212 " pdb=" C GLY D 212 " pdb=" O GLY D 212 " ideal model delta sigma weight residual 121.56 118.26 3.30 1.07e+00 8.73e-01 9.49e+00 angle pdb=" CA THR D 211 " pdb=" C THR D 211 " pdb=" O THR D 211 " ideal model delta sigma weight residual 120.82 117.67 3.15 1.05e+00 9.07e-01 9.02e+00 angle pdb=" N THR D 119 " pdb=" CA THR D 119 " pdb=" CB THR D 119 " ideal model delta sigma weight residual 114.17 110.87 3.30 1.14e+00 7.69e-01 8.37e+00 angle pdb=" N CYS E 221 " pdb=" CA CYS E 221 " pdb=" C CYS E 221 " ideal model delta sigma weight residual 114.56 111.05 3.51 1.27e+00 6.20e-01 7.66e+00 angle pdb=" N THR A 120 " pdb=" CA THR A 120 " pdb=" C THR A 120 " ideal model delta sigma weight residual 110.80 105.50 5.30 2.13e+00 2.20e-01 6.20e+00 ... (remaining 18794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.74: 7750 21.74 - 43.47: 455 43.47 - 65.21: 47 65.21 - 86.95: 14 86.95 - 108.69: 9 Dihedral angle restraints: 8275 sinusoidal: 3281 harmonic: 4994 Sorted by residual: dihedral pdb=" CB CYS E 221 " pdb=" SG CYS E 221 " pdb=" SG CYS E 233 " pdb=" CB CYS E 233 " ideal model delta sinusoidal sigma weight residual -86.00 -174.13 88.13 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 175 " pdb=" CB CYS E 175 " ideal model delta sinusoidal sigma weight residual 93.00 50.70 42.30 1 1.00e+01 1.00e-02 2.50e+01 dihedral pdb=" CB CYS D 145 " pdb=" SG CYS D 145 " pdb=" SG CYS D 159 " pdb=" CB CYS D 159 " ideal model delta sinusoidal sigma weight residual 93.00 52.89 40.11 1 1.00e+01 1.00e-02 2.26e+01 ... (remaining 8272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1616 0.039 - 0.079: 378 0.079 - 0.118: 172 0.118 - 0.157: 15 0.157 - 0.196: 6 Chirality restraints: 2187 Sorted by residual: chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 45 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 45 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 2184 not shown) Planarity restraints: 2347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 408 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C ILE A 408 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE A 408 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 409 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 408 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.10e+00 pdb=" C ILE C 408 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE C 408 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE C 409 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 156 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.15e+00 pdb=" C VAL C 156 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL C 156 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN C 157 " -0.008 2.00e-02 2.50e+03 ... (remaining 2344 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 165 2.59 - 3.17: 12413 3.17 - 3.75: 20340 3.75 - 4.32: 28593 4.32 - 4.90: 47968 Nonbonded interactions: 109479 Sorted by model distance: nonbonded pdb=" O VAL D 118 " pdb=" OG1 THR D 119 " model vdw 2.015 2.440 nonbonded pdb=" O VAL E 134 " pdb=" OG1 THR E 135 " model vdw 2.086 2.440 nonbonded pdb=" O VAL C 118 " pdb=" OG1 THR C 119 " model vdw 2.089 2.440 nonbonded pdb=" O VAL B 118 " pdb=" OG1 THR B 119 " model vdw 2.089 2.440 nonbonded pdb=" NH1 ARG E 50 " pdb=" O PRO E 51 " model vdw 2.161 2.520 ... (remaining 109474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 384 or (resid 385 through 390 and (name N or na \ me CA or name C or name O or name CB )) or resid 391 or (resid 392 through 398 a \ nd (name N or name CA or name C or name O or name CB )) or resid 399 through 418 \ or resid 501 through 503)) selection = (chain 'B' and (resid 15 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 through 384 or (resid 385 through 390 and \ (name N or name CA or name C or name O or name CB )) or resid 391 through 417 or \ (resid 418 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 1 through 503)) selection = (chain 'C' and (resid 15 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 through 392 or (resid 393 through 398 and \ (name N or name CA or name C or name O or name CB )) or resid 399 through 418 or \ resid 501 through 503)) selection = (chain 'D' and (resid 15 through 385 or (resid 386 through 390 and (name N or na \ me CA or name C or name O or name CB )) or resid 391 through 392 or (resid 393 t \ hrough 398 and (name N or name CA or name C or name O or name CB )) or resid 399 \ through 418 or resid 501 through 503)) } 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: 1.120 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: 0.010 Extract box with map and model: 4.400 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.290 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 0.047 13804 Z= 0.279 Angle : 0.541 5.881 18799 Z= 0.284 Chirality : 0.041 0.196 2187 Planarity : 0.003 0.031 2338 Dihedral : 14.141 108.685 5005 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.35 % Allowed : 1.87 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.18), residues: 1669 helix: -0.87 (0.19), residues: 578 sheet: -3.85 (0.20), residues: 394 loop : -2.73 (0.20), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 75 HIS 0.003 0.001 HIS D 116 PHE 0.009 0.001 PHE D 214 TYR 0.017 0.001 TYR C 308 ARG 0.003 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 271 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8228 (p0) cc_final: 0.8024 (p0) REVERT: A 218 GLU cc_start: 0.7432 (pt0) cc_final: 0.6485 (pt0) REVERT: A 286 TYR cc_start: 0.8294 (p90) cc_final: 0.8033 (p90) REVERT: B 232 ILE cc_start: 0.8081 (tp) cc_final: 0.7832 (mt) REVERT: C 23 LYS cc_start: 0.8446 (tttt) cc_final: 0.7869 (tptt) REVERT: D 250 TRP cc_start: 0.7389 (m100) cc_final: 0.7181 (m100) REVERT: E 90 ASN cc_start: 0.6879 (m-40) cc_final: 0.6568 (m-40) REVERT: E 300 LYS cc_start: 0.8249 (mttt) cc_final: 0.7999 (mttt) REVERT: E 329 GLN cc_start: 0.8325 (tp40) cc_final: 0.7986 (tp40) outliers start: 5 outliers final: 1 residues processed: 276 average time/residue: 0.2640 time to fit residues: 103.4764 Evaluate side-chains 190 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 220 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 9.9990 chunk 125 optimal weight: 0.0670 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 66 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 50 optimal weight: 0.0010 chunk 78 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 233 GLN A 273 GLN A 312 ASN B 73 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 122 ASN D 193 GLN E 63 ASN E 82 ASN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13804 Z= 0.199 Angle : 0.632 7.475 18799 Z= 0.317 Chirality : 0.045 0.187 2187 Planarity : 0.004 0.042 2338 Dihedral : 7.719 74.453 2005 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.87 % Allowed : 9.00 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1669 helix: 1.05 (0.21), residues: 563 sheet: -3.02 (0.24), residues: 338 loop : -2.13 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 177 HIS 0.004 0.001 HIS A 208 PHE 0.017 0.001 PHE C 51 TYR 0.022 0.002 TYR B 308 ARG 0.007 0.001 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: A 184 GLN cc_start: 0.7938 (mp10) cc_final: 0.7660 (mp10) REVERT: A 286 TYR cc_start: 0.8348 (p90) cc_final: 0.8105 (p90) REVERT: B 281 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7475 (tp) REVERT: C 23 LYS cc_start: 0.8422 (tttt) cc_final: 0.7903 (tptt) REVERT: D 250 TRP cc_start: 0.7483 (m100) cc_final: 0.7255 (m100) REVERT: E 56 ILE cc_start: 0.8531 (mp) cc_final: 0.8306 (mt) REVERT: E 90 ASN cc_start: 0.7070 (m-40) cc_final: 0.6796 (m-40) REVERT: E 190 ARG cc_start: 0.7066 (ttm110) cc_final: 0.6537 (mtt-85) REVERT: E 300 LYS cc_start: 0.8231 (mttt) cc_final: 0.7987 (mttt) REVERT: E 329 GLN cc_start: 0.8398 (tp40) cc_final: 0.7645 (tp40) outliers start: 27 outliers final: 14 residues processed: 209 average time/residue: 0.2401 time to fit residues: 74.9998 Evaluate side-chains 181 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 0.0370 chunk 162 optimal weight: 5.9990 chunk 133 optimal weight: 0.0020 chunk 148 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.2072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN D 157 GLN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13804 Z= 0.202 Angle : 0.598 7.560 18799 Z= 0.298 Chirality : 0.044 0.239 2187 Planarity : 0.004 0.043 2338 Dihedral : 6.566 71.484 2003 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.29 % Allowed : 11.01 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1669 helix: 1.59 (0.22), residues: 563 sheet: -2.52 (0.25), residues: 357 loop : -1.84 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.002 0.001 HIS A 208 PHE 0.016 0.001 PHE C 406 TYR 0.020 0.001 TYR B 308 ARG 0.004 0.000 ARG E 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8285 (mttm) REVERT: A 286 TYR cc_start: 0.8401 (p90) cc_final: 0.8141 (p90) REVERT: B 270 MET cc_start: 0.8713 (tpp) cc_final: 0.8447 (tpp) REVERT: C 23 LYS cc_start: 0.8513 (tttt) cc_final: 0.7914 (tptt) REVERT: E 90 ASN cc_start: 0.7237 (m-40) cc_final: 0.6984 (m-40) REVERT: E 190 ARG cc_start: 0.7082 (ttm110) cc_final: 0.6535 (mtt180) REVERT: E 247 TYR cc_start: 0.7892 (m-80) cc_final: 0.7668 (m-80) REVERT: E 300 LYS cc_start: 0.8236 (mttt) cc_final: 0.8006 (mttt) REVERT: E 329 GLN cc_start: 0.8426 (tp40) cc_final: 0.7657 (tp40) outliers start: 33 outliers final: 22 residues processed: 220 average time/residue: 0.2370 time to fit residues: 77.1935 Evaluate side-chains 196 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 150 optimal weight: 0.0980 chunk 159 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 312 ASN B 208 HIS ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13804 Z= 0.190 Angle : 0.586 7.071 18799 Z= 0.291 Chirality : 0.044 0.223 2187 Planarity : 0.004 0.041 2338 Dihedral : 6.212 75.920 2003 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.94 % Allowed : 14.13 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1669 helix: 1.84 (0.22), residues: 563 sheet: -2.19 (0.26), residues: 362 loop : -1.62 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 250 HIS 0.008 0.001 HIS B 208 PHE 0.016 0.001 PHE C 406 TYR 0.019 0.001 TYR B 308 ARG 0.007 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8305 (mttm) REVERT: A 286 TYR cc_start: 0.8438 (p90) cc_final: 0.8180 (p90) REVERT: A 312 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8129 (t0) REVERT: C 23 LYS cc_start: 0.8514 (tttt) cc_final: 0.7982 (tptt) REVERT: C 96 MET cc_start: 0.5962 (tpp) cc_final: 0.5598 (tpp) REVERT: E 300 LYS cc_start: 0.8250 (mttt) cc_final: 0.8027 (mttt) outliers start: 28 outliers final: 19 residues processed: 204 average time/residue: 0.2170 time to fit residues: 67.3933 Evaluate side-chains 189 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 2 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 312 ASN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13804 Z= 0.219 Angle : 0.586 7.024 18799 Z= 0.292 Chirality : 0.043 0.237 2187 Planarity : 0.004 0.040 2338 Dihedral : 6.155 75.920 2003 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.84 % Allowed : 14.82 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1669 helix: 1.91 (0.22), residues: 563 sheet: -2.01 (0.25), residues: 402 loop : -1.40 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 177 HIS 0.002 0.001 HIS A 208 PHE 0.016 0.001 PHE C 406 TYR 0.037 0.001 TYR E 325 ARG 0.007 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 193 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 SER cc_start: 0.7320 (m) cc_final: 0.7073 (p) REVERT: A 220 LYS cc_start: 0.8553 (mtpp) cc_final: 0.8333 (mttm) REVERT: A 286 TYR cc_start: 0.8498 (p90) cc_final: 0.8249 (p90) REVERT: C 23 LYS cc_start: 0.8501 (tttt) cc_final: 0.7967 (tptt) REVERT: D 114 ASN cc_start: 0.8509 (p0) cc_final: 0.8247 (p0) REVERT: E 300 LYS cc_start: 0.8260 (mttt) cc_final: 0.7972 (mttt) REVERT: E 329 GLN cc_start: 0.8656 (tp40) cc_final: 0.7574 (tp40) outliers start: 41 outliers final: 29 residues processed: 218 average time/residue: 0.2208 time to fit residues: 73.0520 Evaluate side-chains 210 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 159 optimal weight: 0.0370 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 312 ASN B 208 HIS ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13804 Z= 0.225 Angle : 0.590 6.935 18799 Z= 0.295 Chirality : 0.043 0.257 2187 Planarity : 0.004 0.039 2338 Dihedral : 6.152 78.663 2003 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.98 % Allowed : 16.34 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1669 helix: 2.02 (0.22), residues: 559 sheet: -1.94 (0.25), residues: 402 loop : -1.34 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 177 HIS 0.009 0.001 HIS B 208 PHE 0.016 0.001 PHE D 313 TYR 0.030 0.002 TYR D 308 ARG 0.007 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 199 time to evaluate : 1.565 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8328 (mttm) REVERT: A 286 TYR cc_start: 0.8527 (p90) cc_final: 0.8279 (p90) REVERT: C 23 LYS cc_start: 0.8532 (tttt) cc_final: 0.7980 (tptt) REVERT: D 114 ASN cc_start: 0.8503 (p0) cc_final: 0.8206 (p0) REVERT: E 300 LYS cc_start: 0.8288 (mttt) cc_final: 0.7961 (mttt) outliers start: 43 outliers final: 30 residues processed: 224 average time/residue: 0.2198 time to fit residues: 75.1890 Evaluate side-chains 214 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 208 HIS ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN E 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13804 Z= 0.203 Angle : 0.582 7.008 18799 Z= 0.291 Chirality : 0.043 0.261 2187 Planarity : 0.004 0.038 2338 Dihedral : 6.072 78.500 2003 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.32 % Allowed : 17.38 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1669 helix: 2.02 (0.22), residues: 559 sheet: -1.81 (0.25), residues: 401 loop : -1.29 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 177 HIS 0.008 0.001 HIS B 208 PHE 0.017 0.001 PHE C 406 TYR 0.032 0.001 TYR D 308 ARG 0.008 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 196 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8565 (mtpp) cc_final: 0.8336 (mttm) REVERT: A 226 GLN cc_start: 0.7964 (pt0) cc_final: 0.7721 (pt0) REVERT: A 286 TYR cc_start: 0.8516 (p90) cc_final: 0.8281 (p90) REVERT: B 151 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.8069 (p0) REVERT: C 23 LYS cc_start: 0.8527 (tttt) cc_final: 0.7987 (tptt) REVERT: D 114 ASN cc_start: 0.8508 (p0) cc_final: 0.8185 (p0) REVERT: D 313 PHE cc_start: 0.7659 (t80) cc_final: 0.7238 (t80) REVERT: E 249 MET cc_start: 0.8044 (tmm) cc_final: 0.7804 (ttp) REVERT: E 300 LYS cc_start: 0.8298 (mttt) cc_final: 0.7979 (mttt) outliers start: 48 outliers final: 32 residues processed: 226 average time/residue: 0.2135 time to fit residues: 73.8345 Evaluate side-chains 215 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.1980 chunk 94 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13804 Z= 0.184 Angle : 0.589 9.464 18799 Z= 0.293 Chirality : 0.043 0.263 2187 Planarity : 0.004 0.038 2338 Dihedral : 6.023 79.389 2003 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.63 % Allowed : 18.84 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1669 helix: 2.07 (0.22), residues: 559 sheet: -1.71 (0.25), residues: 397 loop : -1.25 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 250 HIS 0.002 0.001 HIS C 208 PHE 0.023 0.001 PHE C 106 TYR 0.030 0.001 TYR D 308 ARG 0.009 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 197 time to evaluate : 1.591 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8343 (mttm) REVERT: A 270 MET cc_start: 0.7769 (tpp) cc_final: 0.7350 (mpp) REVERT: A 286 TYR cc_start: 0.8506 (p90) cc_final: 0.8260 (p90) REVERT: B 120 THR cc_start: 0.8751 (t) cc_final: 0.8423 (m) REVERT: B 151 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.8042 (p0) REVERT: C 23 LYS cc_start: 0.8523 (tttt) cc_final: 0.7977 (tptt) REVERT: D 114 ASN cc_start: 0.8477 (p0) cc_final: 0.8160 (p0) REVERT: D 313 PHE cc_start: 0.7656 (t80) cc_final: 0.7264 (t80) REVERT: E 249 MET cc_start: 0.8094 (tmm) cc_final: 0.7834 (tmm) REVERT: E 300 LYS cc_start: 0.8307 (mttt) cc_final: 0.7984 (mttt) REVERT: E 329 GLN cc_start: 0.8418 (tp40) cc_final: 0.8131 (tp40) outliers start: 38 outliers final: 33 residues processed: 219 average time/residue: 0.2251 time to fit residues: 74.4383 Evaluate side-chains 218 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 89 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 0.0070 chunk 45 optimal weight: 6.9990 chunk 133 optimal weight: 0.0870 chunk 140 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN E 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13804 Z= 0.157 Angle : 0.586 9.114 18799 Z= 0.289 Chirality : 0.042 0.266 2187 Planarity : 0.004 0.045 2338 Dihedral : 5.905 78.444 2003 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.49 % Allowed : 19.74 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1669 helix: 2.19 (0.22), residues: 559 sheet: -1.52 (0.26), residues: 401 loop : -1.17 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 250 HIS 0.002 0.001 HIS C 208 PHE 0.022 0.001 PHE C 106 TYR 0.029 0.001 TYR D 308 ARG 0.014 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 213 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 270 MET cc_start: 0.7735 (tpp) cc_final: 0.7387 (mpp) REVERT: A 286 TYR cc_start: 0.8488 (p90) cc_final: 0.8239 (p90) REVERT: B 120 THR cc_start: 0.8543 (t) cc_final: 0.8225 (m) REVERT: B 151 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7991 (p0) REVERT: C 19 ASP cc_start: 0.6757 (OUTLIER) cc_final: 0.6417 (t0) REVERT: C 23 LYS cc_start: 0.8515 (tttt) cc_final: 0.8008 (tptt) REVERT: D 114 ASN cc_start: 0.8410 (p0) cc_final: 0.8202 (p0) REVERT: D 313 PHE cc_start: 0.7632 (t80) cc_final: 0.7257 (t80) REVERT: E 192 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8065 (mt) REVERT: E 249 MET cc_start: 0.8188 (tmm) cc_final: 0.7946 (tmm) REVERT: E 300 LYS cc_start: 0.8296 (mttt) cc_final: 0.8021 (mttt) outliers start: 36 outliers final: 29 residues processed: 235 average time/residue: 0.2280 time to fit residues: 80.0705 Evaluate side-chains 227 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 298 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.0980 chunk 95 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN E 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13804 Z= 0.179 Angle : 0.599 8.671 18799 Z= 0.298 Chirality : 0.043 0.270 2187 Planarity : 0.004 0.040 2338 Dihedral : 5.880 79.095 2003 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.42 % Allowed : 19.74 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1669 helix: 2.19 (0.22), residues: 559 sheet: -1.50 (0.25), residues: 401 loop : -1.12 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 250 HIS 0.003 0.001 HIS C 208 PHE 0.021 0.001 PHE C 106 TYR 0.028 0.001 TYR D 308 ARG 0.007 0.000 ARG A 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 198 time to evaluate : 1.624 Fit side-chains revert: symmetry clash REVERT: A 68 ASN cc_start: 0.8043 (t0) cc_final: 0.7706 (t0) REVERT: A 270 MET cc_start: 0.7770 (tpp) cc_final: 0.7447 (mpp) REVERT: A 286 TYR cc_start: 0.8520 (p90) cc_final: 0.8250 (p90) REVERT: B 120 THR cc_start: 0.8550 (t) cc_final: 0.8246 (m) REVERT: C 19 ASP cc_start: 0.6748 (t70) cc_final: 0.6403 (t0) REVERT: C 23 LYS cc_start: 0.8543 (tttt) cc_final: 0.7994 (tptt) REVERT: D 114 ASN cc_start: 0.8419 (p0) cc_final: 0.8133 (p0) REVERT: D 313 PHE cc_start: 0.7634 (t80) cc_final: 0.7215 (t80) REVERT: E 114 LYS cc_start: 0.8568 (pttt) cc_final: 0.8336 (mmtt) REVERT: E 192 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8039 (mt) REVERT: E 249 MET cc_start: 0.8244 (tmm) cc_final: 0.8019 (tmm) REVERT: E 300 LYS cc_start: 0.8318 (mttt) cc_final: 0.8055 (mttt) outliers start: 35 outliers final: 30 residues processed: 219 average time/residue: 0.2220 time to fit residues: 73.8788 Evaluate side-chains 223 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 192 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 409 PHE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0670 chunk 40 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN E 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.154443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137573 restraints weight = 19302.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141219 restraints weight = 9859.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143571 restraints weight = 6183.076| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13804 Z= 0.203 Angle : 0.608 8.337 18799 Z= 0.303 Chirality : 0.043 0.274 2187 Planarity : 0.004 0.036 2338 Dihedral : 5.952 79.728 2003 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.56 % Allowed : 19.81 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1669 helix: 2.14 (0.22), residues: 563 sheet: -1.53 (0.25), residues: 405 loop : -1.11 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 177 HIS 0.002 0.001 HIS C 208 PHE 0.021 0.001 PHE C 106 TYR 0.027 0.001 TYR D 308 ARG 0.006 0.000 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2600.42 seconds wall clock time: 49 minutes 49.91 seconds (2989.91 seconds total)