Starting phenix.real_space_refine on Wed Feb 14 07:10:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv5_32138/02_2024/7vv5_32138_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv5_32138/02_2024/7vv5_32138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv5_32138/02_2024/7vv5_32138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv5_32138/02_2024/7vv5_32138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv5_32138/02_2024/7vv5_32138_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv5_32138/02_2024/7vv5_32138_updated.pdb" } resolution = 2.76 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= 0.006 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 66 5.16 5 C 5660 2.51 5 N 1474 2.21 5 O 1629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 125": "OD1" <-> "OD2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S GLU 208": "OE1" <-> "OE2" Residue "S GLU 222": "OE1" <-> "OE2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "R PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 176": "OD1" <-> "OD2" Residue "R PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 254": "OD1" <-> "OD2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8829 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 427 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1786 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2205 Unusual residues: {'6IB': 1, 'CLR': 1} Classifications: {'peptide': 268, 'undetermined': 2} Link IDs: {'PTRANS': 8, 'TRANS': 259, None: 2} Not linked: pdbres="TRP R 289 " pdbres="CLR R 401 " Not linked: pdbres="CLR R 401 " pdbres="6IB R 402 " Time building chain proxies: 4.87, per 1000 atoms: 0.55 Number of scatterers: 8829 At special positions: 0 Unit cell: (116.772, 108.356, 104.148, 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 66 16.00 O 1629 8.00 N 1474 7.00 C 5660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 33.2% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.862A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.321A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.123A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 23 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 209 through 211 No H-bonds generated for 'chain 'S' and resid 209 through 211' Processing helix chain 'R' and resid 31 through 56 Processing helix chain 'R' and resid 63 through 93 removed outlier: 4.251A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 132 Processing helix chain 'R' and resid 134 through 138 Processing helix chain 'R' and resid 145 through 167 Processing helix chain 'R' and resid 177 through 211 removed outlier: 3.926A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 235 Processing helix chain 'R' and resid 237 through 244 Processing helix chain 'R' and resid 246 through 249 No H-bonds generated for 'chain 'R' and resid 246 through 249' Processing helix chain 'R' and resid 257 through 279 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 281 through 287 removed outlier: 4.497A pdb=" N ARG R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS R 287 " --> pdb=" O GLY R 283 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.377A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.889A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.892A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.618A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.894A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.605A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.472A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.442A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 6.032A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.658A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= M, first strand: chain 'S' and resid 214 through 219 removed outlier: 6.211A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1116 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: 2.45 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 2811 1.35 - 1.48: 2505 1.48 - 1.61: 3616 1.61 - 1.75: 2 1.75 - 1.88: 90 Bond restraints: 9024 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.669 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C ALA S 40 " pdb=" N PRO S 41 " ideal model delta sigma weight residual 1.333 1.415 -0.082 1.44e-02 4.82e+03 3.26e+01 bond pdb=" CG LEU B 79 " pdb=" CD2 LEU B 79 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.62e+00 bond pdb=" CG1 ILE B 123 " pdb=" CD1 ILE B 123 " ideal model delta sigma weight residual 1.513 1.406 0.107 3.90e-02 6.57e+02 7.51e+00 bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.28e-02 6.10e+03 6.99e+00 ... (remaining 9019 not shown) Histogram of bond angle deviations from ideal: 96.18 - 103.83: 91 103.83 - 111.48: 3669 111.48 - 119.13: 3647 119.13 - 126.77: 4683 126.77 - 134.42: 140 Bond angle restraints: 12230 Sorted by residual: angle pdb=" N PRO S 41 " pdb=" CA PRO S 41 " pdb=" C PRO S 41 " ideal model delta sigma weight residual 113.81 121.95 -8.14 1.45e+00 4.76e-01 3.15e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 130.63 -7.89 1.44e+00 4.82e-01 3.01e+01 angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 113.45 120.88 -7.43 1.39e+00 5.18e-01 2.85e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 131.52 -9.98 1.91e+00 2.74e-01 2.73e+01 angle pdb=" C TRP R 250 " pdb=" N LYS R 251 " pdb=" CA LYS R 251 " ideal model delta sigma weight residual 122.08 129.29 -7.21 1.47e+00 4.63e-01 2.41e+01 ... (remaining 12225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4521 17.14 - 34.27: 579 34.27 - 51.41: 199 51.41 - 68.55: 56 68.55 - 85.69: 12 Dihedral angle restraints: 5367 sinusoidal: 2131 harmonic: 3236 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.43 -66.43 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CA THR R 30 " pdb=" C THR R 30 " pdb=" N LEU R 31 " pdb=" CA LEU R 31 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP R 254 " pdb=" C ASP R 254 " pdb=" N VAL R 255 " pdb=" CA VAL R 255 " ideal model delta harmonic sigma weight residual -180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 5364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1130 0.082 - 0.164: 227 0.164 - 0.246: 20 0.246 - 0.329: 7 0.329 - 0.411: 1 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CB VAL A 218 " pdb=" CA VAL A 218 " pdb=" CG1 VAL A 218 " pdb=" CG2 VAL A 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1382 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER S 172 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO S 173 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO S 173 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 173 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.046 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO S 75 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL R 149 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.014 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1855 2.77 - 3.30: 7320 3.30 - 3.83: 15841 3.83 - 4.37: 18554 4.37 - 4.90: 32112 Nonbonded interactions: 75682 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.236 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.286 2.440 nonbonded pdb=" O GLY R 27 " pdb=" OH TYR R 89 " model vdw 2.291 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.297 2.440 nonbonded pdb=" O SER R 264 " pdb=" OG SER R 268 " model vdw 2.306 2.440 ... (remaining 75677 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: 0.170 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: 1.330 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.210 Find NCS groups from input model: 0.370 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:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.012 0.134 9024 Z= 0.759 Angle : 1.174 16.073 12230 Z= 0.632 Chirality : 0.067 0.411 1385 Planarity : 0.008 0.069 1530 Dihedral : 18.052 85.686 3269 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 10.86 % Allowed : 18.27 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.82 (0.21), residues: 1108 helix: -2.79 (0.16), residues: 387 sheet: -0.57 (0.29), residues: 279 loop : -1.65 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP S 47 HIS 0.011 0.003 HIS S 35 PHE 0.028 0.004 PHE B 151 TYR 0.023 0.004 TYR S 50 ARG 0.005 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 216 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8256 (m-30) cc_final: 0.8052 (m-30) REVERT: A 29 LYS cc_start: 0.7879 (tppt) cc_final: 0.7514 (tppt) REVERT: A 32 ARG cc_start: 0.8335 (ptp90) cc_final: 0.7888 (ptp-170) REVERT: A 205 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6655 (mtm180) REVERT: A 248 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8127 (mttp) REVERT: A 273 LEU cc_start: 0.8539 (tp) cc_final: 0.8186 (tp) REVERT: A 305 CYS cc_start: 0.8128 (t) cc_final: 0.7844 (p) REVERT: B 10 GLU cc_start: 0.8181 (tp30) cc_final: 0.7699 (tp30) REVERT: B 15 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8502 (mtmt) REVERT: B 127 LYS cc_start: 0.9073 (mptm) cc_final: 0.8839 (mmtp) REVERT: B 146 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8856 (tp) REVERT: B 172 GLU cc_start: 0.7580 (pp20) cc_final: 0.7307 (tm-30) REVERT: B 188 MET cc_start: 0.8860 (mmm) cc_final: 0.8497 (mmm) REVERT: S 23 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8647 (p) REVERT: R 22 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.5832 (tm) REVERT: R 24 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6586 (mm) REVERT: R 28 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7115 (mmpt) REVERT: R 32 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7658 (tp) REVERT: R 52 LEU cc_start: 0.9279 (mt) cc_final: 0.9052 (mt) REVERT: R 58 ARG cc_start: 0.7892 (mmt-90) cc_final: 0.7662 (mmp80) REVERT: R 152 LEU cc_start: 0.8596 (mt) cc_final: 0.8371 (mt) REVERT: R 278 ILE cc_start: 0.9025 (mt) cc_final: 0.8749 (mt) REVERT: R 289 TRP cc_start: 0.5361 (p-90) cc_final: 0.4344 (m-10) outliers start: 104 outliers final: 34 residues processed: 303 average time/residue: 1.0689 time to fit residues: 346.7000 Evaluate side-chains 223 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 180 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 204 GLN A 213 HIS A 255 ASN B 175 GLN B 259 GLN B 311 HIS S 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9024 Z= 0.175 Angle : 0.570 9.550 12230 Z= 0.290 Chirality : 0.042 0.226 1385 Planarity : 0.004 0.037 1530 Dihedral : 10.067 82.186 1368 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.43 % Allowed : 25.05 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.78 (0.23), residues: 1108 helix: 0.02 (0.24), residues: 390 sheet: -0.10 (0.29), residues: 286 loop : -1.18 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.021 0.001 PHE R 257 TYR 0.016 0.001 TYR R 222 ARG 0.007 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 207 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8270 (ptp90) cc_final: 0.7919 (ptp-170) REVERT: A 242 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7450 (mtt180) REVERT: A 273 LEU cc_start: 0.8533 (tp) cc_final: 0.8115 (tp) REVERT: A 305 CYS cc_start: 0.8063 (t) cc_final: 0.7635 (t) REVERT: A 306 GLN cc_start: 0.8256 (mm110) cc_final: 0.8041 (mm110) REVERT: B 10 GLU cc_start: 0.8178 (tp30) cc_final: 0.7811 (tp30) REVERT: B 23 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8531 (tmmm) REVERT: B 101 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: B 127 LYS cc_start: 0.8865 (mptm) cc_final: 0.8595 (mmtm) REVERT: B 146 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8947 (tp) REVERT: B 188 MET cc_start: 0.8759 (mmm) cc_final: 0.8335 (mmm) REVERT: B 226 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: G 18 GLN cc_start: 0.9013 (tp40) cc_final: 0.8795 (tp40) REVERT: G 32 LYS cc_start: 0.8635 (tttt) cc_final: 0.8425 (tttm) REVERT: G 37 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8707 (mp) REVERT: S 62 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7407 (p0) REVERT: S 87 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7794 (mtp85) REVERT: R 22 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5493 (tm) REVERT: R 58 ARG cc_start: 0.7825 (mmt-90) cc_final: 0.7519 (mmp80) REVERT: R 59 MET cc_start: 0.8277 (mtp) cc_final: 0.8075 (mtp) REVERT: R 246 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9104 (OUTLIER) REVERT: R 278 ILE cc_start: 0.8903 (mt) cc_final: 0.8627 (mt) outliers start: 52 outliers final: 19 residues processed: 233 average time/residue: 1.2782 time to fit residues: 315.8651 Evaluate side-chains 211 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 255 ASN B 32 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9024 Z= 0.182 Angle : 0.550 10.281 12230 Z= 0.277 Chirality : 0.041 0.168 1385 Planarity : 0.003 0.032 1530 Dihedral : 8.382 81.935 1324 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 6.47 % Allowed : 24.74 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.09 (0.25), residues: 1108 helix: 1.15 (0.26), residues: 391 sheet: 0.05 (0.31), residues: 268 loop : -0.85 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.021 0.001 PHE R 257 TYR 0.016 0.001 TYR R 222 ARG 0.008 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 200 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8013 (ttt180) REVERT: A 32 ARG cc_start: 0.8186 (ptp90) cc_final: 0.7812 (ptp-170) REVERT: A 255 ASN cc_start: 0.8984 (m-40) cc_final: 0.8687 (m110) REVERT: A 273 LEU cc_start: 0.8579 (tp) cc_final: 0.8145 (tp) REVERT: A 302 TYR cc_start: 0.8864 (t80) cc_final: 0.8661 (t80) REVERT: A 304 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8255 (tm-30) REVERT: A 308 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7874 (mt-10) REVERT: B 10 GLU cc_start: 0.8241 (tp30) cc_final: 0.7815 (tp30) REVERT: B 23 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8493 (tmmm) REVERT: B 101 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8118 (mtm) REVERT: B 127 LYS cc_start: 0.8842 (mptm) cc_final: 0.8590 (mmtm) REVERT: B 146 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8919 (tp) REVERT: B 188 MET cc_start: 0.8751 (mmm) cc_final: 0.8419 (mmm) REVERT: B 226 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: G 17 GLU cc_start: 0.7806 (tp30) cc_final: 0.7104 (tp30) REVERT: G 32 LYS cc_start: 0.8576 (tttt) cc_final: 0.8326 (tttm) REVERT: G 37 LEU cc_start: 0.8946 (tp) cc_final: 0.8682 (mp) REVERT: S 43 LYS cc_start: 0.8424 (mppt) cc_final: 0.8222 (mppt) REVERT: S 87 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7765 (mtp85) REVERT: R 22 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5449 (tm) REVERT: R 50 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: R 58 ARG cc_start: 0.7824 (mmt-90) cc_final: 0.7561 (mmp80) REVERT: R 278 ILE cc_start: 0.8833 (mt) cc_final: 0.8535 (mt) outliers start: 62 outliers final: 23 residues processed: 231 average time/residue: 1.2856 time to fit residues: 315.0947 Evaluate side-chains 216 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 0.0770 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 204 GLN B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9024 Z= 0.220 Angle : 0.557 10.185 12230 Z= 0.281 Chirality : 0.042 0.157 1385 Planarity : 0.004 0.036 1530 Dihedral : 7.970 81.871 1320 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 6.05 % Allowed : 25.89 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.46 (0.25), residues: 1108 helix: 1.58 (0.26), residues: 390 sheet: 0.01 (0.30), residues: 278 loop : -0.58 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.023 0.001 PHE R 257 TYR 0.016 0.001 TYR R 222 ARG 0.008 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 188 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.7859 (ttt180) REVERT: A 32 ARG cc_start: 0.8201 (ptp90) cc_final: 0.7838 (ptp-170) REVERT: A 255 ASN cc_start: 0.8926 (m-40) cc_final: 0.8607 (m110) REVERT: A 273 LEU cc_start: 0.8592 (tp) cc_final: 0.8374 (tp) REVERT: B 10 GLU cc_start: 0.8267 (tp30) cc_final: 0.7863 (tp30) REVERT: B 15 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8543 (mtmt) REVERT: B 101 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8160 (mtm) REVERT: B 127 LYS cc_start: 0.8843 (mptm) cc_final: 0.8589 (mmtm) REVERT: B 146 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8917 (tp) REVERT: B 188 MET cc_start: 0.8775 (mmm) cc_final: 0.8448 (mmm) REVERT: B 197 ARG cc_start: 0.7539 (mmp-170) cc_final: 0.7241 (mmp-170) REVERT: B 226 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: G 32 LYS cc_start: 0.8599 (tttt) cc_final: 0.8370 (tttm) REVERT: G 37 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8650 (mp) REVERT: S 87 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7171 (mtp85) REVERT: R 22 LEU cc_start: 0.5751 (OUTLIER) cc_final: 0.5418 (tm) REVERT: R 50 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7466 (m-10) REVERT: R 58 ARG cc_start: 0.7802 (mmt-90) cc_final: 0.7543 (mmp80) REVERT: R 208 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7638 (mmm160) REVERT: R 270 LEU cc_start: 0.8814 (tp) cc_final: 0.8518 (tm) REVERT: R 278 ILE cc_start: 0.8852 (mt) cc_final: 0.8534 (mt) outliers start: 58 outliers final: 27 residues processed: 220 average time/residue: 1.3284 time to fit residues: 309.8263 Evaluate side-chains 218 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 204 GLN B 32 GLN B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 77 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9024 Z= 0.302 Angle : 0.595 10.604 12230 Z= 0.301 Chirality : 0.043 0.161 1385 Planarity : 0.004 0.037 1530 Dihedral : 8.051 81.507 1317 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.74 % Allowed : 26.83 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.59 (0.25), residues: 1108 helix: 1.73 (0.26), residues: 390 sheet: 0.02 (0.30), residues: 278 loop : -0.50 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.024 0.002 PHE R 183 TYR 0.015 0.002 TYR R 222 ARG 0.010 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 186 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.7793 (ttt180) REVERT: A 32 ARG cc_start: 0.8239 (ptp90) cc_final: 0.7927 (ptp-170) REVERT: A 273 LEU cc_start: 0.8631 (tp) cc_final: 0.8413 (tp) REVERT: B 10 GLU cc_start: 0.8279 (tp30) cc_final: 0.7871 (tp30) REVERT: B 15 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8555 (mtmt) REVERT: B 101 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8217 (mtm) REVERT: B 127 LYS cc_start: 0.8929 (mptm) cc_final: 0.8680 (mmtm) REVERT: B 146 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8939 (tp) REVERT: B 188 MET cc_start: 0.8838 (mmm) cc_final: 0.8449 (mmm) REVERT: B 226 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: G 37 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8718 (mp) REVERT: S 87 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7870 (mtp85) REVERT: S 232 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8258 (ttpp) REVERT: S 234 GLU cc_start: 0.6983 (mp0) cc_final: 0.6495 (mp0) REVERT: R 22 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.5485 (tm) REVERT: R 24 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6793 (mm) REVERT: R 58 ARG cc_start: 0.7794 (mmt-90) cc_final: 0.7560 (mmp80) REVERT: R 181 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6937 (tt0) REVERT: R 208 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7645 (mmm160) REVERT: R 278 ILE cc_start: 0.8924 (mt) cc_final: 0.8607 (mt) outliers start: 55 outliers final: 30 residues processed: 220 average time/residue: 1.3071 time to fit residues: 304.8920 Evaluate side-chains 221 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 102 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 204 GLN A 306 GLN B 32 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 39 GLN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9024 Z= 0.228 Angle : 0.563 10.231 12230 Z= 0.286 Chirality : 0.042 0.162 1385 Planarity : 0.004 0.042 1530 Dihedral : 7.831 80.946 1317 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.85 % Allowed : 27.45 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.75 (0.25), residues: 1108 helix: 1.87 (0.27), residues: 391 sheet: 0.11 (0.31), residues: 272 loop : -0.41 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.016 0.001 PHE R 257 TYR 0.019 0.001 TYR R 222 ARG 0.011 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 187 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.7853 (ttt180) REVERT: A 32 ARG cc_start: 0.8245 (ptp90) cc_final: 0.7910 (ptp-170) REVERT: A 273 LEU cc_start: 0.8617 (tp) cc_final: 0.8395 (tp) REVERT: B 10 GLU cc_start: 0.8291 (tp30) cc_final: 0.7891 (tp30) REVERT: B 15 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8532 (mtmt) REVERT: B 101 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8142 (mtm) REVERT: B 127 LYS cc_start: 0.8907 (mptm) cc_final: 0.8680 (mmtm) REVERT: B 146 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8916 (tp) REVERT: B 188 MET cc_start: 0.8796 (mmm) cc_final: 0.8367 (mmm) REVERT: B 226 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: G 17 GLU cc_start: 0.7692 (tp30) cc_final: 0.7337 (tp30) REVERT: G 20 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8754 (ttmm) REVERT: G 37 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8689 (mp) REVERT: S 87 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7455 (mtp85) REVERT: R 22 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5484 (tm) REVERT: R 24 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6844 (mm) REVERT: R 50 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7509 (m-10) REVERT: R 58 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7546 (mmp80) REVERT: R 181 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: R 270 LEU cc_start: 0.8789 (tp) cc_final: 0.8516 (tm) REVERT: R 278 ILE cc_start: 0.8882 (mt) cc_final: 0.8558 (mt) outliers start: 56 outliers final: 30 residues processed: 222 average time/residue: 1.2644 time to fit residues: 298.0710 Evaluate side-chains 220 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 59 optimal weight: 0.3980 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 32 GLN B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 77 ASN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9024 Z= 0.234 Angle : 0.570 9.935 12230 Z= 0.289 Chirality : 0.042 0.165 1385 Planarity : 0.004 0.049 1530 Dihedral : 7.757 80.759 1317 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.95 % Allowed : 27.45 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.88 (0.26), residues: 1108 helix: 2.01 (0.27), residues: 385 sheet: 0.18 (0.31), residues: 270 loop : -0.35 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.001 PHE R 183 TYR 0.023 0.002 TYR A 302 ARG 0.011 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 190 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.7845 (ttt180) REVERT: A 32 ARG cc_start: 0.8237 (ptp90) cc_final: 0.7926 (ptp-170) REVERT: A 273 LEU cc_start: 0.8624 (tp) cc_final: 0.8400 (tp) REVERT: B 10 GLU cc_start: 0.8290 (tp30) cc_final: 0.7892 (tp30) REVERT: B 15 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8536 (mtmt) REVERT: B 101 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8116 (mtm) REVERT: B 127 LYS cc_start: 0.8882 (mptm) cc_final: 0.8653 (mmtm) REVERT: B 146 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8916 (tp) REVERT: B 188 MET cc_start: 0.8794 (mmm) cc_final: 0.8469 (mmm) REVERT: B 226 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: G 20 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8768 (ttmm) REVERT: G 37 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8706 (mp) REVERT: S 87 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7905 (mtp85) REVERT: R 22 LEU cc_start: 0.5784 (OUTLIER) cc_final: 0.5556 (tm) REVERT: R 24 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6849 (mm) REVERT: R 50 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7520 (m-10) REVERT: R 58 ARG cc_start: 0.7784 (mmt-90) cc_final: 0.7536 (mmp80) REVERT: R 181 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: R 208 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7602 (mmm160) REVERT: R 270 LEU cc_start: 0.8774 (tp) cc_final: 0.8502 (tm) REVERT: R 278 ILE cc_start: 0.8870 (mt) cc_final: 0.8539 (mt) outliers start: 57 outliers final: 30 residues processed: 228 average time/residue: 1.2876 time to fit residues: 311.1308 Evaluate side-chains 225 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 67 optimal weight: 0.4980 chunk 72 optimal weight: 0.0370 chunk 52 optimal weight: 0.2980 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9024 Z= 0.156 Angle : 0.552 9.349 12230 Z= 0.280 Chirality : 0.041 0.167 1385 Planarity : 0.004 0.048 1530 Dihedral : 7.422 80.189 1315 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.55 % Allowed : 30.79 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.05 (0.26), residues: 1108 helix: 2.15 (0.27), residues: 383 sheet: 0.35 (0.32), residues: 254 loop : -0.27 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.016 0.001 PHE R 257 TYR 0.011 0.001 TYR A 302 ARG 0.013 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 198 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.7822 (ttt180) REVERT: A 32 ARG cc_start: 0.8204 (ptp90) cc_final: 0.7829 (ptp-170) REVERT: A 37 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8806 (tt) REVERT: A 244 HIS cc_start: 0.8347 (m90) cc_final: 0.7938 (m90) REVERT: A 269 ASN cc_start: 0.8642 (m110) cc_final: 0.8105 (m-40) REVERT: A 273 LEU cc_start: 0.8593 (tp) cc_final: 0.8362 (tp) REVERT: A 304 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8195 (tm-30) REVERT: B 8 ARG cc_start: 0.7185 (mpt180) cc_final: 0.6862 (mtt90) REVERT: B 10 GLU cc_start: 0.8284 (tp30) cc_final: 0.7869 (tp30) REVERT: B 15 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8520 (mtmt) REVERT: B 46 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.7275 (ttp80) REVERT: B 101 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7968 (mtm) REVERT: B 127 LYS cc_start: 0.8755 (mptm) cc_final: 0.8534 (mmtm) REVERT: B 146 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8890 (tp) REVERT: B 188 MET cc_start: 0.8719 (mmm) cc_final: 0.8328 (mmm) REVERT: B 226 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: G 17 GLU cc_start: 0.7700 (tp30) cc_final: 0.7341 (tp30) REVERT: G 20 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8770 (ttmm) REVERT: R 24 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6738 (mm) REVERT: R 58 ARG cc_start: 0.7833 (mmt-90) cc_final: 0.7615 (mmp80) REVERT: R 158 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8403 (tp) REVERT: R 208 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7626 (mmm160) REVERT: R 233 LEU cc_start: 0.8881 (tm) cc_final: 0.8680 (tt) REVERT: R 278 ILE cc_start: 0.8714 (mt) cc_final: 0.8409 (mt) outliers start: 34 outliers final: 12 residues processed: 216 average time/residue: 1.3080 time to fit residues: 299.2792 Evaluate side-chains 207 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 306 GLN B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9024 Z= 0.197 Angle : 0.572 9.497 12230 Z= 0.291 Chirality : 0.042 0.169 1385 Planarity : 0.004 0.051 1530 Dihedral : 7.281 80.188 1308 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.34 % Allowed : 31.73 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.09 (0.26), residues: 1108 helix: 2.21 (0.27), residues: 382 sheet: 0.30 (0.31), residues: 268 loop : -0.23 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.026 0.001 PHE R 257 TYR 0.018 0.001 TYR R 222 ARG 0.012 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.7890 (ttt180) REVERT: A 32 ARG cc_start: 0.8211 (ptp90) cc_final: 0.7803 (ptp-170) REVERT: A 244 HIS cc_start: 0.8333 (m90) cc_final: 0.8021 (m90) REVERT: A 269 ASN cc_start: 0.8670 (m110) cc_final: 0.8127 (m-40) REVERT: A 273 LEU cc_start: 0.8581 (tp) cc_final: 0.8295 (tp) REVERT: A 304 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 308 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7783 (mt-10) REVERT: B 10 GLU cc_start: 0.8289 (tp30) cc_final: 0.7872 (tp30) REVERT: B 15 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8562 (mtmt) REVERT: B 101 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8024 (mtm) REVERT: B 127 LYS cc_start: 0.8762 (mptm) cc_final: 0.8530 (mmtm) REVERT: B 146 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8938 (tp) REVERT: B 188 MET cc_start: 0.8773 (mmm) cc_final: 0.8316 (mmm) REVERT: B 226 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: G 20 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8777 (ttmm) REVERT: R 24 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6706 (mm) REVERT: R 58 ARG cc_start: 0.7809 (mmt-90) cc_final: 0.7449 (mmp80) REVERT: R 158 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8417 (tp) REVERT: R 208 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7634 (mmm160) REVERT: R 233 LEU cc_start: 0.8911 (tm) cc_final: 0.8686 (tt) REVERT: R 270 LEU cc_start: 0.8753 (tp) cc_final: 0.8478 (tm) REVERT: R 278 ILE cc_start: 0.8740 (mt) cc_final: 0.8457 (mt) outliers start: 32 outliers final: 17 residues processed: 204 average time/residue: 1.3039 time to fit residues: 282.1824 Evaluate side-chains 207 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 306 GLN B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9024 Z= 0.231 Angle : 0.611 9.384 12230 Z= 0.307 Chirality : 0.042 0.170 1385 Planarity : 0.004 0.054 1530 Dihedral : 7.314 80.205 1307 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.24 % Allowed : 31.84 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.26), residues: 1108 helix: 2.21 (0.27), residues: 379 sheet: 0.32 (0.32), residues: 268 loop : -0.24 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.027 0.001 PHE R 257 TYR 0.015 0.001 TYR A 302 ARG 0.013 0.001 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.7812 (ttt180) REVERT: A 32 ARG cc_start: 0.8207 (ptp90) cc_final: 0.7832 (ptp-170) REVERT: A 244 HIS cc_start: 0.8402 (m90) cc_final: 0.8025 (m90) REVERT: A 273 LEU cc_start: 0.8568 (tp) cc_final: 0.8283 (tp) REVERT: A 304 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8139 (tm-30) REVERT: A 308 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7947 (mt-10) REVERT: B 10 GLU cc_start: 0.8325 (tp30) cc_final: 0.7907 (tp30) REVERT: B 15 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8566 (mtmt) REVERT: B 101 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8057 (mtm) REVERT: B 127 LYS cc_start: 0.8839 (mptm) cc_final: 0.8606 (mmtm) REVERT: B 146 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8919 (tp) REVERT: B 188 MET cc_start: 0.8800 (mmm) cc_final: 0.8348 (mmm) REVERT: B 226 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: G 20 LYS cc_start: 0.9020 (ttmt) cc_final: 0.8775 (ttmm) REVERT: R 24 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6725 (mm) REVERT: R 50 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7529 (m-10) REVERT: R 58 ARG cc_start: 0.7811 (mmt-90) cc_final: 0.7445 (mmp80) REVERT: R 158 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8413 (tp) REVERT: R 208 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7607 (mmm160) REVERT: R 233 LEU cc_start: 0.8921 (tm) cc_final: 0.8701 (tt) REVERT: R 270 LEU cc_start: 0.8774 (tp) cc_final: 0.8502 (tm) REVERT: R 278 ILE cc_start: 0.8746 (mt) cc_final: 0.8461 (mt) outliers start: 31 outliers final: 15 residues processed: 205 average time/residue: 1.3010 time to fit residues: 282.6830 Evaluate side-chains 207 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 306 GLN B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.134270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.093687 restraints weight = 11470.690| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.28 r_work: 0.2947 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9024 Z= 0.212 Angle : 0.573 8.375 12230 Z= 0.290 Chirality : 0.042 0.171 1385 Planarity : 0.004 0.054 1530 Dihedral : 7.190 80.062 1307 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.13 % Allowed : 31.63 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.11 (0.26), residues: 1108 helix: 2.21 (0.27), residues: 379 sheet: 0.34 (0.32), residues: 268 loop : -0.21 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.026 0.001 PHE R 257 TYR 0.017 0.001 TYR R 222 ARG 0.013 0.001 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4867.47 seconds wall clock time: 86 minutes 35.26 seconds (5195.26 seconds total)