Starting phenix.real_space_refine on Tue Apr 9 07:19:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/04_2024/7xda_33140.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/04_2024/7xda_33140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/04_2024/7xda_33140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/04_2024/7xda_33140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/04_2024/7xda_33140.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/04_2024/7xda_33140.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 5110 2.51 5 N 1365 2.21 5 O 1579 1.98 5 H 7646 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 1": "OE1" <-> "OE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 91": "OD1" <-> "OD2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 122": "OD1" <-> "OD2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "E ASP 151": "OD1" <-> "OD2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15729 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3154 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3138 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2996 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3265 Classifications: {'peptide': 227} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 212} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3176 Classifications: {'peptide': 214} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 7.17, per 1000 atoms: 0.46 Number of scatterers: 15729 At special positions: 0 Unit cell: (133.98, 115.5, 129.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 1579 8.00 N 1365 7.00 C 5110 6.00 H 7646 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 141 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 414 " distance=2.03 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 470 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.51 Conformation dependent library (CDL) restraints added in 1.8 seconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 26 sheets defined 7.7% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.518A pdb=" N ASP B 89 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 90 " --> pdb=" O ALA B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 90' Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 122 through 130 removed outlier: 3.754A pdb=" N THR C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.850A pdb=" N PHE A 324 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 removed outlier: 4.004A pdb=" N TRP A 335 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.551A pdb=" N TYR A 351 " --> pdb=" O TYR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.648A pdb=" N TYR A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 399 through 404' Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.565A pdb=" N SER A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.636A pdb=" N THR D 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 198 removed outlier: 4.135A pdb=" N GLY D 198 " --> pdb=" O SER D 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 195 through 198' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.514A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 removed outlier: 3.556A pdb=" N LEU E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 8 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.777A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER B 40 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU B 45 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 121 through 125 removed outlier: 5.994A pdb=" N TYR B 177 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 125 removed outlier: 5.994A pdb=" N TYR B 177 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 155 removed outlier: 3.848A pdb=" N LYS B 210 " --> pdb=" O CYS B 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.646A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C 98 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.646A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.026A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 145 through 150 Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AB4, first strand: chain 'A' and resid 343 through 344 removed outlier: 6.327A pdb=" N CYS A 343 " --> pdb=" O CYS A 507 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 434 through 436 Processing sheet with id=AB6, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.465A pdb=" N GLU D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE D 35 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE D 51 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.465A pdb=" N GLU D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU D 110 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.076A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.076A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AC4, first strand: chain 'E' and resid 4 through 7 removed outlier: 5.887A pdb=" N THR E 69 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N GLN E 27 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N SER E 67 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 11.555A pdb=" N ILE E 29 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N SER E 65 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.703A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 116 through 118 Processing sheet with id=AC8, first strand: chain 'E' and resid 144 through 150 336 hydrogen bonds defined for protein. 831 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: 6.29 Time building geometry restraints manager: 12.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7646 1.03 - 1.23: 231 1.23 - 1.43: 3377 1.43 - 1.63: 4648 1.63 - 1.83: 33 Bond restraints: 15935 Sorted by residual: bond pdb=" N ASN A 316 " pdb=" H1 ASN A 316 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N GLU B 1 " pdb=" H2 GLU B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N GLU D 1 " pdb=" H3 GLU D 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N ASP E 1 " pdb=" H2 ASP E 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N GLU B 1 " pdb=" H3 GLU B 1 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 15930 not shown) Histogram of bond angle deviations from ideal: 4.61 - 30.51: 4 30.51 - 56.40: 0 56.40 - 82.30: 0 82.30 - 108.19: 3150 108.19 - 134.09: 25511 Bond angle restraints: 28665 Sorted by residual: angle pdb=" H1 GLU B 1 " pdb=" N GLU B 1 " pdb=" H2 GLU B 1 " ideal model delta sigma weight residual 109.47 4.61 104.86 3.00e+00 1.11e-01 1.22e+03 angle pdb=" H1 ASP E 1 " pdb=" N ASP E 1 " pdb=" H2 ASP E 1 " ideal model delta sigma weight residual 109.47 5.86 103.61 3.00e+00 1.11e-01 1.19e+03 angle pdb=" H1 GLU C 1 " pdb=" N GLU C 1 " pdb=" H2 GLU C 1 " ideal model delta sigma weight residual 109.47 6.75 102.72 3.00e+00 1.11e-01 1.17e+03 angle pdb=" H1 GLU D 1 " pdb=" N GLU D 1 " pdb=" H3 GLU D 1 " ideal model delta sigma weight residual 109.47 25.94 83.53 3.00e+00 1.11e-01 7.75e+02 angle pdb=" H1 GLU D 1 " pdb=" N GLU D 1 " pdb=" H2 GLU D 1 " ideal model delta sigma weight residual 109.47 84.18 25.29 3.00e+00 1.11e-01 7.11e+01 ... (remaining 28660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6792 17.99 - 35.97: 631 35.97 - 53.96: 240 53.96 - 71.94: 51 71.94 - 89.93: 13 Dihedral angle restraints: 7727 sinusoidal: 4040 harmonic: 3687 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 41.74 51.26 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CA SER C 30 " pdb=" C SER C 30 " pdb=" N SER C 31 " pdb=" CA SER C 31 " ideal model delta harmonic sigma weight residual -180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 97 " pdb=" CB CYS D 97 " ideal model delta sinusoidal sigma weight residual 93.00 56.81 36.19 1 1.00e+01 1.00e-02 1.85e+01 ... (remaining 7724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 679 0.028 - 0.057: 380 0.057 - 0.085: 70 0.085 - 0.114: 80 0.114 - 0.142: 25 Chirality restraints: 1234 Sorted by residual: chirality pdb=" CA ILE E 106 " pdb=" N ILE E 106 " pdb=" C ILE E 106 " pdb=" CB ILE E 106 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE E 21 " pdb=" N ILE E 21 " pdb=" C ILE E 21 " pdb=" CB ILE E 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA VAL A 383 " pdb=" N VAL A 383 " pdb=" C VAL A 383 " pdb=" CB VAL A 383 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1231 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 132 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C LEU D 132 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU D 132 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA D 133 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 156 " -0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO D 157 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 157 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 157 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 149 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO B 150 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " -0.016 5.00e-02 4.00e+02 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 893 2.18 - 2.79: 30589 2.79 - 3.39: 38015 3.39 - 4.00: 54540 4.00 - 4.60: 83451 Nonbonded interactions: 207488 Sorted by model distance: nonbonded pdb=" HG SER A 420 " pdb=" OD2 ASP A 424 " model vdw 1.577 1.850 nonbonded pdb=" HH TYR E 36 " pdb=" OE1 GLN E 89 " model vdw 1.611 1.850 nonbonded pdb=" O HIS C 190 " pdb=" HE ARG C 212 " model vdw 1.635 1.850 nonbonded pdb=" HZ2 LYS A 440 " pdb=" O GLN A 456 " model vdw 1.635 1.850 nonbonded pdb=" HG SER B 131 " pdb=" O ILE C 118 " model vdw 1.649 1.850 ... (remaining 207483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.350 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: 0.250 Extract box with map and model: 28.030 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 51.600 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.005 0.051 8289 Z= 0.312 Angle : 0.543 4.209 11283 Z= 0.296 Chirality : 0.043 0.142 1234 Planarity : 0.003 0.036 1458 Dihedral : 16.341 89.930 2922 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.59 % Rotamer: Outliers : 1.85 % Allowed : 24.07 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -3.63 (0.22), residues: 1061 helix: -4.52 (0.30), residues: 55 sheet: -1.20 (0.22), residues: 472 loop : -3.40 (0.20), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 84 HIS 0.003 0.001 HIS D 100 PHE 0.011 0.001 PHE B 78 TYR 0.018 0.001 TYR E 91 ARG 0.001 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.7989 (tt0) cc_final: 0.7720 (tt0) REVERT: B 200 ASN cc_start: 0.6195 (t0) cc_final: 0.5929 (p0) REVERT: B 209 ASP cc_start: 0.7886 (m-30) cc_final: 0.7624 (m-30) REVERT: A 450 ILE cc_start: 0.8629 (pt) cc_final: 0.8127 (mm) REVERT: D 163 ASN cc_start: 0.6396 (t0) cc_final: 0.5824 (t0) REVERT: E 161 GLU cc_start: 0.6892 (pm20) cc_final: 0.6666 (pm20) outliers start: 16 outliers final: 7 residues processed: 147 average time/residue: 2.0665 time to fit residues: 326.8273 Evaluate side-chains 102 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 214 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 58 ASN C 161 GLN A 370 ASN E 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8289 Z= 0.183 Angle : 0.521 5.819 11283 Z= 0.269 Chirality : 0.044 0.195 1234 Planarity : 0.004 0.059 1458 Dihedral : 4.984 30.307 1164 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 1.85 % Allowed : 27.20 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.23), residues: 1061 helix: -3.91 (0.42), residues: 54 sheet: -0.59 (0.23), residues: 471 loop : -2.61 (0.22), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 111 HIS 0.003 0.001 HIS B 53 PHE 0.010 0.001 PHE B 78 TYR 0.015 0.001 TYR E 91 ARG 0.005 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.7994 (tt0) cc_final: 0.7779 (tt0) REVERT: B 209 ASP cc_start: 0.7973 (m-30) cc_final: 0.7592 (m-30) REVERT: C 79 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8065 (mp) REVERT: C 193 TYR cc_start: 0.6530 (m-80) cc_final: 0.5969 (m-80) REVERT: A 450 ILE cc_start: 0.8730 (pt) cc_final: 0.8246 (mm) REVERT: D 163 ASN cc_start: 0.6414 (t0) cc_final: 0.5854 (t0) REVERT: D 207 ASN cc_start: 0.6429 (t0) cc_final: 0.6153 (t0) REVERT: E 161 GLU cc_start: 0.6876 (pm20) cc_final: 0.6664 (pm20) outliers start: 16 outliers final: 8 residues processed: 116 average time/residue: 1.9194 time to fit residues: 241.7591 Evaluate side-chains 102 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 1 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN C 161 GLN E 138 ASN E 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 8289 Z= 0.401 Angle : 0.603 5.748 11283 Z= 0.317 Chirality : 0.047 0.187 1234 Planarity : 0.004 0.037 1458 Dihedral : 5.326 38.172 1158 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.22 % Favored : 93.69 % Rotamer: Outliers : 3.36 % Allowed : 26.16 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.24), residues: 1061 helix: -3.74 (0.46), residues: 56 sheet: -0.34 (0.23), residues: 476 loop : -2.26 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 48 HIS 0.005 0.001 HIS D 100 PHE 0.015 0.002 PHE E 139 TYR 0.024 0.002 TYR E 91 ARG 0.003 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8058 (tt0) cc_final: 0.7805 (tt0) REVERT: B 209 ASP cc_start: 0.7955 (m-30) cc_final: 0.7656 (m-30) REVERT: C 79 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8114 (mp) REVERT: A 450 ILE cc_start: 0.8848 (pt) cc_final: 0.8402 (mm) REVERT: D 163 ASN cc_start: 0.6423 (t0) cc_final: 0.5872 (t0) REVERT: E 137 ASN cc_start: 0.7976 (m-40) cc_final: 0.7725 (m-40) REVERT: E 161 GLU cc_start: 0.7049 (pm20) cc_final: 0.6802 (pm20) outliers start: 29 outliers final: 19 residues processed: 124 average time/residue: 2.1179 time to fit residues: 282.5729 Evaluate side-chains 107 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 139 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8289 Z= 0.241 Angle : 0.544 7.235 11283 Z= 0.285 Chirality : 0.044 0.185 1234 Planarity : 0.004 0.034 1458 Dihedral : 5.137 38.481 1158 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 3.01 % Allowed : 26.85 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -1.76 (0.25), residues: 1061 helix: -3.50 (0.52), residues: 50 sheet: -0.12 (0.24), residues: 477 loop : -1.95 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 48 HIS 0.003 0.001 HIS B 53 PHE 0.077 0.002 PHE E 139 TYR 0.020 0.001 TYR E 173 ARG 0.004 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8040 (tt0) cc_final: 0.7780 (tt0) REVERT: B 209 ASP cc_start: 0.7985 (m-30) cc_final: 0.7624 (m-30) REVERT: C 18 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7363 (ptm160) REVERT: C 193 TYR cc_start: 0.6501 (m-80) cc_final: 0.6034 (m-80) REVERT: A 450 ILE cc_start: 0.8875 (pt) cc_final: 0.8417 (mm) REVERT: D 113 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6940 (mtm180) REVERT: D 163 ASN cc_start: 0.6384 (t0) cc_final: 0.5834 (t0) REVERT: D 214 LYS cc_start: 0.7525 (mtpt) cc_final: 0.6664 (tmtm) REVERT: E 161 GLU cc_start: 0.7050 (pm20) cc_final: 0.6794 (pm20) outliers start: 26 outliers final: 20 residues processed: 118 average time/residue: 2.0006 time to fit residues: 254.7392 Evaluate side-chains 110 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 139 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN E 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8289 Z= 0.218 Angle : 0.515 5.536 11283 Z= 0.268 Chirality : 0.044 0.187 1234 Planarity : 0.004 0.053 1458 Dihedral : 4.965 39.998 1158 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.25 % Rotamer: Outliers : 3.36 % Allowed : 27.08 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -1.45 (0.25), residues: 1061 helix: -3.43 (0.52), residues: 50 sheet: 0.09 (0.24), residues: 469 loop : -1.71 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 84 HIS 0.002 0.001 HIS B 53 PHE 0.038 0.001 PHE E 139 TYR 0.017 0.001 TYR E 91 ARG 0.009 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8036 (tt0) cc_final: 0.7786 (tt0) REVERT: B 209 ASP cc_start: 0.7978 (m-30) cc_final: 0.7555 (m-30) REVERT: C 18 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7307 (ptm160) REVERT: C 193 TYR cc_start: 0.6506 (m-80) cc_final: 0.6069 (m-80) REVERT: A 450 ILE cc_start: 0.8894 (pt) cc_final: 0.8437 (mm) REVERT: D 113 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6890 (mtm180) REVERT: D 163 ASN cc_start: 0.6431 (t0) cc_final: 0.5868 (t0) REVERT: D 214 LYS cc_start: 0.7474 (mtpt) cc_final: 0.6653 (tmtm) REVERT: E 161 GLU cc_start: 0.7072 (pm20) cc_final: 0.6823 (pm20) outliers start: 29 outliers final: 21 residues processed: 117 average time/residue: 1.9026 time to fit residues: 241.6909 Evaluate side-chains 111 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 139 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 84 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8289 Z= 0.188 Angle : 0.493 5.458 11283 Z= 0.256 Chirality : 0.044 0.183 1234 Planarity : 0.004 0.056 1458 Dihedral : 4.743 41.116 1158 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.00 % Rotamer: Outliers : 3.47 % Allowed : 26.62 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -1.18 (0.25), residues: 1061 helix: -3.35 (0.54), residues: 50 sheet: 0.24 (0.24), residues: 469 loop : -1.48 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 84 HIS 0.002 0.001 HIS D 100 PHE 0.015 0.001 PHE E 139 TYR 0.015 0.001 TYR E 91 ARG 0.007 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8027 (tt0) cc_final: 0.7751 (tt0) REVERT: B 209 ASP cc_start: 0.7993 (m-30) cc_final: 0.7546 (m-30) REVERT: C 18 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7336 (ptm160) REVERT: C 193 TYR cc_start: 0.6437 (m-80) cc_final: 0.6076 (m-80) REVERT: A 450 ILE cc_start: 0.8890 (pt) cc_final: 0.8430 (mm) REVERT: D 113 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6941 (mtm180) REVERT: D 163 ASN cc_start: 0.6425 (t0) cc_final: 0.5866 (t0) REVERT: D 214 LYS cc_start: 0.7521 (mtpt) cc_final: 0.6710 (tmtm) REVERT: E 161 GLU cc_start: 0.7113 (pm20) cc_final: 0.6889 (pm20) outliers start: 30 outliers final: 24 residues processed: 122 average time/residue: 2.0058 time to fit residues: 264.2526 Evaluate side-chains 117 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN E 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8289 Z= 0.219 Angle : 0.507 5.279 11283 Z= 0.263 Chirality : 0.044 0.181 1234 Planarity : 0.004 0.059 1458 Dihedral : 4.816 42.659 1158 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 3.24 % Allowed : 26.97 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -1.03 (0.25), residues: 1061 helix: -3.31 (0.54), residues: 50 sheet: 0.39 (0.24), residues: 466 loop : -1.41 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 48 HIS 0.003 0.001 HIS D 100 PHE 0.009 0.001 PHE B 78 TYR 0.017 0.001 TYR E 91 ARG 0.012 0.001 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8044 (tt0) cc_final: 0.7747 (tt0) REVERT: B 209 ASP cc_start: 0.7975 (m-30) cc_final: 0.7594 (m-30) REVERT: A 450 ILE cc_start: 0.8904 (pt) cc_final: 0.8441 (mm) REVERT: D 113 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6878 (mtm180) REVERT: D 163 ASN cc_start: 0.6343 (t0) cc_final: 0.5792 (t0) REVERT: D 214 LYS cc_start: 0.7545 (mtpt) cc_final: 0.6729 (tmtm) outliers start: 28 outliers final: 25 residues processed: 118 average time/residue: 2.0324 time to fit residues: 259.1841 Evaluate side-chains 114 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8289 Z= 0.197 Angle : 0.498 5.352 11283 Z= 0.257 Chirality : 0.044 0.181 1234 Planarity : 0.004 0.063 1458 Dihedral : 4.753 43.238 1158 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 3.94 % Allowed : 26.27 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1061 helix: -3.28 (0.54), residues: 50 sheet: 0.48 (0.24), residues: 468 loop : -1.32 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 48 HIS 0.002 0.001 HIS D 100 PHE 0.014 0.001 PHE E 139 TYR 0.016 0.001 TYR E 91 ARG 0.011 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 92 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8027 (tt0) cc_final: 0.7752 (tt0) REVERT: B 209 ASP cc_start: 0.8029 (m-30) cc_final: 0.7636 (m-30) REVERT: A 450 ILE cc_start: 0.8905 (pt) cc_final: 0.8434 (mm) REVERT: D 113 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6848 (mtm180) REVERT: D 163 ASN cc_start: 0.6400 (t0) cc_final: 0.5851 (t0) REVERT: D 214 LYS cc_start: 0.7558 (mtpt) cc_final: 0.6747 (tmtm) REVERT: E 78 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6804 (mp) outliers start: 34 outliers final: 26 residues processed: 120 average time/residue: 1.9635 time to fit residues: 255.3306 Evaluate side-chains 119 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN E 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8289 Z= 0.162 Angle : 0.489 5.226 11283 Z= 0.252 Chirality : 0.043 0.177 1234 Planarity : 0.004 0.064 1458 Dihedral : 4.623 43.030 1158 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 3.01 % Allowed : 27.55 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -0.76 (0.26), residues: 1061 helix: -3.22 (0.54), residues: 50 sheet: 0.58 (0.24), residues: 468 loop : -1.23 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 84 HIS 0.002 0.001 HIS D 100 PHE 0.009 0.001 PHE B 78 TYR 0.014 0.001 TYR E 91 ARG 0.013 0.001 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8017 (tt0) cc_final: 0.7746 (tt0) REVERT: B 209 ASP cc_start: 0.7965 (m-30) cc_final: 0.7477 (m-30) REVERT: C 14 SER cc_start: 0.7967 (OUTLIER) cc_final: 0.7667 (t) REVERT: C 193 TYR cc_start: 0.6354 (m-80) cc_final: 0.6005 (m-80) REVERT: A 450 ILE cc_start: 0.8903 (pt) cc_final: 0.8432 (mm) REVERT: D 113 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6721 (mtm110) REVERT: D 163 ASN cc_start: 0.6392 (t0) cc_final: 0.5850 (t0) REVERT: D 214 LYS cc_start: 0.7566 (mtpt) cc_final: 0.6748 (tmtm) REVERT: E 137 ASN cc_start: 0.7971 (m110) cc_final: 0.6981 (p0) outliers start: 26 outliers final: 21 residues processed: 118 average time/residue: 1.9495 time to fit residues: 249.2627 Evaluate side-chains 114 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8289 Z= 0.286 Angle : 0.535 5.344 11283 Z= 0.277 Chirality : 0.045 0.183 1234 Planarity : 0.005 0.068 1458 Dihedral : 4.925 45.806 1158 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.25 % Rotamer: Outliers : 2.89 % Allowed : 27.66 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -0.77 (0.26), residues: 1061 helix: -3.26 (0.54), residues: 50 sheet: 0.57 (0.24), residues: 468 loop : -1.24 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 48 HIS 0.003 0.001 HIS D 100 PHE 0.011 0.001 PHE E 139 TYR 0.020 0.001 TYR E 91 ARG 0.014 0.001 ARG C 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8044 (tt0) cc_final: 0.7793 (tt0) REVERT: B 209 ASP cc_start: 0.7976 (m-30) cc_final: 0.7575 (m-30) REVERT: C 193 TYR cc_start: 0.6409 (m-80) cc_final: 0.5974 (m-80) REVERT: A 450 ILE cc_start: 0.8924 (pt) cc_final: 0.8438 (mm) REVERT: D 113 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6725 (mtm110) REVERT: D 163 ASN cc_start: 0.6447 (t0) cc_final: 0.5906 (t0) REVERT: D 214 LYS cc_start: 0.7576 (mtpt) cc_final: 0.6750 (tmtm) REVERT: E 78 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6800 (mp) REVERT: E 137 ASN cc_start: 0.7980 (m110) cc_final: 0.7072 (p0) outliers start: 25 outliers final: 22 residues processed: 112 average time/residue: 1.8628 time to fit residues: 227.2245 Evaluate side-chains 111 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 0.0000 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 85 optimal weight: 7.9990 chunk 10 optimal weight: 0.0050 chunk 15 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.173291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112367 restraints weight = 28074.806| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.10 r_work: 0.3120 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8289 Z= 0.129 Angle : 0.479 5.420 11283 Z= 0.245 Chirality : 0.043 0.177 1234 Planarity : 0.004 0.060 1458 Dihedral : 4.508 43.853 1158 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 1.97 % Allowed : 28.70 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -0.51 (0.26), residues: 1061 helix: -3.08 (0.55), residues: 50 sheet: 0.76 (0.25), residues: 463 loop : -1.05 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 155 HIS 0.002 0.001 HIS B 201 PHE 0.008 0.001 PHE A 320 TYR 0.010 0.001 TYR E 91 ARG 0.013 0.001 ARG C 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6481.30 seconds wall clock time: 116 minutes 40.48 seconds (7000.48 seconds total)