Starting phenix.real_space_refine on Tue May 7 20:43:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/05_2024/8uh3_42245_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/05_2024/8uh3_42245.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/05_2024/8uh3_42245_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/05_2024/8uh3_42245_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/05_2024/8uh3_42245_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/05_2024/8uh3_42245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/05_2024/8uh3_42245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/05_2024/8uh3_42245_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uh3_42245/05_2024/8uh3_42245_updated.pdb" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5631 2.51 5 N 1457 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 201": "OD1" <-> "OD2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 8759 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2558 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2168 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1762 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 391 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "D" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 132 Unusual residues: {'CLR': 4, 'WOQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.93, per 1000 atoms: 0.56 Number of scatterers: 8759 At special positions: 0 Unit cell: (91.46, 117.284, 123.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1608 8.00 N 1457 7.00 C 5631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.7 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 12 sheets defined 34.9% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.775A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 removed outlier: 4.088A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.766A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 296 through 309 removed outlier: 3.742A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'D' and resid 20 through 49 Processing helix chain 'D' and resid 56 through 74 Processing helix chain 'D' and resid 76 through 85 removed outlier: 3.509A pdb=" N VAL D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 125 removed outlier: 3.623A pdb=" N MET D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 133 removed outlier: 3.968A pdb=" N ARG D 132 " --> pdb=" O ILE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 160 Proline residue: D 156 - end of helix removed outlier: 3.730A pdb=" N PHE D 159 " --> pdb=" O MET D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'D' and resid 192 through 212 removed outlier: 3.785A pdb=" N LYS D 210 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER D 211 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 315 removed outlier: 3.610A pdb=" N TRP D 304 " --> pdb=" O PHE D 300 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Proline residue: D 306 - end of helix Processing helix chain 'D' and resid 323 through 345 removed outlier: 3.788A pdb=" N GLY D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR D 334 " --> pdb=" O THR D 330 " (cutoff:3.500A) Proline residue: D 341 - end of helix Processing helix chain 'D' and resid 349 through 358 Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'G' and resid 14 through 22 Processing helix chain 'G' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'B' and resid 49 through 52 removed outlier: 4.231A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.048A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.648A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.710A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 203 removed outlier: 4.046A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.688A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.574A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.755A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 4 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.704A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.575A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 393 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2747 1.34 - 1.46: 2120 1.46 - 1.58: 3993 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 8951 Sorted by residual: bond pdb=" C3 WOQ D 405 " pdb=" C4 WOQ D 405 " ideal model delta sigma weight residual 1.546 1.321 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" N WOQ D 405 " pdb=" C5 WOQ D 405 " ideal model delta sigma weight residual 1.613 1.459 0.154 2.00e-02 2.50e+03 5.97e+01 bond pdb=" N WOQ D 405 " pdb=" C1 WOQ D 405 " ideal model delta sigma weight residual 1.318 1.463 -0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" C1 WOQ D 405 " pdb=" C2 WOQ D 405 " ideal model delta sigma weight residual 1.654 1.519 0.135 2.00e-02 2.50e+03 4.59e+01 bond pdb=" C2 WOQ D 405 " pdb=" C3 WOQ D 405 " ideal model delta sigma weight residual 1.414 1.495 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 8946 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.80: 118 104.80 - 112.11: 4597 112.11 - 119.43: 2941 119.43 - 126.75: 4365 126.75 - 134.06: 124 Bond angle restraints: 12145 Sorted by residual: angle pdb=" N ARG B 197 " pdb=" CA ARG B 197 " pdb=" C ARG B 197 " ideal model delta sigma weight residual 114.56 109.80 4.76 1.27e+00 6.20e-01 1.40e+01 angle pdb=" C11 WOQ D 405 " pdb=" C6 WOQ D 405 " pdb=" C4 WOQ D 405 " ideal model delta sigma weight residual 110.99 121.48 -10.49 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C13 WOQ D 405 " pdb=" C18 WOQ D 405 " pdb=" C3 WOQ D 405 " ideal model delta sigma weight residual 110.97 120.79 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C5 WOQ D 405 " pdb=" C4 WOQ D 405 " pdb=" C6 WOQ D 405 " ideal model delta sigma weight residual 121.11 111.77 9.34 3.00e+00 1.11e-01 9.69e+00 angle pdb=" C17 WOQ D 405 " pdb=" C18 WOQ D 405 " pdb=" C3 WOQ D 405 " ideal model delta sigma weight residual 128.52 119.40 9.12 3.00e+00 1.11e-01 9.25e+00 ... (remaining 12140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.79: 5203 23.79 - 47.58: 269 47.58 - 71.38: 21 71.38 - 95.17: 3 95.17 - 118.96: 3 Dihedral angle restraints: 5499 sinusoidal: 2309 harmonic: 3190 Sorted by residual: dihedral pdb=" C10 CLR D 402 " pdb=" C1 CLR D 402 " pdb=" C2 CLR D 402 " pdb=" C3 CLR D 402 " ideal model delta sinusoidal sigma weight residual -56.83 62.13 -118.96 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C1 CLR D 402 " pdb=" C2 CLR D 402 " pdb=" C3 CLR D 402 " pdb=" O1 CLR D 402 " ideal model delta sinusoidal sigma weight residual 180.04 70.31 109.73 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C1 CLR D 402 " pdb=" C2 CLR D 402 " pdb=" C3 CLR D 402 " pdb=" C4 CLR D 402 " ideal model delta sinusoidal sigma weight residual 57.41 -50.54 107.95 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 997 0.041 - 0.081: 302 0.081 - 0.122: 86 0.122 - 0.162: 9 0.162 - 0.203: 2 Chirality restraints: 1396 Sorted by residual: chirality pdb=" CB THR D 148 " pdb=" CA THR D 148 " pdb=" OG1 THR D 148 " pdb=" CG2 THR D 148 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU A 268 " pdb=" CB LEU A 268 " pdb=" CD1 LEU A 268 " pdb=" CD2 LEU A 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 1393 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 156 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO D 157 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 157 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 157 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C12 WOQ D 405 " 0.025 2.00e-02 2.50e+03 1.40e-02 3.91e+00 pdb=" C13 WOQ D 405 " -0.012 2.00e-02 2.50e+03 pdb=" C14 WOQ D 405 " -0.017 2.00e-02 2.50e+03 pdb=" C15 WOQ D 405 " -0.003 2.00e-02 2.50e+03 pdb=" C16 WOQ D 405 " 0.014 2.00e-02 2.50e+03 pdb=" C17 WOQ D 405 " 0.010 2.00e-02 2.50e+03 pdb=" C18 WOQ D 405 " -0.005 2.00e-02 2.50e+03 pdb=" C3 WOQ D 405 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 201 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.00e+00 pdb=" CG ASP E 201 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASP E 201 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP E 201 " 0.009 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 625 2.74 - 3.28: 8913 3.28 - 3.82: 14849 3.82 - 4.36: 17842 4.36 - 4.90: 30947 Nonbonded interactions: 73176 Sorted by model distance: nonbonded pdb=" O PHE A 354 " pdb=" OH TYR D 213 " model vdw 2.196 2.440 nonbonded pdb=" OD1 ASP D 119 " pdb=" OH TYR D 130 " model vdw 2.199 2.440 nonbonded pdb=" O ALA A 41 " pdb=" NZ LYS A 46 " model vdw 2.213 2.520 nonbonded pdb=" NH1 ARG E 202 " pdb=" OE1 GLU E 220 " model vdw 2.218 2.520 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.244 2.440 ... (remaining 73171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.430 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.225 8951 Z= 0.311 Angle : 0.627 10.490 12145 Z= 0.319 Chirality : 0.042 0.203 1396 Planarity : 0.004 0.074 1488 Dihedral : 13.676 118.960 3429 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.11 % Allowed : 0.64 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.42 (0.26), residues: 1078 helix: 1.25 (0.27), residues: 392 sheet: -0.40 (0.32), residues: 248 loop : -0.03 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.013 0.001 PHE D 307 TYR 0.016 0.001 TYR E 190 ARG 0.006 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: B 145 TYR cc_start: 0.9099 (p90) cc_final: 0.8605 (p90) REVERT: B 189 SER cc_start: 0.8543 (p) cc_final: 0.8311 (p) REVERT: B 291 ASP cc_start: 0.7488 (t70) cc_final: 0.7276 (t0) REVERT: A 24 ARG cc_start: 0.6786 (ttp-110) cc_final: 0.6572 (ttp-170) REVERT: G 20 LYS cc_start: 0.8423 (ptpp) cc_final: 0.7755 (mtmm) outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.2667 time to fit residues: 69.2635 Evaluate side-chains 171 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8951 Z= 0.344 Angle : 0.577 6.762 12145 Z= 0.298 Chirality : 0.043 0.148 1396 Planarity : 0.004 0.071 1488 Dihedral : 4.989 50.852 1458 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.12 % Allowed : 11.02 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.41 (0.26), residues: 1078 helix: 1.28 (0.26), residues: 388 sheet: -0.62 (0.31), residues: 265 loop : 0.12 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.013 0.002 PHE A 196 TYR 0.016 0.002 TYR D 185 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 181 time to evaluate : 1.047 Fit side-chains REVERT: B 59 TYR cc_start: 0.8512 (m-80) cc_final: 0.8234 (m-80) REVERT: B 163 ASP cc_start: 0.7930 (t0) cc_final: 0.7717 (t0) REVERT: B 291 ASP cc_start: 0.7574 (t70) cc_final: 0.7169 (t0) REVERT: A 33 GLU cc_start: 0.7701 (mm-30) cc_final: 0.6893 (mm-30) REVERT: A 52 GLN cc_start: 0.7243 (mt0) cc_final: 0.6966 (mt0) REVERT: D 27 MET cc_start: 0.7003 (ptp) cc_final: 0.6791 (ttt) REVERT: E 90 ASP cc_start: 0.8153 (t0) cc_final: 0.7832 (t0) outliers start: 20 outliers final: 17 residues processed: 191 average time/residue: 0.2802 time to fit residues: 69.5635 Evaluate side-chains 186 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8951 Z= 0.242 Angle : 0.532 7.175 12145 Z= 0.276 Chirality : 0.041 0.135 1396 Planarity : 0.004 0.070 1488 Dihedral : 4.891 56.650 1458 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.22 % Allowed : 13.98 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.48 (0.26), residues: 1078 helix: 1.39 (0.27), residues: 386 sheet: -0.57 (0.31), residues: 264 loop : 0.09 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS E 167 PHE 0.013 0.001 PHE D 347 TYR 0.012 0.001 TYR E 190 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 0.959 Fit side-chains REVERT: B 59 TYR cc_start: 0.8506 (m-80) cc_final: 0.8274 (m-80) REVERT: B 291 ASP cc_start: 0.7589 (t70) cc_final: 0.7185 (t0) REVERT: A 33 GLU cc_start: 0.7687 (mm-30) cc_final: 0.6861 (mm-30) REVERT: A 52 GLN cc_start: 0.7206 (mt0) cc_final: 0.6969 (mt0) REVERT: A 337 ASP cc_start: 0.8346 (m-30) cc_final: 0.8091 (m-30) REVERT: D 23 MET cc_start: 0.7879 (mtt) cc_final: 0.7360 (mmp) REVERT: D 27 MET cc_start: 0.6949 (ptp) cc_final: 0.6716 (ttt) REVERT: E 90 ASP cc_start: 0.8207 (t0) cc_final: 0.7800 (t0) outliers start: 21 outliers final: 17 residues processed: 191 average time/residue: 0.2866 time to fit residues: 70.2803 Evaluate side-chains 189 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN A 195 HIS ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8951 Z= 0.213 Angle : 0.520 6.518 12145 Z= 0.269 Chirality : 0.041 0.149 1396 Planarity : 0.004 0.069 1488 Dihedral : 4.877 59.690 1458 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.33 % Allowed : 15.78 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.54 (0.26), residues: 1078 helix: 1.39 (0.27), residues: 386 sheet: -0.46 (0.32), residues: 255 loop : 0.11 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS E 167 PHE 0.011 0.001 PHE A 189 TYR 0.012 0.001 TYR E 190 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8490 (m-80) cc_final: 0.8261 (m-80) REVERT: B 291 ASP cc_start: 0.7582 (t70) cc_final: 0.7125 (t0) REVERT: A 52 GLN cc_start: 0.7105 (mt0) cc_final: 0.6886 (mt0) REVERT: A 53 MET cc_start: 0.6557 (mpp) cc_final: 0.5976 (mtm) REVERT: D 23 MET cc_start: 0.7902 (mtt) cc_final: 0.7383 (mmp) REVERT: D 27 MET cc_start: 0.7008 (ptp) cc_final: 0.6775 (ttt) REVERT: D 130 TYR cc_start: 0.7834 (t80) cc_final: 0.7611 (t80) REVERT: E 90 ASP cc_start: 0.8204 (t0) cc_final: 0.7829 (t0) outliers start: 22 outliers final: 20 residues processed: 190 average time/residue: 0.2636 time to fit residues: 65.2106 Evaluate side-chains 196 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8951 Z= 0.274 Angle : 0.539 6.458 12145 Z= 0.278 Chirality : 0.041 0.140 1396 Planarity : 0.004 0.067 1488 Dihedral : 4.940 59.655 1458 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.07 % Allowed : 15.78 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.41 (0.26), residues: 1078 helix: 1.35 (0.27), residues: 386 sheet: -0.61 (0.31), residues: 266 loop : 0.04 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 88 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE A 354 TYR 0.013 0.001 TYR A 302 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8549 (m-80) cc_final: 0.8317 (m-80) REVERT: B 163 ASP cc_start: 0.7879 (t0) cc_final: 0.7592 (t0) REVERT: B 291 ASP cc_start: 0.7621 (t70) cc_final: 0.7144 (t0) REVERT: A 52 GLN cc_start: 0.6971 (mt0) cc_final: 0.6767 (mt0) REVERT: A 53 MET cc_start: 0.6471 (mpp) cc_final: 0.6116 (mtm) REVERT: D 23 MET cc_start: 0.7864 (mtt) cc_final: 0.7380 (mmp) REVERT: D 130 TYR cc_start: 0.7825 (t80) cc_final: 0.7609 (t80) REVERT: E 90 ASP cc_start: 0.8239 (t0) cc_final: 0.7834 (t0) outliers start: 29 outliers final: 23 residues processed: 198 average time/residue: 0.2672 time to fit residues: 68.9849 Evaluate side-chains 199 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 20.0000 chunk 99 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS E 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8951 Z= 0.295 Angle : 0.553 6.465 12145 Z= 0.285 Chirality : 0.042 0.182 1396 Planarity : 0.004 0.068 1488 Dihedral : 5.006 58.013 1458 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.92 % Allowed : 16.42 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.37 (0.26), residues: 1078 helix: 1.33 (0.27), residues: 392 sheet: -0.68 (0.31), residues: 266 loop : 0.02 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 160 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE D 308 TYR 0.015 0.001 TYR E 175 ARG 0.006 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 1.163 Fit side-chains REVERT: B 59 TYR cc_start: 0.8537 (m-80) cc_final: 0.8305 (m-80) REVERT: B 163 ASP cc_start: 0.8025 (t0) cc_final: 0.7666 (t0) REVERT: B 291 ASP cc_start: 0.7638 (t70) cc_final: 0.7154 (t0) REVERT: A 53 MET cc_start: 0.6788 (mpp) cc_final: 0.6559 (mtm) REVERT: D 23 MET cc_start: 0.7781 (mtt) cc_final: 0.7389 (mmp) REVERT: D 105 CYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5864 (t) REVERT: D 130 TYR cc_start: 0.7806 (t80) cc_final: 0.7591 (t80) REVERT: E 90 ASP cc_start: 0.8297 (t0) cc_final: 0.7953 (t0) outliers start: 37 outliers final: 29 residues processed: 201 average time/residue: 0.2522 time to fit residues: 66.1095 Evaluate side-chains 201 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.0670 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 0.0970 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8951 Z= 0.184 Angle : 0.533 8.840 12145 Z= 0.270 Chirality : 0.041 0.164 1396 Planarity : 0.004 0.068 1488 Dihedral : 4.858 55.951 1458 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.39 % Allowed : 17.69 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.49 (0.26), residues: 1078 helix: 1.39 (0.27), residues: 392 sheet: -0.48 (0.32), residues: 255 loop : 0.01 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 88 HIS 0.002 0.001 HIS B 91 PHE 0.012 0.001 PHE D 347 TYR 0.012 0.001 TYR E 190 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8459 (m-80) cc_final: 0.8254 (m-80) REVERT: B 163 ASP cc_start: 0.7894 (t0) cc_final: 0.7605 (t0) REVERT: B 291 ASP cc_start: 0.7633 (t70) cc_final: 0.7122 (t0) REVERT: A 32 ARG cc_start: 0.8277 (mtm110) cc_final: 0.7756 (mtm180) REVERT: D 23 MET cc_start: 0.7777 (mtt) cc_final: 0.7341 (mmp) REVERT: E 90 ASP cc_start: 0.8290 (t0) cc_final: 0.7933 (t0) outliers start: 32 outliers final: 26 residues processed: 200 average time/residue: 0.2557 time to fit residues: 66.7000 Evaluate side-chains 200 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8951 Z= 0.245 Angle : 0.554 7.297 12145 Z= 0.282 Chirality : 0.042 0.170 1396 Planarity : 0.004 0.068 1488 Dihedral : 4.914 55.584 1458 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.60 % Allowed : 18.54 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.42 (0.26), residues: 1078 helix: 1.31 (0.27), residues: 392 sheet: -0.54 (0.32), residues: 257 loop : 0.00 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 88 HIS 0.002 0.001 HIS B 91 PHE 0.012 0.001 PHE D 308 TYR 0.011 0.001 TYR E 190 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 0.994 Fit side-chains REVERT: B 59 TYR cc_start: 0.8489 (m-80) cc_final: 0.8260 (m-80) REVERT: B 163 ASP cc_start: 0.7958 (t0) cc_final: 0.7569 (t0) REVERT: B 291 ASP cc_start: 0.7662 (t70) cc_final: 0.7142 (t0) REVERT: A 32 ARG cc_start: 0.8286 (mtm110) cc_final: 0.7797 (mtm180) REVERT: D 23 MET cc_start: 0.7790 (mtt) cc_final: 0.7365 (mmp) REVERT: D 76 MET cc_start: 0.7914 (mtt) cc_final: 0.7698 (mtp) REVERT: E 90 ASP cc_start: 0.8311 (t0) cc_final: 0.7959 (t0) REVERT: E 237 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8336 (mt) outliers start: 34 outliers final: 29 residues processed: 195 average time/residue: 0.2665 time to fit residues: 67.7095 Evaluate side-chains 204 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 176 GLN Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8951 Z= 0.208 Angle : 0.562 7.557 12145 Z= 0.285 Chirality : 0.042 0.241 1396 Planarity : 0.004 0.070 1488 Dihedral : 4.859 54.606 1458 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.50 % Allowed : 18.75 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1078 helix: 1.35 (0.27), residues: 391 sheet: -0.44 (0.32), residues: 255 loop : -0.04 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 88 HIS 0.002 0.001 HIS B 91 PHE 0.019 0.001 PHE D 347 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 0.937 Fit side-chains REVERT: B 163 ASP cc_start: 0.7767 (t0) cc_final: 0.7375 (t0) REVERT: B 291 ASP cc_start: 0.7653 (t70) cc_final: 0.7124 (t0) REVERT: A 32 ARG cc_start: 0.8328 (mtm110) cc_final: 0.7848 (mtm180) REVERT: D 23 MET cc_start: 0.7776 (mtt) cc_final: 0.7363 (mmp) REVERT: D 76 MET cc_start: 0.7859 (mtt) cc_final: 0.7640 (mtp) REVERT: E 90 ASP cc_start: 0.8312 (t0) cc_final: 0.7961 (t0) REVERT: E 237 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8316 (mt) outliers start: 33 outliers final: 28 residues processed: 187 average time/residue: 0.2595 time to fit residues: 64.2361 Evaluate side-chains 199 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 176 GLN Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 0.0370 chunk 98 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 90 optimal weight: 0.6980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 GLN E 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8951 Z= 0.219 Angle : 0.570 11.222 12145 Z= 0.288 Chirality : 0.043 0.399 1396 Planarity : 0.004 0.073 1488 Dihedral : 4.886 54.165 1458 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.39 % Allowed : 18.96 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.45 (0.26), residues: 1078 helix: 1.37 (0.27), residues: 390 sheet: -0.49 (0.32), residues: 257 loop : -0.03 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 88 HIS 0.002 0.001 HIS D 177 PHE 0.031 0.001 PHE D 347 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG B 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 172 time to evaluate : 1.018 Fit side-chains REVERT: B 163 ASP cc_start: 0.7775 (t0) cc_final: 0.7382 (t0) REVERT: B 291 ASP cc_start: 0.7656 (t70) cc_final: 0.7134 (t0) REVERT: A 32 ARG cc_start: 0.8347 (mtm110) cc_final: 0.7888 (mtm180) REVERT: D 23 MET cc_start: 0.7790 (mtt) cc_final: 0.7387 (mmp) REVERT: E 90 ASP cc_start: 0.8325 (t0) cc_final: 0.7974 (t0) REVERT: E 237 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8309 (mt) outliers start: 32 outliers final: 30 residues processed: 189 average time/residue: 0.2565 time to fit residues: 63.5676 Evaluate side-chains 202 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 176 GLN Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 319 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.168267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120119 restraints weight = 11016.327| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.41 r_work: 0.3264 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8951 Z= 0.213 Angle : 0.577 11.017 12145 Z= 0.291 Chirality : 0.043 0.387 1396 Planarity : 0.004 0.073 1488 Dihedral : 4.891 53.804 1458 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.28 % Allowed : 19.28 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1078 helix: 1.37 (0.27), residues: 390 sheet: -0.42 (0.32), residues: 255 loop : -0.07 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 88 HIS 0.004 0.001 HIS E 167 PHE 0.026 0.001 PHE D 347 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2435.26 seconds wall clock time: 45 minutes 15.96 seconds (2715.96 seconds total)