Starting phenix.real_space_refine on Tue Mar 19 20:34:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shn_10201/03_2024/6shn_10201_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shn_10201/03_2024/6shn_10201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shn_10201/03_2024/6shn_10201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shn_10201/03_2024/6shn_10201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shn_10201/03_2024/6shn_10201_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shn_10201/03_2024/6shn_10201_trim_updated.pdb" } resolution = 3.3 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= 0.001 sd= 0.114 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 80 5.16 5 C 8088 2.51 5 N 2251 2.21 5 O 2403 1.98 5 H 12513 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 419": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 219": "OD1" <-> "OD2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 420": "OE1" <-> "OE2" Residue "C ARG 29": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 219": "OD1" <-> "OD2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 420": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25339 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 6331 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 411, 6312 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 411, 6312 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 6357 Chain: "A" Number of atoms: 6327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6327 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 6341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6341 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6300 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.98, per 1000 atoms: 0.55 Number of scatterers: 25339 At special positions: 0 Unit cell: (106.794, 105.747, 102.606, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 4 15.00 O 2403 8.00 N 2251 7.00 C 8088 6.00 H 12513 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 22.32 Conformation dependent library (CDL) restraints added in 3.8 seconds 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3082 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 25 sheets defined 27.4% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'D' and resid 13 through 19 Proline residue: D 17 - end of helix No H-bonds generated for 'chain 'D' and resid 13 through 19' Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 53 through 64 removed outlier: 4.118A pdb=" N SER D 59 " --> pdb=" O PHE D 56 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN D 60 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE D 62 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN D 63 " --> pdb=" O ASN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 Processing helix chain 'D' and resid 117 through 123 removed outlier: 3.710A pdb=" N VAL D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 131 removed outlier: 3.783A pdb=" N ARG D 130 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR D 131 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.504A pdb=" N ILE D 154 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 158 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 removed outlier: 5.644A pdb=" N SER D 176 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 231 Processing helix chain 'D' and resid 240 through 251 removed outlier: 4.671A pdb=" N ILE D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 280 through 291 removed outlier: 3.756A pdb=" N LEU D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA D 291 " --> pdb=" O ASN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 400 through 406 Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'A' and resid 12 through 19 Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 54 through 63 removed outlier: 4.161A pdb=" N SER A 59 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 60 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 62 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 63 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 118 through 122 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.860A pdb=" N ARG A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.028A pdb=" N ILE A 154 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 5.618A pdb=" N SER A 176 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.661A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 251 removed outlier: 4.770A pdb=" N ILE A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 280 through 290 removed outlier: 3.824A pdb=" N LEU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'C' and resid 13 through 18 Proline residue: C 17 - end of helix No H-bonds generated for 'chain 'C' and resid 13 through 18' Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 54 through 64 removed outlier: 4.087A pdb=" N SER C 59 " --> pdb=" O PHE C 56 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN C 60 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 62 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN C 63 " --> pdb=" O ASN C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 117 through 123 Processing helix chain 'C' and resid 125 through 131 removed outlier: 3.612A pdb=" N ARG C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 removed outlier: 4.300A pdb=" N ILE C 154 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU C 158 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 removed outlier: 5.551A pdb=" N SER C 176 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.525A pdb=" N GLU C 228 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 251 removed outlier: 4.751A pdb=" N ILE C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 280 through 291 removed outlier: 3.740A pdb=" N LEU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 291 " --> pdb=" O ASN C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 406 Processing helix chain 'C' and resid 419 through 425 Processing helix chain 'B' and resid 13 through 19 Proline residue: B 17 - end of helix No H-bonds generated for 'chain 'B' and resid 13 through 19' Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 54 through 63 removed outlier: 4.075A pdb=" N SER B 59 " --> pdb=" O PHE B 56 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN B 60 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 62 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN B 63 " --> pdb=" O ASN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 117 through 121 removed outlier: 3.599A pdb=" N VAL B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 117 through 121' Processing helix chain 'B' and resid 125 through 131 removed outlier: 4.073A pdb=" N ARG B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.506A pdb=" N ASP B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 5.575A pdb=" N SER B 176 " --> pdb=" O GLU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.639A pdb=" N GLU B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 251 removed outlier: 4.765A pdb=" N ILE B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Proline residue: B 246 - end of helix Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 280 through 291 removed outlier: 3.866A pdb=" N LEU B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 406 Processing helix chain 'B' and resid 419 through 425 Processing sheet with id= A, first strand: chain 'D' and resid 98 through 101 removed outlier: 7.421A pdb=" N SER D 20 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLY D 70 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA D 22 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR D 135 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LEU D 23 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 137 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE D 215 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 167 through 171 Processing sheet with id= C, first strand: chain 'D' and resid 317 through 319 Processing sheet with id= D, first strand: chain 'D' and resid 344 through 346 Processing sheet with id= E, first strand: chain 'D' and resid 365 through 367 removed outlier: 6.749A pdb=" N CYS D 382 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 415 " --> pdb=" O VAL D 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 179 through 183 Processing sheet with id= G, first strand: chain 'A' and resid 98 through 101 removed outlier: 7.351A pdb=" N SER A 20 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLY A 70 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 22 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR A 135 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LEU A 23 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A 137 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE A 215 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 167 through 171 Processing sheet with id= I, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= J, first strand: chain 'A' and resid 344 through 346 Processing sheet with id= K, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.796A pdb=" N CYS A 382 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 415 " --> pdb=" O VAL A 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 179 through 183 Processing sheet with id= M, first strand: chain 'C' and resid 98 through 101 removed outlier: 7.496A pdb=" N SER C 20 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY C 70 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA C 22 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR C 135 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LEU C 23 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL C 137 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE C 215 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 167 through 171 Processing sheet with id= O, first strand: chain 'C' and resid 317 through 319 Processing sheet with id= P, first strand: chain 'C' and resid 344 through 346 Processing sheet with id= Q, first strand: chain 'C' and resid 365 through 367 removed outlier: 6.789A pdb=" N CYS C 382 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C 415 " --> pdb=" O VAL C 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 179 through 183 Processing sheet with id= S, first strand: chain 'B' and resid 20 through 24 removed outlier: 7.010A pdb=" N TYR B 135 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N LEU B 23 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 137 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE B 215 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.456A pdb=" N PHE B 98 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL B 71 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP B 100 " --> pdb=" O VAL B 71 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'B' and resid 167 through 171 Processing sheet with id= V, first strand: chain 'B' and resid 317 through 319 Processing sheet with id= W, first strand: chain 'B' and resid 344 through 346 Processing sheet with id= X, first strand: chain 'B' and resid 365 through 367 removed outlier: 6.799A pdb=" N CYS B 382 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 415 " --> pdb=" O VAL B 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'B' and resid 179 through 183 274 hydrogen bonds defined for protein. 708 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: 9.37 Time building geometry restraints manager: 22.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 12478 1.01 - 1.21: 37 1.21 - 1.41: 5506 1.41 - 1.62: 7461 1.62 - 1.82: 124 Bond restraints: 25606 Sorted by residual: bond pdb=" C5 FBP D 501 " pdb=" O5 FBP D 501 " ideal model delta sigma weight residual 1.608 1.405 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C5 FBP C 501 " pdb=" O5 FBP C 501 " ideal model delta sigma weight residual 1.608 1.426 0.182 2.00e-02 2.50e+03 8.30e+01 bond pdb=" C4 FBP D 501 " pdb=" C5 FBP D 501 " ideal model delta sigma weight residual 1.346 1.523 -0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" C4 FBP C 501 " pdb=" C5 FBP C 501 " ideal model delta sigma weight residual 1.346 1.510 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" C2 FBP C 501 " pdb=" O5 FBP C 501 " ideal model delta sigma weight residual 1.294 1.422 -0.128 2.00e-02 2.50e+03 4.11e+01 ... (remaining 25601 not shown) Histogram of bond angle deviations from ideal: 78.94 - 90.06: 15 90.06 - 101.19: 68 101.19 - 112.31: 28856 112.31 - 123.43: 14903 123.43 - 134.56: 2387 Bond angle restraints: 46229 Sorted by residual: angle pdb=" CG1 VAL B 217 " pdb=" CB VAL B 217 " pdb=" HB VAL B 217 " ideal model delta sigma weight residual 108.00 78.94 29.06 3.00e+00 1.11e-01 9.38e+01 angle pdb=" CG2 VAL B 217 " pdb=" CB VAL B 217 " pdb=" HB VAL B 217 " ideal model delta sigma weight residual 108.00 80.67 27.33 3.00e+00 1.11e-01 8.30e+01 angle pdb=" CA VAL B 217 " pdb=" CB VAL B 217 " pdb=" HB VAL B 217 " ideal model delta sigma weight residual 109.00 82.02 26.98 3.00e+00 1.11e-01 8.09e+01 angle pdb=" CD1 LEU D 18 " pdb=" CG LEU D 18 " pdb=" HG LEU D 18 " ideal model delta sigma weight residual 108.00 81.28 26.72 3.00e+00 1.11e-01 7.93e+01 angle pdb=" CD2 LEU D 18 " pdb=" CG LEU D 18 " pdb=" HG LEU D 18 " ideal model delta sigma weight residual 108.00 83.02 24.98 3.00e+00 1.11e-01 6.93e+01 ... (remaining 46224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 10782 17.81 - 35.63: 945 35.63 - 53.44: 309 53.44 - 71.26: 75 71.26 - 89.07: 19 Dihedral angle restraints: 12130 sinusoidal: 6621 harmonic: 5509 Sorted by residual: dihedral pdb=" CA GLY A 342 " pdb=" C GLY A 342 " pdb=" N SER A 343 " pdb=" CA SER A 343 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA GLY B 342 " pdb=" C GLY B 342 " pdb=" N SER B 343 " pdb=" CA SER B 343 " ideal model delta harmonic sigma weight residual 180.00 156.71 23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA GLY C 342 " pdb=" C GLY C 342 " pdb=" N SER C 343 " pdb=" CA SER C 343 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 12127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.385: 1976 0.385 - 0.770: 0 0.770 - 1.154: 0 1.154 - 1.539: 2 1.539 - 1.924: 3 Chirality restraints: 1981 Sorted by residual: chirality pdb=" CG LEU A 18 " pdb=" CB LEU A 18 " pdb=" CD1 LEU A 18 " pdb=" CD2 LEU A 18 " both_signs ideal model delta sigma weight residual False -2.59 -0.67 -1.92 2.00e-01 2.50e+01 9.26e+01 chirality pdb=" CG LEU C 18 " pdb=" CB LEU C 18 " pdb=" CD1 LEU C 18 " pdb=" CD2 LEU C 18 " both_signs ideal model delta sigma weight residual False -2.59 -0.75 -1.84 2.00e-01 2.50e+01 8.50e+01 chirality pdb=" CG LEU B 18 " pdb=" CB LEU B 18 " pdb=" CD1 LEU B 18 " pdb=" CD2 LEU B 18 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.23e+01 ... (remaining 1978 not shown) Planarity restraints: 3872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 178 " 0.042 2.00e-02 2.50e+03 7.35e-02 1.62e+02 pdb=" CG PHE C 178 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 178 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE C 178 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 PHE C 178 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 PHE C 178 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE C 178 " 0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE C 178 " -0.166 2.00e-02 2.50e+03 pdb=" HD2 PHE C 178 " -0.101 2.00e-02 2.50e+03 pdb=" HE1 PHE C 178 " 0.058 2.00e-02 2.50e+03 pdb=" HE2 PHE C 178 " 0.026 2.00e-02 2.50e+03 pdb=" HZ PHE C 178 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 56 " -0.038 2.00e-02 2.50e+03 7.30e-02 1.60e+02 pdb=" CG PHE C 56 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE C 56 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 56 " 0.088 2.00e-02 2.50e+03 pdb=" CE1 PHE C 56 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE C 56 " 0.067 2.00e-02 2.50e+03 pdb=" CZ PHE C 56 " 0.064 2.00e-02 2.50e+03 pdb=" HD1 PHE C 56 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 PHE C 56 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 PHE C 56 " -0.034 2.00e-02 2.50e+03 pdb=" HE2 PHE C 56 " -0.198 2.00e-02 2.50e+03 pdb=" HZ PHE C 56 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 284 " 0.008 2.00e-02 2.50e+03 6.18e-02 1.53e+02 pdb=" CG TRP C 284 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 284 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP C 284 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP C 284 " 0.081 2.00e-02 2.50e+03 pdb=" CE2 TRP C 284 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP C 284 " -0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 284 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 284 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 284 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP C 284 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP C 284 " -0.102 2.00e-02 2.50e+03 pdb=" HE3 TRP C 284 " -0.069 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 284 " -0.101 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 284 " -0.034 2.00e-02 2.50e+03 pdb=" HH2 TRP C 284 " 0.154 2.00e-02 2.50e+03 ... (remaining 3869 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2338 2.20 - 2.80: 54295 2.80 - 3.40: 65616 3.40 - 4.00: 93284 4.00 - 4.60: 146017 Nonbonded interactions: 361550 Sorted by model distance: nonbonded pdb=" O ASN D 60 " pdb=" HG SER D 64 " model vdw 1.596 1.850 nonbonded pdb=" H ALA D 118 " pdb=" O HIS D 238 " model vdw 1.610 1.850 nonbonded pdb=" HE2 HIS D 156 " pdb=" OD1 ASP D 219 " model vdw 1.623 1.850 nonbonded pdb="HH21 ARG A 423 " pdb=" OE2 GLU A 430 " model vdw 1.624 1.850 nonbonded pdb=" HB VAL B 217 " pdb="HG22 VAL B 217 " model vdw 1.648 1.952 ... (remaining 361545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 30 through 73 or (resid \ 74 through 77 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 78 through 92 or (resid 93 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H or \ name HA )) or (resid 94 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 95 through 129 or resid 131 through 431)) selection = (chain 'B' and (resid 10 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 40 through 92 or (resid \ 93 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name OE1 or name OE2 or name H or name HA )) or (resid 94 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 95 through 12 \ 9 or resid 131 through 431)) selection = (chain 'C' and (resid 10 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 30 through 31 or (resid \ 32 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 33 through 38 or (resid 39 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 40 through 73 or (resid 74 through 7 \ 7 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 78 through 92 or (resid 93 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name OE1 or name OE2 or name H or name HA )) \ or (resid 94 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 95 through 129 or resid 131 through 431)) selection = (chain 'D' and (resid 10 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 33 through 38 or (resid \ 39 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 40 through 75 or (resid 76 through 77 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 78 through 129 or resid 1 \ 31 through 431)) } 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=0.50 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: 1.100 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: 0.500 Extract box with map and model: 2.730 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 87.380 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.080 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 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 : 0.021 0.203 13092 Z= 1.382 Angle : 1.170 12.163 17767 Z= 0.626 Chirality : 0.124 1.924 1981 Planarity : 0.009 0.060 2319 Dihedral : 13.950 87.436 4893 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.41 % Favored : 94.47 % Rotamer: Outliers : 4.81 % Allowed : 7.00 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.17), residues: 1629 helix: -2.13 (0.19), residues: 400 sheet: -3.00 (0.29), residues: 208 loop : -1.95 (0.17), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.013 TRP B 304 HIS 0.030 0.009 HIS C 46 PHE 0.046 0.009 PHE B 178 TYR 0.036 0.008 TYR B 145 ARG 0.037 0.005 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 305 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 85 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: D 126 ASP cc_start: 0.7537 (t0) cc_final: 0.7328 (t0) REVERT: D 222 TYR cc_start: 0.8290 (t80) cc_final: 0.7689 (t80) REVERT: D 289 ASP cc_start: 0.7333 (t70) cc_final: 0.7110 (t0) REVERT: D 302 ARG cc_start: 0.8357 (mmt90) cc_final: 0.8111 (mmt-90) REVERT: D 375 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6968 (mtm-85) REVERT: D 424 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8387 (mtpt) REVERT: A 93 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7245 (mm-30) REVERT: A 285 LYS cc_start: 0.8491 (tttt) cc_final: 0.8259 (ttpp) REVERT: A 353 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8301 (mtp-110) REVERT: A 424 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8402 (mtpt) REVERT: C 50 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7797 (ptmt) REVERT: C 74 GLN cc_start: 0.8502 (tt0) cc_final: 0.8098 (tm-30) REVERT: C 76 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7302 (mp10) REVERT: C 95 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.5668 (mmt) REVERT: C 162 ARG cc_start: 0.7885 (mmm160) cc_final: 0.7590 (mmm160) REVERT: C 285 LYS cc_start: 0.8280 (tttt) cc_final: 0.7856 (ttpp) REVERT: C 301 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8133 (t0) REVERT: C 319 VAL cc_start: 0.8842 (m) cc_final: 0.8562 (m) REVERT: C 408 TYR cc_start: 0.8137 (t80) cc_final: 0.6811 (t80) REVERT: C 418 THR cc_start: 0.8829 (m) cc_final: 0.8532 (p) REVERT: B 154 ILE cc_start: 0.8401 (mm) cc_final: 0.8152 (mt) REVERT: B 164 THR cc_start: 0.9110 (t) cc_final: 0.8861 (m) REVERT: B 188 LYS cc_start: 0.7667 (tttt) cc_final: 0.7312 (tttm) REVERT: B 213 MET cc_start: 0.8067 (mtp) cc_final: 0.7743 (mtp) REVERT: B 328 MET cc_start: 0.6610 (mtt) cc_final: 0.5880 (ttt) REVERT: B 399 ASN cc_start: 0.6225 (t0) cc_final: 0.5563 (m-40) outliers start: 65 outliers final: 35 residues processed: 359 average time/residue: 0.6425 time to fit residues: 319.7708 Evaluate side-chains 237 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 310 ASN C 46 HIS C 198 ASN B 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13092 Z= 0.183 Angle : 0.586 10.730 17767 Z= 0.295 Chirality : 0.093 1.697 1981 Planarity : 0.005 0.040 2319 Dihedral : 8.869 72.666 1969 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.06 % Allowed : 11.81 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.19), residues: 1629 helix: -0.95 (0.24), residues: 400 sheet: -2.37 (0.30), residues: 208 loop : -1.57 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 284 HIS 0.007 0.001 HIS B 78 PHE 0.010 0.001 PHE D 259 TYR 0.021 0.001 TYR D 224 ARG 0.006 0.000 ARG D 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 122 THR cc_start: 0.8082 (m) cc_final: 0.7803 (p) REVERT: D 126 ASP cc_start: 0.7516 (t0) cc_final: 0.7279 (t0) REVERT: D 134 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7803 (mt-10) REVERT: D 289 ASP cc_start: 0.7895 (t70) cc_final: 0.7571 (t0) REVERT: A 82 GLN cc_start: 0.8461 (tt0) cc_final: 0.8159 (tt0) REVERT: A 253 LEU cc_start: 0.8010 (mm) cc_final: 0.7731 (mp) REVERT: A 285 LYS cc_start: 0.8340 (tttt) cc_final: 0.8108 (ttpp) REVERT: A 353 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8184 (mtp-110) REVERT: A 423 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7872 (mtp180) REVERT: C 76 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7208 (mp10) REVERT: C 162 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7443 (mmm160) REVERT: C 232 ARG cc_start: 0.8381 (mtt90) cc_final: 0.8010 (mtt90) REVERT: C 285 LYS cc_start: 0.8042 (tttt) cc_final: 0.7800 (ttmm) REVERT: C 289 ASP cc_start: 0.7595 (t70) cc_final: 0.7314 (t0) REVERT: C 301 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8077 (t0) REVERT: C 418 THR cc_start: 0.8860 (m) cc_final: 0.8439 (m) REVERT: C 421 MET cc_start: 0.8550 (mpt) cc_final: 0.7933 (mpt) REVERT: B 151 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7406 (tpm170) REVERT: B 154 ILE cc_start: 0.8323 (mm) cc_final: 0.8107 (mt) REVERT: B 209 SER cc_start: 0.8391 (t) cc_final: 0.7931 (p) REVERT: B 213 MET cc_start: 0.8046 (mtp) cc_final: 0.7765 (mtp) REVERT: B 328 MET cc_start: 0.6581 (mtt) cc_final: 0.6031 (ttt) REVERT: B 399 ASN cc_start: 0.6477 (t0) cc_final: 0.5759 (t0) outliers start: 42 outliers final: 28 residues processed: 263 average time/residue: 0.6015 time to fit residues: 225.1361 Evaluate side-chains 222 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13092 Z= 0.262 Angle : 0.567 10.354 17767 Z= 0.286 Chirality : 0.094 1.721 1981 Planarity : 0.004 0.042 2319 Dihedral : 7.578 73.269 1931 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.35 % Allowed : 13.12 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.19), residues: 1629 helix: -0.59 (0.26), residues: 400 sheet: -1.80 (0.31), residues: 208 loop : -1.38 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 284 HIS 0.004 0.001 HIS B 78 PHE 0.011 0.001 PHE D 218 TYR 0.014 0.001 TYR D 224 ARG 0.003 0.000 ARG D 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 205 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 122 THR cc_start: 0.7979 (m) cc_final: 0.7705 (p) REVERT: D 126 ASP cc_start: 0.7535 (t0) cc_final: 0.7296 (t0) REVERT: D 134 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7817 (mt-10) REVERT: D 222 TYR cc_start: 0.8378 (t80) cc_final: 0.7741 (t80) REVERT: D 289 ASP cc_start: 0.8240 (t70) cc_final: 0.7986 (t0) REVERT: D 424 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8549 (mtpt) REVERT: A 82 GLN cc_start: 0.8436 (tt0) cc_final: 0.8088 (tt0) REVERT: A 285 LYS cc_start: 0.8381 (tttt) cc_final: 0.8157 (ttpp) REVERT: A 310 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7432 (p0) REVERT: A 353 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8253 (mtp-110) REVERT: C 148 ASP cc_start: 0.7424 (t0) cc_final: 0.7094 (t0) REVERT: C 301 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8110 (t0) REVERT: C 363 ASP cc_start: 0.8185 (t0) cc_final: 0.7925 (t0) REVERT: C 408 TYR cc_start: 0.8086 (t80) cc_final: 0.6836 (t80) REVERT: B 151 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7268 (tpm170) REVERT: B 154 ILE cc_start: 0.8310 (mm) cc_final: 0.8057 (mt) REVERT: B 209 SER cc_start: 0.8442 (t) cc_final: 0.8020 (p) REVERT: B 213 MET cc_start: 0.8273 (mtp) cc_final: 0.7761 (mtp) REVERT: B 328 MET cc_start: 0.6554 (mtt) cc_final: 0.6091 (ttt) REVERT: B 399 ASN cc_start: 0.6290 (t0) cc_final: 0.5870 (t0) outliers start: 46 outliers final: 34 residues processed: 244 average time/residue: 0.6141 time to fit residues: 209.9495 Evaluate side-chains 224 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 77 optimal weight: 0.0040 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 100 optimal weight: 0.1980 chunk 149 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13092 Z= 0.188 Angle : 0.536 10.507 17767 Z= 0.265 Chirality : 0.093 1.716 1981 Planarity : 0.004 0.039 2319 Dihedral : 7.012 73.778 1918 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.92 % Allowed : 13.70 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.20), residues: 1629 helix: -0.19 (0.27), residues: 396 sheet: -1.59 (0.32), residues: 208 loop : -1.21 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 284 HIS 0.003 0.001 HIS B 78 PHE 0.008 0.001 PHE D 218 TYR 0.014 0.001 TYR D 224 ARG 0.006 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 193 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 122 THR cc_start: 0.7935 (m) cc_final: 0.7673 (p) REVERT: D 126 ASP cc_start: 0.7544 (t0) cc_final: 0.7302 (t0) REVERT: D 134 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7758 (mt-10) REVERT: D 222 TYR cc_start: 0.8381 (t80) cc_final: 0.7746 (t80) REVERT: D 424 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8546 (mtpt) REVERT: A 82 GLN cc_start: 0.8468 (tt0) cc_final: 0.8150 (tt0) REVERT: A 285 LYS cc_start: 0.8348 (tttt) cc_final: 0.8118 (ttpp) REVERT: A 353 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8265 (mtp-110) REVERT: C 50 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7788 (ptmt) REVERT: C 148 ASP cc_start: 0.7423 (t0) cc_final: 0.6915 (t0) REVERT: C 301 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8074 (t0) REVERT: C 363 ASP cc_start: 0.8255 (t0) cc_final: 0.8003 (t0) REVERT: C 408 TYR cc_start: 0.8056 (t80) cc_final: 0.6873 (t80) REVERT: B 154 ILE cc_start: 0.8299 (mm) cc_final: 0.8013 (mt) REVERT: B 209 SER cc_start: 0.8408 (t) cc_final: 0.7987 (p) REVERT: B 213 MET cc_start: 0.8313 (mtp) cc_final: 0.7804 (mtp) outliers start: 40 outliers final: 34 residues processed: 224 average time/residue: 0.5391 time to fit residues: 175.5484 Evaluate side-chains 215 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 178 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13092 Z= 0.484 Angle : 0.635 10.325 17767 Z= 0.328 Chirality : 0.095 1.724 1981 Planarity : 0.005 0.043 2319 Dihedral : 7.228 70.854 1910 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.43 % Allowed : 14.29 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.20), residues: 1629 helix: -0.40 (0.26), residues: 396 sheet: -1.83 (0.32), residues: 220 loop : -1.36 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 284 HIS 0.010 0.001 HIS A 326 PHE 0.016 0.002 PHE D 218 TYR 0.010 0.002 TYR C 283 ARG 0.004 0.000 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 174 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 126 ASP cc_start: 0.7639 (t0) cc_final: 0.7348 (t0) REVERT: D 424 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8561 (mtpt) REVERT: A 69 MET cc_start: 0.8565 (mtm) cc_final: 0.8245 (mtm) REVERT: A 249 THR cc_start: 0.8789 (m) cc_final: 0.8518 (p) REVERT: A 285 LYS cc_start: 0.8294 (tttt) cc_final: 0.8073 (ttpp) REVERT: A 302 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7618 (mtp-110) REVERT: A 353 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8333 (mtp-110) REVERT: C 301 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8111 (t0) REVERT: C 408 TYR cc_start: 0.8087 (t80) cc_final: 0.6911 (t80) REVERT: B 126 ASP cc_start: 0.8290 (p0) cc_final: 0.8080 (m-30) REVERT: B 209 SER cc_start: 0.8382 (t) cc_final: 0.7975 (p) REVERT: B 348 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8399 (t) outliers start: 47 outliers final: 37 residues processed: 209 average time/residue: 0.5475 time to fit residues: 169.0062 Evaluate side-chains 204 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13092 Z= 0.188 Angle : 0.538 10.582 17767 Z= 0.266 Chirality : 0.094 1.712 1981 Planarity : 0.004 0.040 2319 Dihedral : 6.780 71.252 1908 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.41 % Allowed : 16.18 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.20), residues: 1629 helix: -0.04 (0.27), residues: 392 sheet: -1.68 (0.33), residues: 220 loop : -1.16 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 284 HIS 0.004 0.001 HIS A 78 PHE 0.009 0.001 PHE D 218 TYR 0.012 0.001 TYR D 224 ARG 0.004 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 126 ASP cc_start: 0.7560 (t0) cc_final: 0.7259 (t0) REVERT: D 134 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7791 (mt-10) REVERT: D 424 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8516 (mtpt) REVERT: A 249 THR cc_start: 0.8757 (m) cc_final: 0.8497 (p) REVERT: A 285 LYS cc_start: 0.8246 (tttt) cc_final: 0.8020 (ttpp) REVERT: A 302 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7437 (mtp-110) REVERT: A 353 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8330 (mtp-110) REVERT: C 50 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7856 (ptmt) REVERT: C 301 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8099 (t0) REVERT: C 408 TYR cc_start: 0.8016 (t80) cc_final: 0.6902 (t80) outliers start: 33 outliers final: 27 residues processed: 199 average time/residue: 0.5847 time to fit residues: 168.8709 Evaluate side-chains 195 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN B 310 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13092 Z= 0.246 Angle : 0.544 10.609 17767 Z= 0.270 Chirality : 0.094 1.719 1981 Planarity : 0.004 0.039 2319 Dihedral : 6.576 72.085 1902 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.70 % Allowed : 15.96 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1629 helix: 0.12 (0.27), residues: 388 sheet: -1.67 (0.33), residues: 220 loop : -1.04 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 284 HIS 0.004 0.001 HIS D 156 PHE 0.009 0.001 PHE D 218 TYR 0.009 0.001 TYR D 224 ARG 0.007 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 126 ASP cc_start: 0.7558 (t0) cc_final: 0.7253 (t0) REVERT: D 134 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7802 (mt-10) REVERT: D 424 LYS cc_start: 0.8727 (mtmt) cc_final: 0.8506 (mtpt) REVERT: A 82 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: A 162 ARG cc_start: 0.7402 (mmm160) cc_final: 0.6877 (mmm-85) REVERT: A 249 THR cc_start: 0.8784 (m) cc_final: 0.8525 (p) REVERT: A 265 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6610 (pm20) REVERT: A 285 LYS cc_start: 0.8253 (tttt) cc_final: 0.8032 (ttpp) REVERT: A 302 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7464 (mtp-110) REVERT: A 353 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8317 (mtp-110) REVERT: C 148 ASP cc_start: 0.7220 (t0) cc_final: 0.6718 (t0) REVERT: C 232 ARG cc_start: 0.8526 (mtt90) cc_final: 0.8261 (mtt90) REVERT: C 301 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8126 (t0) REVERT: C 408 TYR cc_start: 0.8003 (t80) cc_final: 0.6937 (t80) REVERT: B 82 GLN cc_start: 0.8503 (tt0) cc_final: 0.8152 (tt0) outliers start: 37 outliers final: 28 residues processed: 203 average time/residue: 0.5951 time to fit residues: 171.7526 Evaluate side-chains 195 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 100 optimal weight: 0.0000 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13092 Z= 0.163 Angle : 0.527 10.717 17767 Z= 0.258 Chirality : 0.093 1.709 1981 Planarity : 0.004 0.039 2319 Dihedral : 6.306 72.616 1897 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.55 % Allowed : 16.55 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.21), residues: 1629 helix: 0.21 (0.27), residues: 392 sheet: -1.41 (0.33), residues: 212 loop : -0.93 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 284 HIS 0.005 0.001 HIS A 78 PHE 0.007 0.001 PHE D 218 TYR 0.011 0.001 TYR D 224 ARG 0.004 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 126 ASP cc_start: 0.7568 (t0) cc_final: 0.7274 (t0) REVERT: D 134 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7784 (mt-10) REVERT: D 424 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8489 (mtpt) REVERT: D 425 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.9004 (mp) REVERT: A 82 GLN cc_start: 0.8347 (tt0) cc_final: 0.7974 (tt0) REVERT: A 249 THR cc_start: 0.8784 (m) cc_final: 0.8525 (p) REVERT: A 265 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6538 (pm20) REVERT: A 285 LYS cc_start: 0.8232 (tttt) cc_final: 0.8004 (ttpp) REVERT: A 302 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7457 (mtp-110) REVERT: A 353 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8264 (mtp-110) REVERT: C 50 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7800 (ptmt) REVERT: C 148 ASP cc_start: 0.7109 (t0) cc_final: 0.6614 (t0) REVERT: C 232 ARG cc_start: 0.8436 (mtt90) cc_final: 0.8219 (mtt90) REVERT: C 301 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8113 (t0) REVERT: C 408 TYR cc_start: 0.7980 (t80) cc_final: 0.6847 (t80) REVERT: B 82 GLN cc_start: 0.8474 (tt0) cc_final: 0.8131 (tt0) REVERT: B 250 GLU cc_start: 0.8606 (tp30) cc_final: 0.8281 (tp30) outliers start: 35 outliers final: 26 residues processed: 198 average time/residue: 0.6018 time to fit residues: 169.1986 Evaluate side-chains 201 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13092 Z= 0.290 Angle : 0.553 10.467 17767 Z= 0.275 Chirality : 0.093 1.692 1981 Planarity : 0.004 0.041 2319 Dihedral : 6.306 72.759 1895 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.48 % Allowed : 16.62 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1629 helix: 0.15 (0.27), residues: 392 sheet: -1.64 (0.33), residues: 220 loop : -0.88 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 284 HIS 0.005 0.001 HIS A 78 PHE 0.010 0.001 PHE D 218 TYR 0.008 0.001 TYR D 224 ARG 0.004 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 126 ASP cc_start: 0.7563 (t0) cc_final: 0.7248 (t0) REVERT: D 424 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8498 (mtpt) REVERT: D 425 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8989 (mp) REVERT: A 82 GLN cc_start: 0.8469 (tt0) cc_final: 0.8059 (tt0) REVERT: A 168 MET cc_start: 0.6452 (tpt) cc_final: 0.6194 (ttt) REVERT: A 249 THR cc_start: 0.8817 (m) cc_final: 0.8550 (p) REVERT: A 265 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6621 (pm20) REVERT: A 285 LYS cc_start: 0.8259 (tttt) cc_final: 0.8037 (ttpp) REVERT: A 302 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7411 (mtp-110) REVERT: C 148 ASP cc_start: 0.7218 (t0) cc_final: 0.6710 (t0) REVERT: C 301 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8155 (t0) REVERT: C 408 TYR cc_start: 0.7988 (t80) cc_final: 0.6909 (t80) REVERT: B 348 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8550 (t) outliers start: 34 outliers final: 27 residues processed: 194 average time/residue: 0.5886 time to fit residues: 162.0534 Evaluate side-chains 194 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13092 Z= 0.280 Angle : 0.552 10.511 17767 Z= 0.275 Chirality : 0.093 1.704 1981 Planarity : 0.004 0.043 2319 Dihedral : 6.277 72.379 1893 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.33 % Allowed : 16.84 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.21), residues: 1629 helix: 0.30 (0.28), residues: 388 sheet: -1.61 (0.33), residues: 220 loop : -0.90 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 284 HIS 0.004 0.001 HIS D 78 PHE 0.010 0.001 PHE D 218 TYR 0.008 0.001 TYR D 224 ARG 0.004 0.000 ARG D 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue TYR 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 126 ASP cc_start: 0.7565 (t0) cc_final: 0.7249 (t0) REVERT: D 424 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8424 (mtpt) REVERT: D 425 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8970 (mp) REVERT: A 168 MET cc_start: 0.6505 (tpt) cc_final: 0.6206 (ttt) REVERT: A 249 THR cc_start: 0.8849 (m) cc_final: 0.8576 (p) REVERT: A 265 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6593 (pm20) REVERT: A 285 LYS cc_start: 0.8311 (tttt) cc_final: 0.8089 (ttpp) REVERT: A 302 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7449 (mtp-110) REVERT: C 50 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7864 (ptmt) REVERT: C 148 ASP cc_start: 0.7236 (t0) cc_final: 0.6687 (t0) REVERT: C 186 ASN cc_start: 0.8335 (t0) cc_final: 0.7956 (t0) REVERT: C 301 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8203 (t0) REVERT: C 347 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7525 (mm-40) REVERT: C 408 TYR cc_start: 0.8019 (t80) cc_final: 0.6907 (t80) outliers start: 32 outliers final: 25 residues processed: 193 average time/residue: 0.5910 time to fit residues: 163.2386 Evaluate side-chains 194 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 423 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 39 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.165633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125463 restraints weight = 47099.979| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.01 r_work: 0.3427 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13092 Z= 0.180 Angle : 0.531 10.691 17767 Z= 0.261 Chirality : 0.093 1.703 1981 Planarity : 0.004 0.075 2319 Dihedral : 6.057 72.678 1889 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.26 % Allowed : 16.98 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1629 helix: 0.41 (0.28), residues: 388 sheet: -1.36 (0.34), residues: 212 loop : -0.84 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 284 HIS 0.004 0.001 HIS D 78 PHE 0.008 0.001 PHE D 218 TYR 0.010 0.001 TYR D 224 ARG 0.010 0.000 ARG C 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5885.76 seconds wall clock time: 104 minutes 35.85 seconds (6275.85 seconds total)