Starting phenix.real_space_refine on Sun Dec 10 21:53:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/12_2023/7xda_33140.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/12_2023/7xda_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_33140/12_2023/7xda_33140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/12_2023/7xda_33140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/12_2023/7xda_33140.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/12_2023/7xda_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.22, 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: 11.57 Conformation dependent library (CDL) restraints added in 1.6 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: 1.43 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: 6.21 Time building geometry restraints manager: 12.07 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: 6702 17.99 - 35.97: 595 35.97 - 53.96: 180 53.96 - 71.94: 32 71.94 - 89.93: 13 Dihedral angle restraints: 7522 sinusoidal: 3835 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 7519 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: 8.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 29.070 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 50.430 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.290 ------------------------------------------------------------------------------- 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 : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 147 average time/residue: 1.9882 time to fit residues: 314.3310 Evaluate side-chains 102 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.4186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 50 GLN B 58 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN E 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8289 Z= 0.195 Angle : 0.521 6.707 11283 Z= 0.271 Chirality : 0.044 0.183 1234 Planarity : 0.004 0.051 1458 Dihedral : 4.741 29.850 1156 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 2.55 % Allowed : 27.43 % Favored : 70.02 % 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: -2.73 (0.23), residues: 1061 helix: -3.98 (0.40), residues: 55 sheet: -0.65 (0.23), residues: 471 loop : -2.72 (0.22), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 84 HIS 0.003 0.001 HIS B 53 PHE 0.010 0.001 PHE B 78 TYR 0.016 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 122 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 119 average time/residue: 1.7638 time to fit residues: 227.8804 Evaluate side-chains 103 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 1.0482 time to fit residues: 5.1147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN E 79 GLN E 138 ASN E 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 8289 Z= 0.527 Angle : 0.674 7.143 11283 Z= 0.355 Chirality : 0.050 0.203 1234 Planarity : 0.005 0.039 1458 Dihedral : 5.715 41.574 1156 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.35 % Favored : 92.55 % Rotamer: Outliers : 4.86 % Allowed : 25.12 % Favored : 70.02 % 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: -2.32 (0.24), residues: 1061 helix: -3.85 (0.43), residues: 56 sheet: -0.38 (0.23), residues: 473 loop : -2.42 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 48 HIS 0.006 0.001 HIS D 100 PHE 0.015 0.002 PHE C 37 TYR 0.028 0.002 TYR E 91 ARG 0.003 0.001 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 136 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 94 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 26 residues processed: 127 average time/residue: 1.8170 time to fit residues: 250.1332 Evaluate side-chains 103 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 77 time to evaluate : 1.271 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 23 residues processed: 3 average time/residue: 1.0064 time to fit residues: 5.0245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8289 Z= 0.186 Angle : 0.520 5.539 11283 Z= 0.271 Chirality : 0.044 0.183 1234 Planarity : 0.004 0.034 1458 Dihedral : 5.093 39.937 1156 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 4.05 % Allowed : 26.16 % 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: -1.85 (0.24), residues: 1061 helix: -3.54 (0.51), residues: 50 sheet: -0.10 (0.24), residues: 474 loop : -2.11 (0.23), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 84 HIS 0.003 0.001 HIS B 53 PHE 0.009 0.001 PHE B 78 TYR 0.016 0.001 TYR E 91 ARG 0.008 0.000 ARG C 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 128 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 93 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 28 residues processed: 126 average time/residue: 1.9058 time to fit residues: 259.6109 Evaluate side-chains 115 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 87 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 26 residues processed: 2 average time/residue: 1.4014 time to fit residues: 4.5259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 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: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8289 Z= 0.246 Angle : 0.531 5.723 11283 Z= 0.278 Chirality : 0.044 0.193 1234 Planarity : 0.004 0.051 1458 Dihedral : 5.023 42.198 1156 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.13 % Favored : 93.78 % Rotamer: Outliers : 4.05 % Allowed : 26.97 % Favored : 68.98 % 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: -1.59 (0.25), residues: 1061 helix: -3.49 (0.52), residues: 50 sheet: 0.08 (0.24), residues: 474 loop : -1.92 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 48 HIS 0.003 0.001 HIS B 53 PHE 0.017 0.001 PHE E 139 TYR 0.018 0.001 TYR E 91 ARG 0.007 0.000 ARG E 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 125 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 90 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 28 residues processed: 121 average time/residue: 1.7669 time to fit residues: 233.2343 Evaluate side-chains 111 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 83 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 0.3403 time to fit residues: 2.0887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 ASN ** 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: 0.8294 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8289 Z= 0.285 Angle : 0.542 5.805 11283 Z= 0.284 Chirality : 0.045 0.193 1234 Planarity : 0.004 0.054 1458 Dihedral : 5.132 44.779 1156 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.50 % Favored : 93.40 % Rotamer: Outliers : 3.59 % Allowed : 26.85 % Favored : 69.56 % 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: -1.41 (0.25), residues: 1061 helix: -3.25 (0.58), residues: 44 sheet: 0.18 (0.24), residues: 472 loop : -1.80 (0.24), residues: 545 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 0.009 0.001 PHE B 78 TYR 0.020 0.001 TYR E 91 ARG 0.009 0.001 ARG C 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 119 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 28 residues processed: 116 average time/residue: 1.9225 time to fit residues: 242.5907 Evaluate side-chains 108 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 0.3148 time to fit residues: 2.0194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8289 Z= 0.208 Angle : 0.513 5.589 11283 Z= 0.268 Chirality : 0.044 0.186 1234 Planarity : 0.004 0.060 1458 Dihedral : 4.958 45.206 1156 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 3.36 % Allowed : 27.20 % 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: -1.20 (0.25), residues: 1061 helix: -3.17 (0.58), residues: 44 sheet: 0.31 (0.24), residues: 472 loop : -1.64 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 162 HIS 0.002 0.001 HIS D 172 PHE 0.019 0.001 PHE E 139 TYR 0.017 0.001 TYR E 91 ARG 0.010 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 115 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 28 residues processed: 113 average time/residue: 1.8517 time to fit residues: 228.0582 Evaluate side-chains 105 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 0.3195 time to fit residues: 2.0668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 ASN ** 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: 0.8279 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8289 Z= 0.225 Angle : 0.517 5.618 11283 Z= 0.270 Chirality : 0.044 0.188 1234 Planarity : 0.004 0.064 1458 Dihedral : 4.949 46.436 1156 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.87 % Rotamer: Outliers : 3.59 % Allowed : 26.97 % 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: -1.07 (0.25), residues: 1061 helix: -3.18 (0.59), residues: 44 sheet: 0.40 (0.24), residues: 474 loop : -1.56 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 162 HIS 0.002 0.001 HIS D 100 PHE 0.009 0.001 PHE B 78 TYR 0.017 0.001 TYR E 91 ARG 0.009 0.000 ARG E 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 113 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 82 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 27 residues processed: 110 average time/residue: 1.7726 time to fit residues: 212.3348 Evaluate side-chains 104 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 1.4254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 93 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3180 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= 0.152 Angle : 0.489 5.520 11283 Z= 0.254 Chirality : 0.043 0.185 1234 Planarity : 0.004 0.055 1458 Dihedral : 4.702 45.908 1156 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 3.36 % Allowed : 26.97 % Favored : 69.68 % 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: -1.00 (0.25), residues: 1061 helix: -3.35 (0.53), residues: 50 sheet: 0.45 (0.25), residues: 466 loop : -1.43 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 162 HIS 0.002 0.001 HIS D 172 PHE 0.018 0.001 PHE E 139 TYR 0.013 0.001 TYR E 91 ARG 0.008 0.000 ARG E 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 119 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 24 residues processed: 117 average time/residue: 1.8604 time to fit residues: 237.2090 Evaluate side-chains 103 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 2 average time/residue: 0.5361 time to fit residues: 4.1922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8289 Z= 0.297 Angle : 0.548 5.543 11283 Z= 0.285 Chirality : 0.045 0.189 1234 Planarity : 0.004 0.052 1458 Dihedral : 5.025 48.656 1156 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.41 % Favored : 93.50 % Rotamer: Outliers : 2.89 % Allowed : 27.78 % 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: -0.95 (0.25), residues: 1061 helix: -3.14 (0.59), residues: 44 sheet: 0.43 (0.24), residues: 478 loop : -1.42 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 162 HIS 0.003 0.001 HIS D 100 PHE 0.010 0.001 PHE E 94 TYR 0.021 0.002 TYR E 91 ARG 0.009 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 110 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 24 residues processed: 109 average time/residue: 1.7121 time to fit residues: 204.6402 Evaluate side-chains 105 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 1.455 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 1.6966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 12 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.0670 chunk 73 optimal weight: 0.9980 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.171538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110371 restraints weight = 27911.116| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.07 r_work: 0.3102 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3342 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= 0.154 Angle : 0.497 5.547 11283 Z= 0.257 Chirality : 0.043 0.186 1234 Planarity : 0.004 0.054 1458 Dihedral : 4.759 48.161 1156 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 2.89 % Allowed : 28.01 % Favored : 69.10 % 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: -0.78 (0.26), residues: 1061 helix: -3.29 (0.53), residues: 50 sheet: 0.60 (0.25), residues: 464 loop : -1.26 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 162 HIS 0.002 0.001 HIS D 172 PHE 0.019 0.001 PHE E 139 TYR 0.013 0.001 TYR E 91 ARG 0.010 0.001 ARG C 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6199.01 seconds wall clock time: 110 minutes 25.58 seconds (6625.58 seconds total)