Starting phenix.real_space_refine on Sun Aug 4 22:56:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzx_18784/08_2024/8qzx_18784.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzx_18784/08_2024/8qzx_18784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzx_18784/08_2024/8qzx_18784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzx_18784/08_2024/8qzx_18784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzx_18784/08_2024/8qzx_18784.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzx_18784/08_2024/8qzx_18784.cif" } resolution = 3.01 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= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 68 5.16 5 C 7471 2.51 5 N 1965 2.21 5 O 2196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 33": "OD1" <-> "OD2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "D ASP 34": "OD1" <-> "OD2" Residue "D PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 211": "NH1" <-> "NH2" Residue "D TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11708 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2620 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 317} Chain breaks: 2 Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2618 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 318} Chain breaks: 1 Chain: "C" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2629 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain breaks: 1 Chain: "D" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2580 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Chain breaks: 3 Chain: "E" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1055 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1B NAD A 401 " occ=0.73 ... (42 atoms not shown) pdb=" PN NAD A 401 " occ=0.73 residue: pdb=" C1B NAD B 401 " occ=0.88 ... (42 atoms not shown) pdb=" PN NAD B 401 " occ=0.88 residue: pdb=" C1B NAD C 401 " occ=0.75 ... (42 atoms not shown) pdb=" PN NAD C 401 " occ=0.75 residue: pdb=" C1B NAD D 402 " occ=0.79 ... (42 atoms not shown) pdb=" PN NAD D 402 " occ=0.79 Time building chain proxies: 7.29, per 1000 atoms: 0.62 Number of scatterers: 11708 At special positions: 0 Unit cell: (79.4864, 96.3984, 145.443, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 8 15.00 O 2196 8.00 N 1965 7.00 C 7471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.73 Conformation dependent library (CDL) restraints added in 2.2 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2660 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 10 sheets defined 53.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'A' and resid 52 through 69 removed outlier: 3.868A pdb=" N ASN A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.573A pdb=" N PHE A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.796A pdb=" N PHE A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 174 through 200 removed outlier: 4.089A pdb=" N TYR A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Proline residue: A 187 - end of helix Processing helix chain 'A' and resid 204 through 217 removed outlier: 4.008A pdb=" N ASN A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 removed outlier: 3.576A pdb=" N TRP A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.530A pdb=" N ASP A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.243A pdb=" N ASP A 315 " --> pdb=" O HIS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 removed outlier: 3.720A pdb=" N ALA A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.538A pdb=" N VAL A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'B' and resid 39 through 46 removed outlier: 3.623A pdb=" N GLN B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 51 through 69 removed outlier: 3.639A pdb=" N ASN B 56 " --> pdb=" O PHE B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.907A pdb=" N ILE B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.532A pdb=" N HIS B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 removed outlier: 3.827A pdb=" N PHE B 141 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 175 through 200 removed outlier: 3.972A pdb=" N CYS B 179 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) Proline residue: B 187 - end of helix Processing helix chain 'B' and resid 204 through 217 removed outlier: 3.762A pdb=" N ASN B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 removed outlier: 3.627A pdb=" N TRP B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 254 removed outlier: 3.703A pdb=" N TYR B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN B 253 " --> pdb=" O PHE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 312 through 316 removed outlier: 4.404A pdb=" N ASP B 315 " --> pdb=" O HIS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 330 removed outlier: 3.571A pdb=" N ALA B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 48 through 51 removed outlier: 4.560A pdb=" N GLY C 51 " --> pdb=" O LYS C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 52 through 69 removed outlier: 3.821A pdb=" N ASN C 56 " --> pdb=" O PHE C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 removed outlier: 4.017A pdb=" N ILE C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.614A pdb=" N LEU C 121 " --> pdb=" O TYR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.709A pdb=" N PHE C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 163 Processing helix chain 'C' and resid 174 through 200 removed outlier: 4.122A pdb=" N TYR C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS C 179 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 204 through 215 Processing helix chain 'C' and resid 221 through 229 removed outlier: 3.657A pdb=" N TRP C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 254 removed outlier: 3.607A pdb=" N ASP C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN C 253 " --> pdb=" O PHE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 271 removed outlier: 3.795A pdb=" N ASP C 264 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 297 removed outlier: 3.569A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 removed outlier: 4.018A pdb=" N ASP C 315 " --> pdb=" O HIS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 329 removed outlier: 3.608A pdb=" N ALA C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.702A pdb=" N VAL C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) Proline residue: C 350 - end of helix Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 51 through 69 removed outlier: 3.671A pdb=" N ASN D 56 " --> pdb=" O PHE D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 removed outlier: 4.109A pdb=" N ILE D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 124 Processing helix chain 'D' and resid 133 through 146 removed outlier: 3.738A pdb=" N PHE D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 163 Processing helix chain 'D' and resid 175 through 200 removed outlier: 4.099A pdb=" N CYS D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Proline residue: D 187 - end of helix Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 241 through 252 removed outlier: 3.686A pdb=" N TYR D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 271 removed outlier: 3.939A pdb=" N ASP D 264 " --> pdb=" O ASP D 260 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 266 " --> pdb=" O VAL D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 298 removed outlier: 3.926A pdb=" N TYR D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 removed outlier: 4.251A pdb=" N ASP D 315 " --> pdb=" O HIS D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 330 removed outlier: 3.784A pdb=" N ALA D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 356 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 356 through 363 removed outlier: 3.541A pdb=" N PHE D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 140 Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 234 removed outlier: 7.047A pdb=" N VAL A 130 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 304 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 305 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL A 341 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR A 307 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 131 removed outlier: 6.553A pdb=" N ILE B 101 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL B 131 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU B 103 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL B 305 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL B 341 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR B 307 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.574A pdb=" N ASN B 166 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 233 through 234 removed outlier: 7.059A pdb=" N VAL C 130 " --> pdb=" O TYR C 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 149 through 150 Processing sheet with id=AA6, first strand: chain 'D' and resid 233 through 234 removed outlier: 6.877A pdb=" N VAL D 130 " --> pdb=" O TYR D 234 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL D 129 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE D 101 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL D 131 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU D 103 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 305 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL D 341 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR D 307 " --> pdb=" O VAL D 341 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 165 through 168 Processing sheet with id=AA8, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.241A pdb=" N VAL E 47 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR E 68 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 91 through 92 removed outlier: 6.664A pdb=" N GLN E 107 " --> pdb=" O ILE E 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.724A pdb=" N ASP E 161 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU E 151 " --> pdb=" O ILE E 159 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE E 159 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER E 153 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1494 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: 3.40 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.19: 7 1.19 - 1.37: 3991 1.37 - 1.55: 7832 1.55 - 1.72: 51 1.72 - 1.90: 105 Bond restraints: 11986 Sorted by residual: bond pdb=" C ILE E 159 " pdb=" N VAL E 160 " ideal model delta sigma weight residual 1.335 1.015 0.320 1.22e-02 6.72e+03 6.89e+02 bond pdb=" C ASN E 143 " pdb=" N ASP E 144 " ideal model delta sigma weight residual 1.331 1.022 0.308 1.41e-02 5.03e+03 4.78e+02 bond pdb=" C VAL E 146 " pdb=" N VAL E 147 " ideal model delta sigma weight residual 1.330 1.021 0.309 1.48e-02 4.57e+03 4.37e+02 bond pdb=" C TYR E 37 " pdb=" O TYR E 37 " ideal model delta sigma weight residual 1.234 1.475 -0.241 1.25e-02 6.40e+03 3.72e+02 bond pdb=" C ASP E 134 " pdb=" N LEU E 135 " ideal model delta sigma weight residual 1.333 1.049 0.284 1.55e-02 4.16e+03 3.36e+02 ... (remaining 11981 not shown) Histogram of bond angle deviations from ideal: 95.96 - 109.22: 1694 109.22 - 122.49: 12479 122.49 - 135.76: 2086 135.76 - 149.03: 5 149.03 - 162.30: 2 Bond angle restraints: 16266 Sorted by residual: angle pdb=" C GLY E 104 " pdb=" N HIS E 105 " pdb=" CA HIS E 105 " ideal model delta sigma weight residual 121.85 162.30 -40.45 1.77e+00 3.19e-01 5.22e+02 angle pdb=" C ASN E 143 " pdb=" N ASP E 144 " pdb=" CA ASP E 144 " ideal model delta sigma weight residual 121.50 150.36 -28.86 1.43e+00 4.89e-01 4.07e+02 angle pdb=" O ASN E 143 " pdb=" C ASN E 143 " pdb=" N ASP E 144 " ideal model delta sigma weight residual 122.39 95.96 26.43 1.48e+00 4.57e-01 3.19e+02 angle pdb=" CA TYR E 37 " pdb=" C TYR E 37 " pdb=" O TYR E 37 " ideal model delta sigma weight residual 121.66 100.37 21.29 1.22e+00 6.72e-01 3.05e+02 angle pdb=" CA ASN E 143 " pdb=" C ASN E 143 " pdb=" N ASP E 144 " ideal model delta sigma weight residual 118.44 142.98 -24.54 1.41e+00 5.03e-01 3.03e+02 ... (remaining 16261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.08: 6395 19.08 - 38.16: 571 38.16 - 57.25: 141 57.25 - 76.33: 44 76.33 - 95.41: 22 Dihedral angle restraints: 7173 sinusoidal: 3002 harmonic: 4171 Sorted by residual: dihedral pdb=" CA GLY E 104 " pdb=" C GLY E 104 " pdb=" N HIS E 105 " pdb=" CA HIS E 105 " ideal model delta harmonic sigma weight residual 180.00 122.21 57.79 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" C PHE D 52 " pdb=" N PHE D 52 " pdb=" CA PHE D 52 " pdb=" CB PHE D 52 " ideal model delta harmonic sigma weight residual -122.60 -138.72 16.12 0 2.50e+00 1.60e-01 4.16e+01 dihedral pdb=" C ASP D 303 " pdb=" N ASP D 303 " pdb=" CA ASP D 303 " pdb=" CB ASP D 303 " ideal model delta harmonic sigma weight residual -122.60 -135.59 12.99 0 2.50e+00 1.60e-01 2.70e+01 ... (remaining 7170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1058 0.110 - 0.219: 591 0.219 - 0.329: 124 0.329 - 0.439: 9 0.439 - 0.548: 3 Chirality restraints: 1785 Sorted by residual: chirality pdb=" CA PHE D 52 " pdb=" N PHE D 52 " pdb=" C PHE D 52 " pdb=" CB PHE D 52 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.52e+00 chirality pdb=" CA GLN E 130 " pdb=" N GLN E 130 " pdb=" C GLN E 130 " pdb=" CB GLN E 130 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" CB VAL B 130 " pdb=" CA VAL B 130 " pdb=" CG1 VAL B 130 " pdb=" CG2 VAL B 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.96e+00 ... (remaining 1782 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD C 401 " -0.096 2.00e-02 2.50e+03 7.76e-02 1.20e+02 pdb=" C2N NAD C 401 " 0.170 2.00e-02 2.50e+03 pdb=" C3N NAD C 401 " 0.020 2.00e-02 2.50e+03 pdb=" C4N NAD C 401 " -0.030 2.00e-02 2.50e+03 pdb=" C5N NAD C 401 " 0.017 2.00e-02 2.50e+03 pdb=" C6N NAD C 401 " -0.017 2.00e-02 2.50e+03 pdb=" C7N NAD C 401 " -0.087 2.00e-02 2.50e+03 pdb=" N1N NAD C 401 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 401 " 0.081 2.00e-02 2.50e+03 6.79e-02 9.23e+01 pdb=" C2N NAD A 401 " -0.018 2.00e-02 2.50e+03 pdb=" C3N NAD A 401 " 0.014 2.00e-02 2.50e+03 pdb=" C4N NAD A 401 " 0.111 2.00e-02 2.50e+03 pdb=" C5N NAD A 401 " 0.008 2.00e-02 2.50e+03 pdb=" C6N NAD A 401 " -0.120 2.00e-02 2.50e+03 pdb=" C7N NAD A 401 " -0.049 2.00e-02 2.50e+03 pdb=" N1N NAD A 401 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 402 " 0.107 2.00e-02 2.50e+03 6.71e-02 9.01e+01 pdb=" C2N NAD D 402 " -0.112 2.00e-02 2.50e+03 pdb=" C3N NAD D 402 " 0.002 2.00e-02 2.50e+03 pdb=" C4N NAD D 402 " 0.083 2.00e-02 2.50e+03 pdb=" C5N NAD D 402 " -0.007 2.00e-02 2.50e+03 pdb=" C6N NAD D 402 " -0.060 2.00e-02 2.50e+03 pdb=" C7N NAD D 402 " 0.021 2.00e-02 2.50e+03 pdb=" N1N NAD D 402 " -0.034 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4405 2.90 - 3.40: 11287 3.40 - 3.90: 20052 3.90 - 4.40: 24306 4.40 - 4.90: 38363 Nonbonded interactions: 98413 Sorted by model distance: nonbonded pdb=" O ASP E 134 " pdb=" CA LEU E 135 " model vdw 2.405 2.776 nonbonded pdb=" O ALA D 226 " pdb=" N ILE D 231 " model vdw 2.408 3.120 nonbonded pdb=" N PHE E 136 " pdb=" N ASN E 137 " model vdw 2.420 2.560 nonbonded pdb=" O VAL E 146 " pdb=" CA VAL E 147 " model vdw 2.438 2.776 nonbonded pdb=" O ILE E 159 " pdb=" CA VAL E 160 " model vdw 2.453 2.776 ... (remaining 98408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 34 or resid 38 through 73 or resid 81 through 1 \ 50 or resid 154 through 363)) selection = (chain 'B' and (resid 26 through 34 or resid 38 through 150 or resid 154 through \ 168 or resid 171 through 363)) selection = (chain 'C' and (resid 26 through 34 or resid 38 through 73 or resid 81 through 1 \ 50 or resid 154 through 168 or resid 171 through 363)) selection = (chain 'D' and (resid 26 through 73 or resid 81 through 168 or resid 171 through \ 363)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.73 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.770 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 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 : 0.015 0.320 11986 Z= 0.961 Angle : 1.923 40.445 16266 Z= 1.437 Chirality : 0.128 0.548 1785 Planarity : 0.008 0.078 2070 Dihedral : 16.904 95.409 4513 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 7.06 % Allowed : 12.51 % Favored : 80.43 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1440 helix: 1.62 (0.19), residues: 664 sheet: 0.57 (0.40), residues: 156 loop : -0.21 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 329 HIS 0.006 0.002 HIS B 250 PHE 0.032 0.003 PHE E 136 TYR 0.030 0.003 TYR C 70 ARG 0.009 0.001 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 273 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7447 (tpt) cc_final: 0.7169 (tpt) REVERT: A 150 MET cc_start: 0.6676 (mtp) cc_final: 0.5670 (mmt) REVERT: A 155 HIS cc_start: 0.4025 (OUTLIER) cc_final: 0.2898 (m90) REVERT: A 166 ASN cc_start: 0.7661 (t0) cc_final: 0.6897 (t0) REVERT: A 220 ASP cc_start: 0.5449 (t0) cc_final: 0.5193 (t0) REVERT: A 298 TYR cc_start: 0.7939 (m-80) cc_final: 0.7698 (m-10) REVERT: B 47 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6597 (mmt) REVERT: B 67 MET cc_start: 0.6728 (mtt) cc_final: 0.6436 (mtm) REVERT: B 130 VAL cc_start: 0.5044 (OUTLIER) cc_final: 0.4827 (t) REVERT: B 138 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6175 (tm-30) REVERT: B 145 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7094 (mt) REVERT: B 278 THR cc_start: 0.7760 (p) cc_final: 0.7560 (p) REVERT: B 299 ARG cc_start: 0.5600 (ptp-110) cc_final: 0.5315 (tpt170) REVERT: B 329 TRP cc_start: 0.6341 (OUTLIER) cc_final: 0.5625 (m-10) REVERT: C 313 ASP cc_start: 0.6943 (p0) cc_final: 0.6569 (t0) REVERT: D 41 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.6783 (t0) REVERT: D 73 GLU cc_start: 0.7044 (mp0) cc_final: 0.6391 (tm-30) REVERT: D 109 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6162 (mp) REVERT: D 163 ARG cc_start: 0.6646 (mtt180) cc_final: 0.6143 (mmt90) REVERT: D 176 LYS cc_start: 0.7309 (tttt) cc_final: 0.6633 (tptt) REVERT: D 361 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6238 (mp) outliers start: 88 outliers final: 15 residues processed: 345 average time/residue: 0.2210 time to fit residues: 110.4627 Evaluate side-chains 196 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 329 TRP Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 329 TRP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 361 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 108 ASN A 166 ASN A 296 ASN B 177 ASN B 230 ASN B 296 ASN C 46 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 46 GLN D 124 HIS E 84 HIS E 105 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11986 Z= 0.237 Angle : 0.656 9.803 16266 Z= 0.348 Chirality : 0.046 0.160 1785 Planarity : 0.005 0.069 2070 Dihedral : 13.244 85.974 1849 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.13 % Allowed : 15.48 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1440 helix: 1.05 (0.19), residues: 694 sheet: 0.46 (0.37), residues: 188 loop : -0.14 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 203 HIS 0.006 0.001 HIS D 124 PHE 0.023 0.002 PHE A 357 TYR 0.020 0.002 TYR A 224 ARG 0.003 0.001 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6376 (mtp) cc_final: 0.5443 (mmt) REVERT: A 155 HIS cc_start: 0.4010 (OUTLIER) cc_final: 0.3569 (m90) REVERT: B 47 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.4743 (mpt) REVERT: B 299 ARG cc_start: 0.5591 (ptp-110) cc_final: 0.5065 (tpt170) REVERT: C 313 ASP cc_start: 0.7357 (p0) cc_final: 0.6685 (t0) REVERT: D 41 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6525 (t0) REVERT: D 145 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7268 (mt) REVERT: D 176 LYS cc_start: 0.7089 (tttt) cc_final: 0.6467 (tptp) REVERT: D 186 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6879 (mtt) REVERT: D 359 LYS cc_start: 0.5335 (mptt) cc_final: 0.4408 (ptmt) outliers start: 39 outliers final: 21 residues processed: 228 average time/residue: 0.2511 time to fit residues: 82.6003 Evaluate side-chains 190 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 329 TRP Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 147 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 291 HIS B 108 ASN B 124 HIS B 296 ASN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS E 58 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11986 Z= 0.356 Angle : 0.702 7.680 16266 Z= 0.372 Chirality : 0.050 0.169 1785 Planarity : 0.005 0.066 2070 Dihedral : 11.915 73.823 1824 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.77 % Allowed : 16.36 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1440 helix: 0.34 (0.19), residues: 696 sheet: 0.12 (0.38), residues: 181 loop : -0.27 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 329 HIS 0.008 0.002 HIS A 290 PHE 0.020 0.003 PHE A 357 TYR 0.020 0.002 TYR A 224 ARG 0.007 0.001 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 179 time to evaluate : 1.367 Fit side-chains revert: symmetry clash REVERT: A 155 HIS cc_start: 0.4102 (OUTLIER) cc_final: 0.3597 (m90) REVERT: B 47 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.4717 (mpt) REVERT: B 85 LEU cc_start: 0.7660 (mm) cc_final: 0.7435 (mm) REVERT: B 138 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6188 (tm-30) REVERT: B 246 MET cc_start: 0.7667 (mmt) cc_final: 0.7306 (mmp) REVERT: C 313 ASP cc_start: 0.7638 (p0) cc_final: 0.6186 (t0) REVERT: D 41 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.6714 (t0) REVERT: D 176 LYS cc_start: 0.7154 (tttt) cc_final: 0.6500 (tptp) REVERT: D 186 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6961 (mtt) REVERT: D 291 HIS cc_start: 0.6389 (OUTLIER) cc_final: 0.6023 (t-170) REVERT: D 359 LYS cc_start: 0.5518 (mptt) cc_final: 0.4473 (ptmt) outliers start: 47 outliers final: 27 residues processed: 211 average time/residue: 0.2297 time to fit residues: 71.0549 Evaluate side-chains 194 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 329 TRP Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 329 TRP Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 68 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS B 108 ASN B 149 HIS B 269 ASN C 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11986 Z= 0.191 Angle : 0.571 6.864 16266 Z= 0.298 Chirality : 0.044 0.176 1785 Planarity : 0.005 0.060 2070 Dihedral : 10.436 72.104 1822 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.61 % Allowed : 17.48 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1440 helix: 0.54 (0.19), residues: 699 sheet: 0.24 (0.38), residues: 176 loop : -0.11 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 203 HIS 0.006 0.001 HIS A 124 PHE 0.021 0.001 PHE A 357 TYR 0.022 0.002 TYR D 224 ARG 0.005 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 176 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: A 155 HIS cc_start: 0.4082 (OUTLIER) cc_final: 0.3564 (m90) REVERT: B 43 MET cc_start: 0.6892 (tmm) cc_final: 0.6018 (tmm) REVERT: B 47 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.4251 (mpt) REVERT: B 145 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7090 (mm) REVERT: B 220 ASP cc_start: 0.6665 (t0) cc_final: 0.6441 (t0) REVERT: B 246 MET cc_start: 0.7572 (mmt) cc_final: 0.7361 (mmp) REVERT: C 313 ASP cc_start: 0.7596 (p0) cc_final: 0.6059 (t0) REVERT: D 41 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.6725 (t0) REVERT: D 145 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7297 (mt) REVERT: D 176 LYS cc_start: 0.7050 (tttt) cc_final: 0.6328 (tptp) REVERT: D 186 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6839 (mtt) outliers start: 45 outliers final: 22 residues processed: 204 average time/residue: 0.2384 time to fit residues: 71.4092 Evaluate side-chains 187 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 329 TRP Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 118 optimal weight: 0.0170 chunk 96 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11986 Z= 0.300 Angle : 0.624 7.001 16266 Z= 0.328 Chirality : 0.047 0.300 1785 Planarity : 0.005 0.059 2070 Dihedral : 10.067 73.302 1822 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.53 % Allowed : 17.72 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.22), residues: 1440 helix: 0.40 (0.19), residues: 699 sheet: 0.27 (0.39), residues: 180 loop : -0.18 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 203 HIS 0.008 0.001 HIS A 124 PHE 0.016 0.002 PHE C 153 TYR 0.014 0.002 TYR B 298 ARG 0.005 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 163 time to evaluate : 1.290 Fit side-chains REVERT: A 62 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: A 114 MET cc_start: 0.6730 (mmt) cc_final: 0.6440 (mmt) REVERT: A 155 HIS cc_start: 0.4141 (OUTLIER) cc_final: 0.3695 (m90) REVERT: A 234 TYR cc_start: 0.8156 (m-80) cc_final: 0.7947 (m-80) REVERT: B 47 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.4167 (mpt) REVERT: B 145 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7101 (mm) REVERT: B 220 ASP cc_start: 0.6643 (t0) cc_final: 0.6371 (t0) REVERT: B 246 MET cc_start: 0.7669 (mmt) cc_final: 0.7389 (mmp) REVERT: B 300 ASN cc_start: 0.7323 (OUTLIER) cc_final: 0.6796 (t0) REVERT: C 313 ASP cc_start: 0.7744 (p0) cc_final: 0.6152 (t0) REVERT: D 39 ASP cc_start: 0.5919 (OUTLIER) cc_final: 0.5716 (m-30) REVERT: D 41 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.6710 (t0) REVERT: D 145 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7422 (mm) REVERT: D 163 ARG cc_start: 0.6468 (mtt180) cc_final: 0.5842 (mtt-85) REVERT: D 176 LYS cc_start: 0.7156 (tttt) cc_final: 0.6408 (tptp) REVERT: D 186 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6852 (mtt) outliers start: 44 outliers final: 24 residues processed: 192 average time/residue: 0.2516 time to fit residues: 70.6975 Evaluate side-chains 186 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 139 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11986 Z= 0.276 Angle : 0.613 11.733 16266 Z= 0.319 Chirality : 0.046 0.168 1785 Planarity : 0.005 0.059 2070 Dihedral : 9.615 72.805 1820 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.13 % Allowed : 18.68 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1440 helix: 0.36 (0.19), residues: 700 sheet: 0.17 (0.39), residues: 181 loop : -0.24 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 203 HIS 0.006 0.001 HIS D 124 PHE 0.015 0.002 PHE A 120 TYR 0.015 0.002 TYR C 70 ARG 0.005 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 HIS cc_start: 0.4261 (OUTLIER) cc_final: 0.3643 (m90) REVERT: B 47 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.4066 (mpt) REVERT: B 82 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5424 (mp) REVERT: B 145 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7156 (mm) REVERT: B 246 MET cc_start: 0.7655 (mmt) cc_final: 0.7361 (mmp) REVERT: B 300 ASN cc_start: 0.7395 (OUTLIER) cc_final: 0.6923 (t0) REVERT: C 313 ASP cc_start: 0.7835 (p0) cc_final: 0.6211 (t0) REVERT: D 41 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.6742 (t0) REVERT: D 145 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7339 (mm) REVERT: D 163 ARG cc_start: 0.6435 (mtt180) cc_final: 0.5819 (mtt-85) REVERT: D 176 LYS cc_start: 0.7162 (tttt) cc_final: 0.6395 (tptp) REVERT: D 186 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6838 (mtt) REVERT: E 60 HIS cc_start: 0.5491 (OUTLIER) cc_final: 0.3689 (t-90) outliers start: 39 outliers final: 27 residues processed: 184 average time/residue: 0.2396 time to fit residues: 63.5244 Evaluate side-chains 188 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 107 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 86 optimal weight: 0.0040 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11986 Z= 0.182 Angle : 0.549 8.329 16266 Z= 0.287 Chirality : 0.043 0.176 1785 Planarity : 0.004 0.053 2070 Dihedral : 9.112 71.305 1820 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.29 % Allowed : 18.93 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1440 helix: 0.56 (0.19), residues: 701 sheet: 0.24 (0.40), residues: 175 loop : -0.10 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 203 HIS 0.005 0.001 HIS E 105 PHE 0.014 0.001 PHE A 120 TYR 0.017 0.001 TYR D 224 ARG 0.004 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: A 155 HIS cc_start: 0.4159 (OUTLIER) cc_final: 0.3608 (m90) REVERT: B 47 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.3930 (mpt) REVERT: B 145 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7170 (mm) REVERT: B 220 ASP cc_start: 0.6478 (t0) cc_final: 0.6009 (t0) REVERT: B 246 MET cc_start: 0.7549 (mmt) cc_final: 0.7303 (mmp) REVERT: B 300 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.6913 (t0) REVERT: C 313 ASP cc_start: 0.7724 (p0) cc_final: 0.6150 (t0) REVERT: D 41 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6692 (t0) REVERT: D 145 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7379 (mt) REVERT: D 176 LYS cc_start: 0.7051 (tttt) cc_final: 0.6303 (tptt) REVERT: D 186 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6799 (mtt) outliers start: 41 outliers final: 24 residues processed: 194 average time/residue: 0.2222 time to fit residues: 63.4731 Evaluate side-chains 188 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 156 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11986 Z= 0.260 Angle : 0.591 8.147 16266 Z= 0.309 Chirality : 0.045 0.153 1785 Planarity : 0.005 0.055 2070 Dihedral : 9.039 72.377 1820 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.53 % Allowed : 18.77 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1440 helix: 0.48 (0.19), residues: 700 sheet: 0.26 (0.39), residues: 179 loop : -0.26 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 203 HIS 0.006 0.001 HIS D 124 PHE 0.016 0.002 PHE C 153 TYR 0.017 0.002 TYR D 224 ARG 0.005 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 155 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: A 114 MET cc_start: 0.6602 (mmt) cc_final: 0.6326 (tpt) REVERT: A 155 HIS cc_start: 0.4228 (OUTLIER) cc_final: 0.3625 (m90) REVERT: B 47 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.3896 (mpt) REVERT: B 145 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7134 (mm) REVERT: B 246 MET cc_start: 0.7619 (mmt) cc_final: 0.7329 (mmp) REVERT: B 300 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6922 (t0) REVERT: C 313 ASP cc_start: 0.7811 (p0) cc_final: 0.6166 (t0) REVERT: D 41 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.6712 (t0) REVERT: D 145 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7401 (mt) REVERT: D 163 ARG cc_start: 0.6531 (mtt180) cc_final: 0.5908 (mtt-85) REVERT: D 176 LYS cc_start: 0.7090 (tttt) cc_final: 0.6454 (tptp) REVERT: D 186 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6762 (mtt) REVERT: E 60 HIS cc_start: 0.5572 (OUTLIER) cc_final: 0.3678 (t-90) outliers start: 44 outliers final: 28 residues processed: 187 average time/residue: 0.2428 time to fit residues: 67.5333 Evaluate side-chains 185 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 77 optimal weight: 0.0270 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN D 149 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11986 Z= 0.210 Angle : 0.569 8.852 16266 Z= 0.298 Chirality : 0.044 0.149 1785 Planarity : 0.005 0.054 2070 Dihedral : 8.901 71.417 1820 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.05 % Allowed : 19.41 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1440 helix: 0.55 (0.19), residues: 700 sheet: 0.21 (0.39), residues: 173 loop : -0.23 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 203 HIS 0.004 0.001 HIS D 124 PHE 0.014 0.001 PHE A 120 TYR 0.019 0.001 TYR D 224 ARG 0.006 0.000 ARG D 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: A 114 MET cc_start: 0.6573 (mmt) cc_final: 0.6289 (tpt) REVERT: A 155 HIS cc_start: 0.4221 (OUTLIER) cc_final: 0.3631 (m90) REVERT: B 47 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.3795 (mpt) REVERT: B 145 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7167 (mm) REVERT: B 246 MET cc_start: 0.7583 (mmt) cc_final: 0.7289 (mmp) REVERT: B 300 ASN cc_start: 0.7336 (OUTLIER) cc_final: 0.6899 (t0) REVERT: C 278 THR cc_start: 0.7135 (OUTLIER) cc_final: 0.6929 (p) REVERT: C 313 ASP cc_start: 0.7757 (p0) cc_final: 0.6118 (t0) REVERT: D 41 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6706 (t0) REVERT: D 145 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7368 (mt) REVERT: D 176 LYS cc_start: 0.7050 (tttt) cc_final: 0.6415 (tptt) REVERT: D 186 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6723 (mtt) REVERT: E 60 HIS cc_start: 0.5584 (OUTLIER) cc_final: 0.3681 (t-90) outliers start: 38 outliers final: 27 residues processed: 186 average time/residue: 0.1979 time to fit residues: 54.4006 Evaluate side-chains 188 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 107 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 0.0270 chunk 143 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 114 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN D 108 ASN D 149 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11986 Z= 0.204 Angle : 0.567 8.589 16266 Z= 0.297 Chirality : 0.044 0.154 1785 Planarity : 0.005 0.054 2070 Dihedral : 8.798 71.136 1820 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.37 % Allowed : 19.17 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1440 helix: 0.59 (0.20), residues: 700 sheet: 0.19 (0.39), residues: 173 loop : -0.25 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 203 HIS 0.004 0.001 HIS D 124 PHE 0.014 0.001 PHE A 120 TYR 0.021 0.001 TYR D 224 ARG 0.003 0.000 ARG B 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 155 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: A 114 MET cc_start: 0.6559 (mmt) cc_final: 0.6310 (tpt) REVERT: A 155 HIS cc_start: 0.4228 (OUTLIER) cc_final: 0.3634 (m90) REVERT: B 47 MET cc_start: 0.6403 (OUTLIER) cc_final: 0.3810 (mpt) REVERT: B 145 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7189 (mm) REVERT: B 246 MET cc_start: 0.7596 (mmt) cc_final: 0.7305 (mmp) REVERT: B 300 ASN cc_start: 0.7301 (OUTLIER) cc_final: 0.6918 (t0) REVERT: C 278 THR cc_start: 0.7119 (OUTLIER) cc_final: 0.6914 (p) REVERT: C 313 ASP cc_start: 0.7739 (p0) cc_final: 0.6066 (t0) REVERT: D 41 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6712 (t0) REVERT: D 145 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7310 (mt) REVERT: D 176 LYS cc_start: 0.7031 (tttt) cc_final: 0.6371 (tptt) REVERT: D 186 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6697 (mtt) REVERT: E 60 HIS cc_start: 0.5601 (OUTLIER) cc_final: 0.3623 (t-90) outliers start: 42 outliers final: 28 residues processed: 187 average time/residue: 0.2300 time to fit residues: 63.2807 Evaluate side-chains 190 residues out of total 1247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 105 optimal weight: 0.0370 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 0.0020 chunk 47 optimal weight: 0.0970 chunk 117 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN C 210 HIS D 149 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.193747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.170729 restraints weight = 15103.977| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.79 r_work: 0.3960 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11986 Z= 0.162 Angle : 0.539 8.931 16266 Z= 0.281 Chirality : 0.043 0.153 1785 Planarity : 0.004 0.049 2070 Dihedral : 8.560 69.278 1820 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.89 % Allowed : 19.65 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.22), residues: 1440 helix: 0.74 (0.20), residues: 701 sheet: 0.33 (0.40), residues: 173 loop : -0.14 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 203 HIS 0.004 0.001 HIS C 124 PHE 0.013 0.001 PHE A 120 TYR 0.021 0.001 TYR D 224 ARG 0.003 0.000 ARG E 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2887.99 seconds wall clock time: 54 minutes 38.26 seconds (3278.26 seconds total)