Starting phenix.real_space_refine on Thu Jan 18 08:31:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwc_27752/01_2024/8dwc_27752.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwc_27752/01_2024/8dwc_27752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwc_27752/01_2024/8dwc_27752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwc_27752/01_2024/8dwc_27752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwc_27752/01_2024/8dwc_27752.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwc_27752/01_2024/8dwc_27752.pdb" } resolution = 2.87 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5318 2.51 5 N 1413 2.21 5 O 1511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8298 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 109 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2480 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1925 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1704 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 4.94, per 1000 atoms: 0.60 Number of scatterers: 8298 At special positions: 0 Unit cell: (104.72, 115.28, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1511 8.00 N 1413 7.00 C 5318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 3.04 Conformation dependent library (CDL) restraints added in 1.8 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 38.5% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 Processing helix chain 'C' and resid 4 through 24 removed outlier: 3.667A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.559A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.503A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 55 removed outlier: 3.565A pdb=" N GLY R 44 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 86 removed outlier: 3.686A pdb=" N TYR R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 126 removed outlier: 3.991A pdb=" N ILE R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) Proline residue: R 100 - end of helix removed outlier: 4.759A pdb=" N PHE R 104 " --> pdb=" O PRO R 100 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE R 107 " --> pdb=" O MET R 103 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 137 through 161 Processing helix chain 'R' and resid 170 through 204 removed outlier: 3.807A pdb=" N GLN R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR R 175 " --> pdb=" O ALA R 171 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER R 176 " --> pdb=" O TRP R 172 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR R 180 " --> pdb=" O SER R 176 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 227 Processing helix chain 'R' and resid 230 through 239 removed outlier: 3.607A pdb=" N ILE R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 253 Processing helix chain 'R' and resid 253 through 273 Proline residue: R 269 - end of helix Processing helix chain 'R' and resid 273 through 278 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.191A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.518A pdb=" N GLU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.997A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.622A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.965A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.779A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.133A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.620A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.533A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.729A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.180A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.896A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.011A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.657A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 175 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.647A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.538A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.648A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.515A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.663A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS E 96 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY E 114 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR E 94 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR E 116 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA E 92 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.556A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.597A pdb=" N ASP B 85 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ALA B 105 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1176 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: 2.60 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2603 1.33 - 1.45: 1529 1.45 - 1.57: 4274 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8482 Sorted by residual: bond pdb=" N VAL B 219 " pdb=" CA VAL B 219 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.29e-02 6.01e+03 6.29e+00 bond pdb=" N ASP B 220 " pdb=" CA ASP B 220 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.19e+00 bond pdb=" N THR B 221 " pdb=" CA THR B 221 " ideal model delta sigma weight residual 1.455 1.484 -0.030 1.37e-02 5.33e+03 4.69e+00 bond pdb=" N ALA B 218 " pdb=" CA ALA B 218 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.33e-02 5.65e+03 3.86e+00 bond pdb=" CG1 ILE B 49 " pdb=" CD1 ILE B 49 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.46e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.81: 117 105.81 - 112.88: 4610 112.88 - 119.95: 2693 119.95 - 127.02: 4023 127.02 - 134.09: 102 Bond angle restraints: 11545 Sorted by residual: angle pdb=" N THR B 221 " pdb=" CA THR B 221 " pdb=" C THR B 221 " ideal model delta sigma weight residual 113.72 109.31 4.41 1.30e+00 5.92e-01 1.15e+01 angle pdb=" N ALA B 218 " pdb=" CA ALA B 218 " pdb=" C ALA B 218 " ideal model delta sigma weight residual 113.23 109.46 3.77 1.24e+00 6.50e-01 9.26e+00 angle pdb=" N VAL B 219 " pdb=" CA VAL B 219 " pdb=" C VAL B 219 " ideal model delta sigma weight residual 112.80 109.75 3.05 1.15e+00 7.56e-01 7.03e+00 angle pdb=" CA ASP B 220 " pdb=" C ASP B 220 " pdb=" O ASP B 220 " ideal model delta sigma weight residual 120.92 118.34 2.58 1.14e+00 7.69e-01 5.13e+00 angle pdb=" C ASP B 42 " pdb=" N ASN B 43 " pdb=" CA ASN B 43 " ideal model delta sigma weight residual 124.82 128.66 -3.84 1.78e+00 3.16e-01 4.66e+00 ... (remaining 11540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 4465 15.94 - 31.87: 379 31.87 - 47.81: 78 47.81 - 63.74: 10 63.74 - 79.68: 3 Dihedral angle restraints: 4935 sinusoidal: 1742 harmonic: 3193 Sorted by residual: dihedral pdb=" CA MET E 128 " pdb=" C MET E 128 " pdb=" N THR E 129 " pdb=" CA THR E 129 " ideal model delta harmonic sigma weight residual 180.00 -156.87 -23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP C 258 " pdb=" C ASP C 258 " pdb=" N GLN C 259 " pdb=" CA GLN C 259 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 125.65 -32.65 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 4932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 872 0.042 - 0.084: 349 0.084 - 0.126: 109 0.126 - 0.168: 9 0.168 - 0.210: 3 Chirality restraints: 1342 Sorted by residual: chirality pdb=" CB VAL B 109 " pdb=" CA VAL B 109 " pdb=" CG1 VAL B 109 " pdb=" CG2 VAL B 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU B 143 " pdb=" CB LEU B 143 " pdb=" CD1 LEU B 143 " pdb=" CD2 LEU B 143 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA VAL B 219 " pdb=" N VAL B 219 " pdb=" C VAL B 219 " pdb=" CB VAL B 219 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1339 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 217 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C CYS B 217 " 0.033 2.00e-02 2.50e+03 pdb=" O CYS B 217 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA B 218 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO C 194 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 209 " 0.012 2.00e-02 2.50e+03 1.37e-02 2.82e+00 pdb=" CG HIS B 209 " -0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS B 209 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 209 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS B 209 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 209 " 0.004 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 111 2.66 - 3.22: 7580 3.22 - 3.78: 12389 3.78 - 4.34: 17741 4.34 - 4.90: 29887 Nonbonded interactions: 67708 Sorted by model distance: nonbonded pdb=" OH TYR R 130 " pdb=" OH TYR B 243 " model vdw 2.095 2.440 nonbonded pdb=" NH2 ARG B 93 " pdb=" OD1 ASP B 124 " model vdw 2.123 2.520 nonbonded pdb=" O SER B 44 " pdb=" ND2 ASN B 144 " model vdw 2.149 2.520 nonbonded pdb=" OD2 ASP R 177 " pdb=" NE1 TRP R 241 " model vdw 2.229 2.520 nonbonded pdb=" O GLN C 75 " pdb=" OG SER C 98 " model vdw 2.232 2.440 ... (remaining 67703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.170 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.030 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.008 0.073 8482 Z= 0.503 Angle : 0.645 7.370 11545 Z= 0.354 Chirality : 0.047 0.210 1342 Planarity : 0.004 0.044 1448 Dihedral : 12.543 79.679 2867 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.14 (0.24), residues: 1082 helix: -1.16 (0.24), residues: 365 sheet: 0.11 (0.31), residues: 282 loop : -0.78 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 63 HIS 0.016 0.002 HIS B 82 PHE 0.020 0.003 PHE B 215 TYR 0.026 0.002 TYR C 59 ARG 0.013 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.807 Fit side-chains REVERT: C 163 ASP cc_start: 0.7475 (p0) cc_final: 0.7192 (p0) REVERT: C 188 MET cc_start: 0.7933 (mmp) cc_final: 0.7514 (mmp) REVERT: B 25 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6879 (tm-30) REVERT: B 114 ASP cc_start: 0.7198 (t70) cc_final: 0.6969 (t70) REVERT: B 229 ASN cc_start: 0.8236 (m-40) cc_final: 0.7986 (m-40) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 1.0257 time to fit residues: 221.3446 Evaluate side-chains 188 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8482 Z= 0.252 Angle : 0.563 8.430 11545 Z= 0.296 Chirality : 0.043 0.180 1342 Planarity : 0.004 0.038 1448 Dihedral : 4.525 17.672 1181 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.06 % Allowed : 10.98 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.18 (0.25), residues: 1082 helix: 1.05 (0.27), residues: 348 sheet: 0.30 (0.31), residues: 285 loop : -0.66 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.009 0.001 HIS B 82 PHE 0.017 0.002 PHE C 199 TYR 0.015 0.002 TYR E 178 ARG 0.006 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 0.975 Fit side-chains REVERT: C 223 THR cc_start: 0.7912 (p) cc_final: 0.7696 (t) REVERT: C 259 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: R 85 LEU cc_start: 0.7086 (mt) cc_final: 0.6856 (mm) REVERT: R 211 LEU cc_start: 0.7991 (mp) cc_final: 0.7739 (tp) REVERT: E 69 THR cc_start: 0.8425 (p) cc_final: 0.8191 (t) REVERT: E 192 SER cc_start: 0.8174 (t) cc_final: 0.7955 (t) REVERT: B 25 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6795 (tm-30) REVERT: B 229 ASN cc_start: 0.8175 (m-40) cc_final: 0.7930 (m-40) outliers start: 9 outliers final: 6 residues processed: 195 average time/residue: 1.0807 time to fit residues: 225.6434 Evaluate side-chains 193 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 154 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 0.0170 chunk 107 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8482 Z= 0.219 Angle : 0.525 8.560 11545 Z= 0.275 Chirality : 0.042 0.144 1342 Planarity : 0.004 0.038 1448 Dihedral : 4.269 16.456 1181 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.30 % Allowed : 14.76 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.62 (0.26), residues: 1082 helix: 1.79 (0.27), residues: 349 sheet: 0.34 (0.30), residues: 297 loop : -0.62 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.008 0.001 HIS B 82 PHE 0.017 0.001 PHE C 199 TYR 0.014 0.001 TYR E 178 ARG 0.007 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 1.051 Fit side-chains REVERT: C 223 THR cc_start: 0.7912 (p) cc_final: 0.7676 (t) REVERT: C 307 VAL cc_start: 0.8604 (t) cc_final: 0.8354 (p) REVERT: R 85 LEU cc_start: 0.7031 (mt) cc_final: 0.6812 (mm) REVERT: R 144 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8151 (t) REVERT: R 211 LEU cc_start: 0.7967 (mp) cc_final: 0.7693 (tp) REVERT: E 69 THR cc_start: 0.8413 (p) cc_final: 0.8153 (t) REVERT: E 83 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7557 (mtt) REVERT: E 166 LEU cc_start: 0.8510 (tt) cc_final: 0.8254 (tm) REVERT: E 192 SER cc_start: 0.8175 (t) cc_final: 0.7970 (t) REVERT: B 25 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6736 (tm-30) REVERT: B 29 LYS cc_start: 0.7820 (mttt) cc_final: 0.7560 (mtmt) REVERT: B 196 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 229 ASN cc_start: 0.8169 (m-40) cc_final: 0.7887 (m-40) outliers start: 11 outliers final: 2 residues processed: 198 average time/residue: 0.9918 time to fit residues: 210.9557 Evaluate side-chains 195 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain B residue 128 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN B 22 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8482 Z= 0.249 Angle : 0.521 9.037 11545 Z= 0.274 Chirality : 0.042 0.138 1342 Planarity : 0.004 0.040 1448 Dihedral : 4.209 16.175 1181 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.65 % Allowed : 15.94 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.80 (0.26), residues: 1082 helix: 2.08 (0.27), residues: 349 sheet: 0.39 (0.30), residues: 292 loop : -0.61 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.007 0.001 HIS B 82 PHE 0.017 0.002 PHE C 199 TYR 0.013 0.002 TYR E 178 ARG 0.008 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 0.953 Fit side-chains REVERT: C 223 THR cc_start: 0.7939 (p) cc_final: 0.7713 (t) REVERT: C 259 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: C 307 VAL cc_start: 0.8601 (t) cc_final: 0.8369 (p) REVERT: R 144 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8170 (t) REVERT: R 211 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7713 (tp) REVERT: E 69 THR cc_start: 0.8440 (p) cc_final: 0.8124 (t) REVERT: E 83 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7655 (mtt) REVERT: E 166 LEU cc_start: 0.8506 (tt) cc_final: 0.8254 (tm) REVERT: E 192 SER cc_start: 0.8162 (t) cc_final: 0.7962 (t) REVERT: B 25 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6709 (tm-30) REVERT: B 29 LYS cc_start: 0.7816 (mttt) cc_final: 0.7505 (mtmt) REVERT: B 195 LYS cc_start: 0.7644 (ttpp) cc_final: 0.7389 (ttpp) REVERT: B 196 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7187 (mm-30) REVERT: B 229 ASN cc_start: 0.8188 (m-40) cc_final: 0.7948 (m-40) outliers start: 14 outliers final: 7 residues processed: 198 average time/residue: 1.0211 time to fit residues: 217.0461 Evaluate side-chains 202 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.3980 chunk 1 optimal weight: 0.0030 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.0470 chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.4688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN R 67 ASN B 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8482 Z= 0.184 Angle : 0.487 8.071 11545 Z= 0.257 Chirality : 0.041 0.138 1342 Planarity : 0.004 0.056 1448 Dihedral : 4.059 15.575 1181 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.89 % Allowed : 16.77 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.06 (0.26), residues: 1082 helix: 2.39 (0.27), residues: 353 sheet: 0.53 (0.31), residues: 288 loop : -0.56 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.006 0.001 HIS B 82 PHE 0.016 0.001 PHE C 199 TYR 0.014 0.001 TYR E 178 ARG 0.010 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 196 time to evaluate : 0.924 Fit side-chains REVERT: C 59 TYR cc_start: 0.7650 (m-80) cc_final: 0.7211 (m-80) REVERT: C 259 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: C 307 VAL cc_start: 0.8583 (t) cc_final: 0.8365 (p) REVERT: R 144 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8172 (t) REVERT: R 211 LEU cc_start: 0.7930 (mp) cc_final: 0.7699 (tp) REVERT: E 69 THR cc_start: 0.8429 (p) cc_final: 0.8136 (t) REVERT: E 166 LEU cc_start: 0.8474 (tt) cc_final: 0.8239 (tm) REVERT: E 192 SER cc_start: 0.8165 (t) cc_final: 0.7963 (t) REVERT: B 25 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6708 (tm-30) REVERT: B 29 LYS cc_start: 0.7780 (mttt) cc_final: 0.7461 (mtmt) REVERT: B 195 LYS cc_start: 0.7646 (ttpp) cc_final: 0.7382 (ttpp) REVERT: B 196 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7203 (mm-30) REVERT: B 229 ASN cc_start: 0.8188 (m-40) cc_final: 0.7943 (m-40) REVERT: B 233 ASP cc_start: 0.7469 (t0) cc_final: 0.7105 (t70) outliers start: 16 outliers final: 8 residues processed: 199 average time/residue: 0.9913 time to fit residues: 212.2541 Evaluate side-chains 203 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 193 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 87 optimal weight: 0.0170 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 101 optimal weight: 0.0170 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 132 ASN R 67 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8482 Z= 0.137 Angle : 0.460 7.407 11545 Z= 0.244 Chirality : 0.040 0.137 1342 Planarity : 0.004 0.047 1448 Dihedral : 3.858 14.948 1181 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.77 % Allowed : 17.36 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.32 (0.26), residues: 1082 helix: 2.66 (0.28), residues: 355 sheet: 0.66 (0.32), residues: 275 loop : -0.43 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 82 PHE 0.017 0.001 PHE R 250 TYR 0.014 0.001 TYR E 178 ARG 0.010 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 0.815 Fit side-chains REVERT: C 59 TYR cc_start: 0.7600 (m-80) cc_final: 0.7204 (m-80) REVERT: C 259 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: C 307 VAL cc_start: 0.8559 (t) cc_final: 0.8333 (p) REVERT: R 144 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.8176 (t) REVERT: E 69 THR cc_start: 0.8388 (p) cc_final: 0.8123 (t) REVERT: E 78 THR cc_start: 0.8069 (m) cc_final: 0.7815 (t) REVERT: E 166 LEU cc_start: 0.8448 (tt) cc_final: 0.8242 (tm) REVERT: E 192 SER cc_start: 0.8154 (t) cc_final: 0.7947 (t) REVERT: B 25 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6750 (tm-30) REVERT: B 29 LYS cc_start: 0.7740 (mttt) cc_final: 0.7407 (mtmt) REVERT: B 195 LYS cc_start: 0.7651 (ttpp) cc_final: 0.7374 (ttpp) REVERT: B 229 ASN cc_start: 0.8170 (m-40) cc_final: 0.7935 (m-40) outliers start: 15 outliers final: 6 residues processed: 202 average time/residue: 0.9756 time to fit residues: 211.3838 Evaluate side-chains 203 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 88 ASN C 132 ASN R 67 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8482 Z= 0.248 Angle : 0.524 7.862 11545 Z= 0.271 Chirality : 0.042 0.135 1342 Planarity : 0.004 0.054 1448 Dihedral : 4.038 15.368 1181 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.13 % Allowed : 17.24 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.27 (0.26), residues: 1082 helix: 2.63 (0.27), residues: 353 sheet: 0.66 (0.32), residues: 272 loop : -0.47 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.006 0.001 HIS B 209 PHE 0.017 0.002 PHE C 199 TYR 0.012 0.001 TYR E 103 ARG 0.012 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 196 time to evaluate : 0.959 Fit side-chains REVERT: C 59 TYR cc_start: 0.7685 (m-80) cc_final: 0.7253 (m-80) REVERT: C 68 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8377 (ttt-90) REVERT: C 150 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8000 (mmt180) REVERT: C 163 ASP cc_start: 0.7210 (p0) cc_final: 0.6928 (p0) REVERT: C 259 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: C 307 VAL cc_start: 0.8559 (t) cc_final: 0.8355 (p) REVERT: R 144 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8196 (t) REVERT: E 166 LEU cc_start: 0.8464 (tt) cc_final: 0.8234 (tm) REVERT: E 192 SER cc_start: 0.8176 (t) cc_final: 0.7971 (t) REVERT: B 25 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6744 (tm-30) REVERT: B 29 LYS cc_start: 0.7800 (mttt) cc_final: 0.7414 (mtmt) REVERT: B 195 LYS cc_start: 0.7579 (ttpp) cc_final: 0.7327 (ttpp) REVERT: B 196 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7198 (mm-30) REVERT: B 229 ASN cc_start: 0.8180 (m-40) cc_final: 0.7942 (m-40) REVERT: B 233 ASP cc_start: 0.7444 (t0) cc_final: 0.7117 (t70) outliers start: 18 outliers final: 7 residues processed: 201 average time/residue: 1.0164 time to fit residues: 219.1462 Evaluate side-chains 203 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 88 ASN C 132 ASN R 67 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8482 Z= 0.208 Angle : 0.494 7.416 11545 Z= 0.260 Chirality : 0.041 0.136 1342 Planarity : 0.004 0.049 1448 Dihedral : 3.982 15.419 1181 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.01 % Allowed : 17.71 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.34 (0.26), residues: 1082 helix: 2.69 (0.27), residues: 354 sheet: 0.70 (0.32), residues: 273 loop : -0.44 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 PHE 0.019 0.001 PHE E 68 TYR 0.013 0.001 TYR E 178 ARG 0.012 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 0.953 Fit side-chains REVERT: C 59 TYR cc_start: 0.7685 (m-80) cc_final: 0.7257 (m-80) REVERT: C 150 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7871 (mmt180) REVERT: C 163 ASP cc_start: 0.7182 (p0) cc_final: 0.6904 (p0) REVERT: C 259 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: R 144 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8198 (t) REVERT: E 166 LEU cc_start: 0.8453 (tt) cc_final: 0.8231 (tm) REVERT: E 192 SER cc_start: 0.8156 (t) cc_final: 0.7952 (t) REVERT: B 25 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6748 (tm-30) REVERT: B 29 LYS cc_start: 0.7790 (mttt) cc_final: 0.7408 (mtmt) REVERT: B 195 LYS cc_start: 0.7577 (ttpp) cc_final: 0.7314 (ttpp) REVERT: B 196 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 229 ASN cc_start: 0.8183 (m-40) cc_final: 0.7952 (m-40) outliers start: 17 outliers final: 10 residues processed: 194 average time/residue: 1.0219 time to fit residues: 212.3118 Evaluate side-chains 203 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.5980 chunk 100 optimal weight: 0.0570 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 88 ASN C 132 ASN R 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8482 Z= 0.197 Angle : 0.490 7.420 11545 Z= 0.258 Chirality : 0.041 0.136 1342 Planarity : 0.004 0.047 1448 Dihedral : 3.953 15.095 1181 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.01 % Allowed : 17.83 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.38 (0.26), residues: 1082 helix: 2.71 (0.27), residues: 355 sheet: 0.69 (0.32), residues: 273 loop : -0.39 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 PHE 0.016 0.001 PHE C 199 TYR 0.013 0.001 TYR E 178 ARG 0.012 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 0.899 Fit side-chains REVERT: C 59 TYR cc_start: 0.7663 (m-80) cc_final: 0.7209 (m-80) REVERT: C 150 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7895 (mmt180) REVERT: C 259 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: R 144 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8179 (t) REVERT: E 68 PHE cc_start: 0.7721 (m-10) cc_final: 0.7370 (m-80) REVERT: E 166 LEU cc_start: 0.8444 (tt) cc_final: 0.8232 (tm) REVERT: E 192 SER cc_start: 0.8156 (t) cc_final: 0.7953 (t) REVERT: B 25 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6745 (tm-30) REVERT: B 29 LYS cc_start: 0.7793 (mttt) cc_final: 0.7421 (mtmt) REVERT: B 195 LYS cc_start: 0.7576 (ttpp) cc_final: 0.7314 (ttpp) REVERT: B 196 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7197 (mm-30) REVERT: B 229 ASN cc_start: 0.8174 (m-40) cc_final: 0.7942 (m-40) outliers start: 17 outliers final: 10 residues processed: 195 average time/residue: 1.0297 time to fit residues: 215.3446 Evaluate side-chains 204 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ARG Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 88 ASN C 132 ASN R 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8482 Z= 0.147 Angle : 0.464 6.634 11545 Z= 0.245 Chirality : 0.040 0.137 1342 Planarity : 0.003 0.032 1448 Dihedral : 3.793 14.696 1181 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.65 % Allowed : 17.47 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.53 (0.27), residues: 1082 helix: 2.89 (0.27), residues: 356 sheet: 0.73 (0.32), residues: 274 loop : -0.33 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.004 0.001 HIS B 82 PHE 0.014 0.001 PHE C 199 TYR 0.014 0.001 TYR E 178 ARG 0.007 0.000 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 0.984 Fit side-chains REVERT: C 59 TYR cc_start: 0.7608 (m-80) cc_final: 0.7181 (m-80) REVERT: C 259 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: R 144 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8181 (t) REVERT: E 68 PHE cc_start: 0.7566 (m-10) cc_final: 0.7282 (m-80) REVERT: E 192 SER cc_start: 0.8145 (t) cc_final: 0.7938 (t) REVERT: B 25 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6806 (tm-30) REVERT: B 29 LYS cc_start: 0.7794 (mttt) cc_final: 0.7412 (mtmt) REVERT: B 195 LYS cc_start: 0.7650 (ttpp) cc_final: 0.7371 (ttpp) REVERT: B 196 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7231 (mm-30) outliers start: 14 outliers final: 8 residues processed: 200 average time/residue: 0.9798 time to fit residues: 210.4924 Evaluate side-chains 200 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 88 ASN C 132 ASN R 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100066 restraints weight = 11791.365| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.73 r_work: 0.3150 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8482 Z= 0.200 Angle : 0.494 6.702 11545 Z= 0.260 Chirality : 0.041 0.134 1342 Planarity : 0.004 0.064 1448 Dihedral : 3.870 14.993 1181 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.53 % Allowed : 18.89 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.48 (0.26), residues: 1082 helix: 2.87 (0.27), residues: 354 sheet: 0.63 (0.32), residues: 270 loop : -0.31 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 PHE 0.017 0.001 PHE E 80 TYR 0.013 0.001 TYR E 178 ARG 0.016 0.001 ARG B 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3742.96 seconds wall clock time: 66 minutes 51.68 seconds (4011.68 seconds total)