Starting phenix.real_space_refine on Sat Jan 20 15:56:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/01_2024/7xda_33140.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/01_2024/7xda_33140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/01_2024/7xda_33140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/01_2024/7xda_33140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/01_2024/7xda_33140.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xda_33140/01_2024/7xda_33140.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 5110 2.51 5 N 1365 2.21 5 O 1579 1.98 5 H 7646 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 1": "OE1" <-> "OE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 91": "OD1" <-> "OD2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 122": "OD1" <-> "OD2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "E ASP 151": "OD1" <-> "OD2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 7.25, 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: 13.96 Conformation dependent library (CDL) restraints added in 1.8 seconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 26 sheets defined 7.7% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 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: 7.12 Time building geometry restraints manager: 14.06 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: 6739 17.99 - 35.97: 595 35.97 - 53.96: 180 53.96 - 71.94: 32 71.94 - 89.93: 13 Dihedral angle restraints: 7559 sinusoidal: 3872 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 7556 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: 20.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 32.730 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 60.490 Find NCS groups from input model: 0.390 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:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.160 ------------------------------------------------------------------------------- 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 : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.7989 (tt0) cc_final: 0.7720 (tt0) REVERT: B 200 ASN cc_start: 0.6195 (t0) cc_final: 0.5929 (p0) REVERT: B 209 ASP cc_start: 0.7886 (m-30) cc_final: 0.7624 (m-30) REVERT: A 450 ILE cc_start: 0.8629 (pt) cc_final: 0.8127 (mm) REVERT: D 163 ASN cc_start: 0.6396 (t0) cc_final: 0.5824 (t0) REVERT: E 161 GLU cc_start: 0.6892 (pm20) cc_final: 0.6666 (pm20) outliers start: 16 outliers final: 7 residues processed: 147 average time/residue: 2.0600 time to fit residues: 326.1168 Evaluate side-chains 102 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 214 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 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: 0.6980 chunk 95 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 58 ASN C 161 GLN A 370 ASN E 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8289 Z= 0.191 Angle : 0.523 6.350 11283 Z= 0.271 Chirality : 0.044 0.198 1234 Planarity : 0.004 0.060 1458 Dihedral : 4.980 30.405 1164 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 1.85 % Allowed : 27.31 % Favored : 70.83 % 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: -2.62 (0.23), residues: 1061 helix: -3.94 (0.41), residues: 54 sheet: -0.60 (0.23), residues: 471 loop : -2.62 (0.22), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 111 HIS 0.003 0.001 HIS B 53 PHE 0.010 0.001 PHE B 78 TYR 0.015 0.001 TYR E 91 ARG 0.005 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.7995 (tt0) cc_final: 0.7781 (tt0) REVERT: B 209 ASP cc_start: 0.7976 (m-30) cc_final: 0.7596 (m-30) REVERT: C 79 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8066 (mp) REVERT: C 193 TYR cc_start: 0.6526 (m-80) cc_final: 0.5965 (m-80) REVERT: A 450 ILE cc_start: 0.8732 (pt) cc_final: 0.8249 (mm) REVERT: D 163 ASN cc_start: 0.6413 (t0) cc_final: 0.5854 (t0) REVERT: D 207 ASN cc_start: 0.6427 (t0) cc_final: 0.6156 (t0) REVERT: E 161 GLU cc_start: 0.6879 (pm20) cc_final: 0.6666 (pm20) outliers start: 16 outliers final: 7 residues processed: 116 average time/residue: 1.9094 time to fit residues: 239.7036 Evaluate side-chains 101 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 1 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN E 138 ASN E 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 8289 Z= 0.471 Angle : 0.636 6.286 11283 Z= 0.335 Chirality : 0.048 0.191 1234 Planarity : 0.004 0.037 1458 Dihedral : 5.494 39.686 1158 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.79 % Favored : 93.12 % Rotamer: Outliers : 3.94 % Allowed : 25.81 % Favored : 70.25 % 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: -2.24 (0.24), residues: 1061 helix: -3.78 (0.45), residues: 56 sheet: -0.36 (0.23), residues: 474 loop : -2.33 (0.23), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 48 HIS 0.006 0.001 HIS D 100 PHE 0.014 0.002 PHE E 139 TYR 0.026 0.002 TYR E 91 ARG 0.004 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 131 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 97 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 ASP cc_start: 0.7957 (m-30) cc_final: 0.7681 (m-30) REVERT: C 18 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7439 (ptm160) REVERT: A 450 ILE cc_start: 0.8881 (pt) cc_final: 0.8419 (mm) REVERT: D 113 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6997 (mtm180) REVERT: D 163 ASN cc_start: 0.6425 (t0) cc_final: 0.5876 (t0) REVERT: E 161 GLU cc_start: 0.7084 (pm20) cc_final: 0.6830 (pm20) outliers start: 34 outliers final: 19 residues processed: 124 average time/residue: 1.9956 time to fit residues: 266.8929 Evaluate side-chains 103 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 139 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.8263 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8289 Z= 0.193 Angle : 0.523 6.418 11283 Z= 0.274 Chirality : 0.044 0.182 1234 Planarity : 0.004 0.034 1458 Dihedral : 5.064 38.753 1158 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 2.78 % Allowed : 27.43 % 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: -1.78 (0.25), residues: 1061 helix: -3.49 (0.52), residues: 50 sheet: -0.12 (0.24), residues: 477 loop : -1.99 (0.24), residues: 534 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 0.075 0.001 PHE E 139 TYR 0.023 0.001 TYR E 173 ARG 0.009 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 123 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8069 (tt0) cc_final: 0.7699 (tt0) REVERT: B 209 ASP cc_start: 0.7955 (m-30) cc_final: 0.7558 (m-30) REVERT: C 193 TYR cc_start: 0.6547 (m-80) cc_final: 0.6019 (m-80) REVERT: A 450 ILE cc_start: 0.8857 (pt) cc_final: 0.8398 (mm) REVERT: D 163 ASN cc_start: 0.6368 (t0) cc_final: 0.5819 (t0) REVERT: D 214 LYS cc_start: 0.7525 (mtpt) cc_final: 0.6665 (tmtm) REVERT: E 161 GLU cc_start: 0.7050 (pm20) cc_final: 0.6781 (pm20) outliers start: 24 outliers final: 17 residues processed: 119 average time/residue: 1.9522 time to fit residues: 251.4562 Evaluate side-chains 105 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 139 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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: 0.8289 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8289 Z= 0.268 Angle : 0.535 5.625 11283 Z= 0.279 Chirality : 0.045 0.193 1234 Planarity : 0.004 0.052 1458 Dihedral : 5.110 42.424 1158 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.75 % Favored : 94.16 % Rotamer: Outliers : 3.24 % Allowed : 26.97 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.25), residues: 1061 helix: -3.45 (0.53), residues: 50 sheet: 0.08 (0.24), residues: 476 loop : -1.73 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 48 HIS 0.003 0.001 HIS D 100 PHE 0.031 0.001 PHE E 139 TYR 0.019 0.001 TYR E 91 ARG 0.005 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 121 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 ASP cc_start: 0.7954 (m-30) cc_final: 0.7616 (m-30) REVERT: C 193 TYR cc_start: 0.6544 (m-80) cc_final: 0.6081 (m-80) REVERT: A 450 ILE cc_start: 0.8907 (pt) cc_final: 0.8446 (mm) REVERT: D 113 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6936 (mtm180) REVERT: D 163 ASN cc_start: 0.6374 (t0) cc_final: 0.5819 (t0) REVERT: D 214 LYS cc_start: 0.7496 (mtpt) cc_final: 0.6677 (tmtm) REVERT: E 139 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7714 (p90) REVERT: E 161 GLU cc_start: 0.7118 (pm20) cc_final: 0.6888 (pm20) outliers start: 28 outliers final: 20 residues processed: 116 average time/residue: 1.9207 time to fit residues: 241.5667 Evaluate side-chains 107 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 139 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8270 moved from start: 0.2871 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= 0.207 Angle : 0.505 5.562 11283 Z= 0.262 Chirality : 0.044 0.186 1234 Planarity : 0.004 0.055 1458 Dihedral : 4.904 43.181 1158 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.72 % Rotamer: Outliers : 2.78 % Allowed : 27.20 % 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: -1.24 (0.25), residues: 1061 helix: -3.39 (0.53), residues: 50 sheet: 0.21 (0.24), residues: 470 loop : -1.53 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 48 HIS 0.002 0.001 HIS D 100 PHE 0.017 0.001 PHE E 139 TYR 0.016 0.001 TYR E 91 ARG 0.011 0.000 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 117 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8087 (tt0) cc_final: 0.7753 (tt0) REVERT: B 209 ASP cc_start: 0.7933 (m-30) cc_final: 0.7566 (m-30) REVERT: C 18 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7233 (ptm160) REVERT: C 193 TYR cc_start: 0.6524 (m-80) cc_final: 0.6050 (m-80) REVERT: A 450 ILE cc_start: 0.8907 (pt) cc_final: 0.8435 (mm) REVERT: D 113 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6910 (mtm180) REVERT: D 163 ASN cc_start: 0.6400 (t0) cc_final: 0.5842 (t0) REVERT: D 214 LYS cc_start: 0.7521 (mtpt) cc_final: 0.6708 (tmtm) REVERT: E 161 GLU cc_start: 0.7154 (pm20) cc_final: 0.6917 (pm20) outliers start: 24 outliers final: 19 residues processed: 113 average time/residue: 1.9123 time to fit residues: 234.5332 Evaluate side-chains 108 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.0770 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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: 0.8254 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8289 Z= 0.162 Angle : 0.486 5.328 11283 Z= 0.252 Chirality : 0.043 0.179 1234 Planarity : 0.004 0.059 1458 Dihedral : 4.698 43.255 1158 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 3.01 % Allowed : 27.31 % 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: -1.02 (0.25), residues: 1061 helix: -3.31 (0.54), residues: 50 sheet: 0.38 (0.24), residues: 467 loop : -1.38 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 162 HIS 0.002 0.001 HIS D 100 PHE 0.009 0.001 PHE B 78 TYR 0.014 0.001 TYR E 91 ARG 0.012 0.001 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8084 (tt0) cc_final: 0.7742 (tt0) REVERT: B 209 ASP cc_start: 0.7926 (m-30) cc_final: 0.7564 (m-30) REVERT: C 193 TYR cc_start: 0.6479 (m-80) cc_final: 0.6041 (m-80) REVERT: A 450 ILE cc_start: 0.8902 (pt) cc_final: 0.8435 (mm) REVERT: D 113 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6859 (mtm180) REVERT: D 163 ASN cc_start: 0.6344 (t0) cc_final: 0.5775 (t0) REVERT: D 214 LYS cc_start: 0.7547 (mtpt) cc_final: 0.6733 (tmtm) outliers start: 26 outliers final: 19 residues processed: 114 average time/residue: 1.9332 time to fit residues: 238.2427 Evaluate side-chains 107 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 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: 0.8292 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8289 Z= 0.281 Angle : 0.535 5.504 11283 Z= 0.278 Chirality : 0.045 0.187 1234 Planarity : 0.005 0.063 1458 Dihedral : 5.015 45.991 1158 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.22 % Favored : 93.69 % Rotamer: Outliers : 3.82 % Allowed : 26.04 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1061 helix: -3.34 (0.54), residues: 50 sheet: 0.38 (0.24), residues: 466 loop : -1.39 (0.25), 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 0.011 0.001 PHE E 139 TYR 0.020 0.001 TYR E 91 ARG 0.011 0.001 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8104 (tt0) cc_final: 0.7723 (tt0) REVERT: B 209 ASP cc_start: 0.7898 (m-30) cc_final: 0.7592 (m-30) REVERT: C 193 TYR cc_start: 0.6490 (m-80) cc_final: 0.6072 (m-80) REVERT: A 450 ILE cc_start: 0.8916 (pt) cc_final: 0.8433 (mm) REVERT: A 466 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: D 163 ASN cc_start: 0.6334 (t0) cc_final: 0.5790 (t0) REVERT: D 214 LYS cc_start: 0.7541 (mtpt) cc_final: 0.6729 (tmtm) REVERT: E 137 ASN cc_start: 0.7990 (m110) cc_final: 0.6958 (p0) outliers start: 33 outliers final: 23 residues processed: 118 average time/residue: 1.8177 time to fit residues: 232.5019 Evaluate side-chains 113 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.8272 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8289 Z= 0.208 Angle : 0.511 5.475 11283 Z= 0.265 Chirality : 0.044 0.184 1234 Planarity : 0.004 0.057 1458 Dihedral : 4.874 46.329 1158 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 3.01 % Allowed : 27.08 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1061 helix: -3.25 (0.54), residues: 50 sheet: 0.45 (0.24), residues: 466 loop : -1.30 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 48 HIS 0.002 0.001 HIS D 100 PHE 0.009 0.001 PHE B 78 TYR 0.016 0.001 TYR E 91 ARG 0.012 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8100 (tt0) cc_final: 0.7762 (tt0) REVERT: B 209 ASP cc_start: 0.7848 (m-30) cc_final: 0.7513 (m-30) REVERT: C 193 TYR cc_start: 0.6501 (m-80) cc_final: 0.6064 (m-80) REVERT: A 450 ILE cc_start: 0.8912 (pt) cc_final: 0.8418 (mm) REVERT: A 466 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: D 163 ASN cc_start: 0.6318 (t0) cc_final: 0.5770 (t0) REVERT: D 214 LYS cc_start: 0.7577 (mtpt) cc_final: 0.6755 (tmtm) REVERT: E 78 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6784 (mp) REVERT: E 137 ASN cc_start: 0.7991 (m110) cc_final: 0.7071 (p0) outliers start: 26 outliers final: 23 residues processed: 112 average time/residue: 1.7888 time to fit residues: 217.8937 Evaluate side-chains 111 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.0270 chunk 66 optimal weight: 0.9980 overall best weight: 1.0044 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8289 Z= 0.208 Angle : 0.511 5.435 11283 Z= 0.264 Chirality : 0.044 0.183 1234 Planarity : 0.005 0.062 1458 Dihedral : 4.849 47.126 1158 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.25 % Rotamer: Outliers : 2.89 % Allowed : 27.55 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.26), residues: 1061 helix: -3.20 (0.55), residues: 50 sheet: 0.48 (0.24), residues: 470 loop : -1.25 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 162 HIS 0.002 0.001 HIS D 100 PHE 0.014 0.001 PHE E 139 TYR 0.016 0.001 TYR E 91 ARG 0.013 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 113 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8090 (tt0) cc_final: 0.7750 (tt0) REVERT: B 209 ASP cc_start: 0.7832 (m-30) cc_final: 0.7524 (m-30) REVERT: C 161 GLN cc_start: 0.7174 (mt0) cc_final: 0.5907 (pt0) REVERT: C 193 TYR cc_start: 0.6472 (m-80) cc_final: 0.6065 (m-80) REVERT: A 450 ILE cc_start: 0.8916 (pt) cc_final: 0.8424 (mm) REVERT: D 163 ASN cc_start: 0.6325 (t0) cc_final: 0.5776 (t0) REVERT: D 214 LYS cc_start: 0.7595 (mtpt) cc_final: 0.6767 (tmtm) REVERT: E 137 ASN cc_start: 0.7990 (m110) cc_final: 0.7087 (p0) outliers start: 25 outliers final: 22 residues processed: 109 average time/residue: 1.9097 time to fit residues: 228.8204 Evaluate side-chains 107 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.0199 > 50: distance: 147 - 359: 28.155 distance: 150 - 356: 27.028 distance: 228 - 244: 34.819 distance: 244 - 245: 39.712 distance: 244 - 248: 43.934 distance: 245 - 246: 44.872 distance: 245 - 249: 33.867 distance: 246 - 247: 20.288 distance: 246 - 251: 55.815 distance: 251 - 252: 19.408 distance: 252 - 253: 25.847 distance: 252 - 255: 15.128 distance: 252 - 262: 33.630 distance: 253 - 254: 19.917 distance: 253 - 268: 23.123 distance: 255 - 256: 14.425 distance: 255 - 263: 16.414 distance: 255 - 264: 8.496 distance: 256 - 257: 22.152 distance: 256 - 258: 25.247 distance: 257 - 259: 27.596 distance: 257 - 265: 23.503 distance: 258 - 260: 19.630 distance: 258 - 266: 19.844 distance: 259 - 260: 14.666 distance: 259 - 267: 11.268 distance: 268 - 269: 26.692 distance: 268 - 276: 34.971 distance: 269 - 270: 18.584 distance: 269 - 272: 18.584 distance: 269 - 277: 15.806 distance: 270 - 271: 3.900 distance: 270 - 280: 39.071 distance: 272 - 273: 42.922 distance: 272 - 278: 13.135 distance: 272 - 279: 51.795 distance: 273 - 274: 13.788 distance: 273 - 275: 17.943 distance: 280 - 281: 7.022 distance: 280 - 292: 17.718 distance: 281 - 282: 6.859 distance: 281 - 284: 17.080 distance: 281 - 293: 25.847 distance: 282 - 301: 3.380 distance: 284 - 285: 7.800 distance: 284 - 294: 7.169 distance: 285 - 287: 20.843 distance: 286 - 288: 10.673 distance: 286 - 296: 10.909 distance: 287 - 289: 11.209 distance: 287 - 297: 4.847 distance: 288 - 290: 8.288 distance: 288 - 298: 14.633 distance: 289 - 290: 25.531 distance: 289 - 299: 14.884 distance: 290 - 291: 11.250 distance: 291 - 300: 12.632 distance: 301 - 302: 49.484 distance: 301 - 315: 16.024 distance: 302 - 303: 26.331 distance: 302 - 305: 31.948 distance: 302 - 316: 35.354 distance: 303 - 304: 34.948 distance: 303 - 325: 20.828 distance: 305 - 306: 29.692 distance: 305 - 317: 16.624 distance: 305 - 318: 16.586 distance: 306 - 307: 42.146 distance: 306 - 308: 23.912 distance: 307 - 309: 23.237 distance: 307 - 319: 16.663 distance: 308 - 310: 20.337 distance: 308 - 311: 24.897 distance: 309 - 310: 16.299 distance: 309 - 320: 4.071 distance: 310 - 312: 5.121 distance: 311 - 313: 20.144 distance: 311 - 321: 10.153 distance: 312 - 314: 8.014 distance: 312 - 322: 6.611 distance: 313 - 314: 22.063 distance: 313 - 323: 15.800 distance: 314 - 324: 17.290 distance: 325 - 326: 7.164 distance: 325 - 329: 33.263 distance: 326 - 327: 43.679 distance: 326 - 330: 6.265 distance: 326 - 331: 45.467 distance: 327 - 328: 37.075 distance: 327 - 332: 6.237 distance: 332 - 333: 37.270 distance: 332 - 341: 40.647 distance: 333 - 334: 43.976 distance: 333 - 336: 16.947 distance: 333 - 342: 22.116 distance: 334 - 335: 13.085 distance: 334 - 349: 57.615 distance: 336 - 337: 37.541 distance: 336 - 343: 5.019 distance: 336 - 344: 9.360 distance: 337 - 338: 19.744 distance: 337 - 345: 16.500 distance: 337 - 346: 8.935 distance: 338 - 339: 5.852 distance: 338 - 340: 35.748 distance: 350 - 351: 53.176 distance: 350 - 355: 17.190 distance: 351 - 352: 39.605 distance: 351 - 356: 22.844 distance: 356 - 357: 9.940 distance: 356 - 363: 25.016 distance: 357 - 358: 33.732 distance: 357 - 360: 34.123 distance: 357 - 364: 25.312 distance: 358 - 359: 38.368 distance: 358 - 370: 17.548 distance: 360 - 361: 5.992 distance: 360 - 362: 5.430 distance: 360 - 365: 9.000 distance: 361 - 366: 6.523 distance: 362 - 367: 39.300 distance: 362 - 368: 40.217 distance: 362 - 369: 38.946 distance: 370 - 371: 22.954 distance: 370 - 378: 34.893 distance: 371 - 372: 23.943 distance: 371 - 374: 35.328 distance: 371 - 379: 18.773 distance: 372 - 373: 20.311 distance: 372 - 389: 21.879 distance: 374 - 375: 30.426 distance: 374 - 380: 40.119 distance: 374 - 381: 28.696 distance: 375 - 376: 15.977 distance: 376 - 383: 22.106 distance: 376 - 384: 25.585 distance: 376 - 385: 47.012 distance: 377 - 387: 3.178