Starting phenix.real_space_refine on Wed Feb 14 08:09:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vie_32006/02_2024/7vie_32006_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vie_32006/02_2024/7vie_32006.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vie_32006/02_2024/7vie_32006_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vie_32006/02_2024/7vie_32006_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vie_32006/02_2024/7vie_32006_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vie_32006/02_2024/7vie_32006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vie_32006/02_2024/7vie_32006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vie_32006/02_2024/7vie_32006_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vie_32006/02_2024/7vie_32006_updated.pdb" } resolution = 2.86 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= -0.002 sd= 0.049 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 1 5.49 5 S 65 5.16 5 C 5680 2.51 5 N 1505 2.21 5 O 1654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 129": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 275": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8905 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1808 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "F" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2229 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 2 Chain: "D" Number of atoms: 1806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1800 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 225, 1800 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 1822 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS D 305 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 305 " occ=0.50 Time building chain proxies: 5.39, per 1000 atoms: 0.61 Number of scatterers: 8905 At special positions: 0 Unit cell: (91.3, 119.52, 129.48, 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 65 16.00 P 1 15.00 O 1654 8.00 N 1505 7.00 C 5680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 282 " - pdb=" SG CYS F 287 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.8 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 13 sheets defined 35.4% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.609A pdb=" N ASN A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' 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 'F' and resid 24 through 32 Processing helix chain 'F' and resid 49 through 72 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 79 through 104 Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 114 through 147 Processing helix chain 'F' and resid 157 through 180 removed outlier: 3.550A pdb=" N TRP F 168 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER F 171 " --> pdb=" O CYS F 167 " (cutoff:3.500A) Proline residue: F 178 - end of helix Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 200 through 233 Processing helix chain 'F' and resid 250 through 281 Proline residue: F 271 - end of helix removed outlier: 4.437A pdb=" N VAL F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 294 through 313 removed outlier: 3.711A pdb=" N SER F 304 " --> pdb=" O ALA F 300 " (cutoff:3.500A) Proline residue: F 308 - end of helix Processing helix chain 'F' and resid 316 through 323 Processing helix chain 'D' and resid 7 through 31 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 208 through 215 removed outlier: 5.381A pdb=" N HIS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N CYS D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE D 215 " --> pdb=" O TRP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 230 Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 271 through 279 removed outlier: 3.736A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 285 No H-bonds generated for 'chain 'D' and resid 283 through 285' Processing helix chain 'D' and resid 296 through 310 removed outlier: 3.738A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 350 Processing sheet with id= A, first strand: chain 'A' and resid 57 through 61 removed outlier: 6.825A pdb=" N ALA A 72 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N MET A 60 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 70 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 73 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASP A 82 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS A 88 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 104 removed outlier: 6.829A pdb=" N GLY A 114 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS A 102 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA A 112 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR A 104 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N TYR A 110 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASN A 124 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A 134 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 150 removed outlier: 6.652A pdb=" N SER A 159 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS A 148 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 157 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE A 150 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLN A 155 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP A 169 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLN A 175 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 186 through 191 removed outlier: 7.065A pdb=" N GLY A 201 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU A 189 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 199 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU A 191 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU A 197 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP A 211 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N CYS A 217 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 228 through 233 removed outlier: 6.713A pdb=" N GLY A 243 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 231 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA A 241 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE A 233 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 239 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP A 253 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU A 259 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 272 through 277 removed outlier: 6.663A pdb=" N GLY A 287 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A 275 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 285 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE A 277 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU A 283 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASP A 297 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG A 303 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.647A pdb=" N ILE A 337 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR A 49 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 335 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.669A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.938A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL E 149 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLU E 246 " --> pdb=" O VAL E 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.602A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.318A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 319 through 323 removed outlier: 6.705A pdb=" N ILE D 264 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N HIS D 322 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU D 266 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N HIS D 195 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU D 36 " --> pdb=" O HIS D 195 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS D 197 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU D 38 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE D 199 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLY D 40 " --> pdb=" O PHE D 199 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1186 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: 2.44 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1428 1.30 - 1.43: 2384 1.43 - 1.56: 5174 1.56 - 1.68: 2 1.68 - 1.81: 92 Bond restraints: 9080 Sorted by residual: bond pdb=" C MET F 124 " pdb=" O MET F 124 " ideal model delta sigma weight residual 1.236 1.172 0.065 1.15e-02 7.56e+03 3.16e+01 bond pdb=" O1 S1P F 401 " pdb=" P22 S1P F 401 " ideal model delta sigma weight residual 1.661 1.592 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C11 S1P F 401 " pdb=" C12 S1P F 401 " ideal model delta sigma weight residual 1.573 1.506 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C12 S1P F 401 " pdb=" C13 S1P F 401 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C13 S1P F 401 " pdb=" C14 S1P F 401 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.26e+00 ... (remaining 9075 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.50: 112 105.50 - 112.62: 4821 112.62 - 119.75: 2921 119.75 - 126.87: 4324 126.87 - 134.00: 104 Bond angle restraints: 12282 Sorted by residual: angle pdb=" CA MET F 124 " pdb=" C MET F 124 " pdb=" O MET F 124 " ideal model delta sigma weight residual 120.82 116.51 4.31 1.05e+00 9.07e-01 1.69e+01 angle pdb=" CA PHE F 125 " pdb=" C PHE F 125 " pdb=" O PHE F 125 " ideal model delta sigma weight residual 120.55 116.34 4.21 1.06e+00 8.90e-01 1.58e+01 angle pdb=" CA GLY F 122 " pdb=" C GLY F 122 " pdb=" N SER F 123 " ideal model delta sigma weight residual 117.80 113.43 4.37 1.11e+00 8.12e-01 1.55e+01 angle pdb=" C MET F 124 " pdb=" CA MET F 124 " pdb=" CB MET F 124 " ideal model delta sigma weight residual 110.88 105.60 5.28 1.57e+00 4.06e-01 1.13e+01 angle pdb=" N SER F 123 " pdb=" CA SER F 123 " pdb=" C SER F 123 " ideal model delta sigma weight residual 111.03 107.37 3.66 1.11e+00 8.12e-01 1.09e+01 ... (remaining 12277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4948 17.93 - 35.86: 365 35.86 - 53.79: 71 53.79 - 71.73: 10 71.73 - 89.66: 9 Dihedral angle restraints: 5403 sinusoidal: 2113 harmonic: 3290 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.36 34.64 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" CA GLU E 234 " pdb=" C GLU E 234 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 162.85 17.15 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1199 0.058 - 0.116: 190 0.116 - 0.175: 18 0.175 - 0.233: 2 0.233 - 0.291: 1 Chirality restraints: 1410 Sorted by residual: chirality pdb=" C3 S1P F 401 " pdb=" C2 S1P F 401 " pdb=" C4 S1P F 401 " pdb=" O3 S1P F 401 " both_signs ideal model delta sigma weight residual False -2.52 -2.23 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA MET F 124 " pdb=" N MET F 124 " pdb=" C MET F 124 " pdb=" CB MET F 124 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CG LEU F 177 " pdb=" CB LEU F 177 " pdb=" CD1 LEU F 177 " pdb=" CD2 LEU F 177 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.94e-01 ... (remaining 1407 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 122 " 0.022 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C GLY F 122 " -0.080 2.00e-02 2.50e+03 pdb=" O GLY F 122 " 0.031 2.00e-02 2.50e+03 pdb=" N SER F 123 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 281 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO D 282 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 282 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 282 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO E 236 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.033 5.00e-02 4.00e+02 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 616 2.74 - 3.28: 8938 3.28 - 3.82: 15076 3.82 - 4.36: 18383 4.36 - 4.90: 32209 Nonbonded interactions: 75222 Sorted by model distance: nonbonded pdb=" O LEU D 234 " pdb=" NH1 ARG D 242 " model vdw 2.198 2.520 nonbonded pdb=" O LEU F 174 " pdb=" OH TYR F 202 " model vdw 2.216 2.440 nonbonded pdb=" OD2 ASP E 73 " pdb=" NZ LYS E 76 " model vdw 2.253 2.520 nonbonded pdb=" O ILE A 57 " pdb=" OG SER A 315 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR E 175 " pdb=" OE2 GLU D 8 " model vdw 2.280 2.440 ... (remaining 75217 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.320 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.710 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.004 0.076 9080 Z= 0.241 Angle : 0.605 10.458 12282 Z= 0.326 Chirality : 0.042 0.291 1410 Planarity : 0.005 0.062 1535 Dihedral : 13.482 89.658 3269 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.51 % Allowed : 0.31 % Favored : 99.18 % 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: 0.89 (0.25), residues: 1117 helix: 2.28 (0.26), residues: 394 sheet: 0.15 (0.29), residues: 286 loop : -0.64 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 81 HIS 0.004 0.001 HIS D 244 PHE 0.018 0.001 PHE F 125 TYR 0.029 0.001 TYR E 235 ARG 0.004 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 0.941 Fit side-chains REVERT: D 17 LYS cc_start: 0.8314 (mmtp) cc_final: 0.8094 (mtmt) outliers start: 5 outliers final: 2 residues processed: 153 average time/residue: 1.2348 time to fit residues: 201.5727 Evaluate side-chains 112 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain D residue 354 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 87 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9080 Z= 0.199 Angle : 0.502 10.229 12282 Z= 0.260 Chirality : 0.041 0.203 1410 Planarity : 0.004 0.055 1535 Dihedral : 6.613 84.687 1247 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.47 % Allowed : 9.15 % Favored : 88.39 % 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: 0.98 (0.25), residues: 1117 helix: 2.45 (0.25), residues: 394 sheet: 0.13 (0.29), residues: 292 loop : -0.66 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 81 HIS 0.003 0.001 HIS D 244 PHE 0.011 0.001 PHE A 198 TYR 0.035 0.001 TYR E 235 ARG 0.005 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.005 Fit side-chains REVERT: C 20 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7366 (mtpp) REVERT: D 247 MET cc_start: 0.8931 (mtp) cc_final: 0.8729 (mtm) outliers start: 24 outliers final: 11 residues processed: 128 average time/residue: 1.1976 time to fit residues: 163.7707 Evaluate side-chains 118 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain D residue 18 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 77 ASN E 186 GLN E 194 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9080 Z= 0.213 Angle : 0.498 10.666 12282 Z= 0.260 Chirality : 0.041 0.217 1410 Planarity : 0.004 0.052 1535 Dihedral : 6.268 84.435 1245 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.80 % Allowed : 9.87 % Favored : 86.33 % 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: 0.95 (0.25), residues: 1117 helix: 2.48 (0.25), residues: 393 sheet: 0.09 (0.29), residues: 287 loop : -0.69 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 81 HIS 0.003 0.001 HIS D 244 PHE 0.011 0.001 PHE A 198 TYR 0.035 0.001 TYR E 235 ARG 0.002 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 117 time to evaluate : 1.218 Fit side-chains REVERT: A 188 SER cc_start: 0.8898 (p) cc_final: 0.8617 (t) REVERT: C 20 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7354 (mtpp) REVERT: C 37 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7449 (mp) REVERT: E 3 GLN cc_start: 0.7825 (pt0) cc_final: 0.7520 (pt0) REVERT: E 235 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6751 (t80) outliers start: 37 outliers final: 17 residues processed: 135 average time/residue: 1.2271 time to fit residues: 176.7427 Evaluate side-chains 129 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 51 optimal weight: 0.0010 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 77 ASN F 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9080 Z= 0.156 Angle : 0.467 11.175 12282 Z= 0.244 Chirality : 0.040 0.201 1410 Planarity : 0.004 0.051 1535 Dihedral : 5.836 72.410 1245 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.29 % Allowed : 12.02 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1117 helix: 2.54 (0.25), residues: 394 sheet: 0.17 (0.29), residues: 292 loop : -0.65 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 81 HIS 0.003 0.001 HIS D 244 PHE 0.010 0.001 PHE A 198 TYR 0.034 0.001 TYR E 235 ARG 0.003 0.000 ARG F 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 1.042 Fit side-chains REVERT: A 188 SER cc_start: 0.8891 (p) cc_final: 0.8621 (t) REVERT: C 20 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7330 (mtpp) REVERT: E 235 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6537 (t80) REVERT: F 124 MET cc_start: 0.7245 (ttp) cc_final: 0.6909 (ttt) REVERT: F 164 ILE cc_start: 0.6267 (mm) cc_final: 0.6048 (tp) outliers start: 32 outliers final: 16 residues processed: 135 average time/residue: 1.2906 time to fit residues: 186.0532 Evaluate side-chains 131 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 0.0270 chunk 26 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 77 ASN E 186 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9080 Z= 0.166 Angle : 0.466 11.499 12282 Z= 0.243 Chirality : 0.040 0.198 1410 Planarity : 0.004 0.053 1535 Dihedral : 5.580 69.724 1243 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.49 % Allowed : 13.57 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1117 helix: 2.58 (0.25), residues: 393 sheet: 0.20 (0.29), residues: 298 loop : -0.64 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 81 HIS 0.003 0.001 HIS D 244 PHE 0.010 0.001 PHE A 198 TYR 0.034 0.001 TYR E 235 ARG 0.002 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 1.049 Fit side-chains REVERT: A 303 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7261 (tmm-80) REVERT: C 20 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7329 (mtpp) REVERT: E 235 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.6470 (t80) REVERT: F 197 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7323 (tt) REVERT: D 242 ARG cc_start: 0.7024 (mtt-85) cc_final: 0.6820 (mtt-85) outliers start: 34 outliers final: 21 residues processed: 134 average time/residue: 1.1562 time to fit residues: 165.9941 Evaluate side-chains 136 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 102 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9080 Z= 0.159 Angle : 0.464 11.907 12282 Z= 0.241 Chirality : 0.039 0.196 1410 Planarity : 0.004 0.051 1535 Dihedral : 5.477 71.414 1243 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.98 % Allowed : 14.70 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1117 helix: 2.59 (0.25), residues: 393 sheet: 0.23 (0.29), residues: 298 loop : -0.64 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 81 HIS 0.003 0.001 HIS D 244 PHE 0.010 0.001 PHE A 198 TYR 0.034 0.001 TYR E 235 ARG 0.003 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.005 Fit side-chains REVERT: A 303 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7271 (tmm-80) REVERT: C 20 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7315 (mtpp) REVERT: C 37 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7399 (mp) REVERT: E 235 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.6388 (t80) REVERT: F 197 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7385 (tt) REVERT: D 247 MET cc_start: 0.8952 (mtp) cc_final: 0.8747 (mtm) outliers start: 29 outliers final: 20 residues processed: 131 average time/residue: 1.1649 time to fit residues: 163.2794 Evaluate side-chains 131 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN E 186 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9080 Z= 0.189 Angle : 0.485 12.353 12282 Z= 0.252 Chirality : 0.040 0.206 1410 Planarity : 0.004 0.053 1535 Dihedral : 5.522 71.749 1243 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.19 % Allowed : 15.21 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1117 helix: 2.56 (0.25), residues: 394 sheet: 0.22 (0.29), residues: 293 loop : -0.63 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 81 HIS 0.002 0.001 HIS D 244 PHE 0.011 0.001 PHE F 58 TYR 0.035 0.001 TYR E 235 ARG 0.002 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 1.108 Fit side-chains REVERT: A 303 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7276 (tmm-80) REVERT: C 20 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7333 (mtpp) REVERT: C 37 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7481 (mp) REVERT: E 43 LYS cc_start: 0.8210 (mptt) cc_final: 0.7903 (mtmt) REVERT: E 235 TYR cc_start: 0.6927 (OUTLIER) cc_final: 0.6483 (t80) REVERT: D 240 MET cc_start: 0.6616 (pmm) cc_final: 0.5201 (ppp) outliers start: 31 outliers final: 21 residues processed: 135 average time/residue: 1.3507 time to fit residues: 194.3251 Evaluate side-chains 137 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN E 77 ASN E 186 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9080 Z= 0.185 Angle : 0.489 12.653 12282 Z= 0.253 Chirality : 0.040 0.206 1410 Planarity : 0.004 0.051 1535 Dihedral : 5.504 72.712 1243 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.08 % Allowed : 16.75 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1117 helix: 2.54 (0.25), residues: 395 sheet: 0.25 (0.29), residues: 291 loop : -0.60 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 81 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE F 58 TYR 0.035 0.001 TYR E 235 ARG 0.011 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.051 Fit side-chains REVERT: C 20 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7317 (mtpp) REVERT: E 43 LYS cc_start: 0.8221 (mptt) cc_final: 0.7910 (mtpt) REVERT: E 235 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.6450 (t80) REVERT: F 197 LEU cc_start: 0.7641 (tp) cc_final: 0.7394 (tt) REVERT: F 235 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7451 (pp) outliers start: 30 outliers final: 22 residues processed: 135 average time/residue: 1.2620 time to fit residues: 181.7991 Evaluate side-chains 139 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN E 186 GLN E 194 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9080 Z= 0.329 Angle : 0.568 12.933 12282 Z= 0.296 Chirality : 0.044 0.249 1410 Planarity : 0.004 0.052 1535 Dihedral : 5.968 70.494 1243 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.29 % Allowed : 16.55 % Favored : 80.16 % 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: 0.74 (0.25), residues: 1117 helix: 2.05 (0.25), residues: 402 sheet: 0.08 (0.29), residues: 294 loop : -0.69 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 98 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 150 TYR 0.040 0.002 TYR E 235 ARG 0.009 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 1.038 Fit side-chains REVERT: A 188 SER cc_start: 0.8911 (p) cc_final: 0.8646 (t) REVERT: C 20 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7305 (mtpp) REVERT: C 37 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7689 (mp) REVERT: E 43 LYS cc_start: 0.8219 (mptt) cc_final: 0.7900 (mtpt) REVERT: E 235 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.7080 (t80) REVERT: F 158 PHE cc_start: 0.6429 (m-80) cc_final: 0.6201 (t80) REVERT: F 235 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7520 (pp) REVERT: D 17 LYS cc_start: 0.8325 (mmtp) cc_final: 0.8091 (mtmt) REVERT: D 240 MET cc_start: 0.6695 (pmm) cc_final: 0.5350 (ppp) outliers start: 32 outliers final: 19 residues processed: 132 average time/residue: 1.2842 time to fit residues: 180.7450 Evaluate side-chains 130 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 0.0870 chunk 87 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.0270 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN E 186 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9080 Z= 0.148 Angle : 0.487 12.759 12282 Z= 0.251 Chirality : 0.040 0.204 1410 Planarity : 0.004 0.050 1535 Dihedral : 5.587 76.622 1243 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.85 % Allowed : 17.88 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1117 helix: 2.34 (0.25), residues: 401 sheet: 0.33 (0.30), residues: 279 loop : -0.67 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 81 HIS 0.002 0.000 HIS D 244 PHE 0.011 0.001 PHE A 198 TYR 0.035 0.001 TYR E 235 ARG 0.006 0.000 ARG C 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.031 Fit side-chains REVERT: A 188 SER cc_start: 0.8901 (p) cc_final: 0.8623 (t) REVERT: C 20 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7265 (mtpp) REVERT: E 43 LYS cc_start: 0.8220 (mptt) cc_final: 0.7872 (mtpt) REVERT: E 160 ARG cc_start: 0.7562 (mtm110) cc_final: 0.7076 (mtm-85) REVERT: E 235 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.6456 (t80) REVERT: F 124 MET cc_start: 0.7335 (ttp) cc_final: 0.6918 (mtp) REVERT: F 197 LEU cc_start: 0.7590 (tp) cc_final: 0.7374 (tt) REVERT: F 235 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7440 (pp) REVERT: D 17 LYS cc_start: 0.8315 (mmtp) cc_final: 0.8102 (mtmt) outliers start: 18 outliers final: 14 residues processed: 129 average time/residue: 1.3134 time to fit residues: 180.3098 Evaluate side-chains 131 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 186 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117378 restraints weight = 17734.445| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.30 r_work: 0.3176 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9080 Z= 0.181 Angle : 0.497 12.697 12282 Z= 0.256 Chirality : 0.041 0.200 1410 Planarity : 0.004 0.052 1535 Dihedral : 5.541 76.322 1243 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.47 % Allowed : 17.68 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1117 helix: 2.35 (0.25), residues: 401 sheet: 0.32 (0.30), residues: 279 loop : -0.66 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 81 HIS 0.002 0.001 HIS A 141 PHE 0.011 0.001 PHE F 58 TYR 0.035 0.001 TYR E 235 ARG 0.006 0.000 ARG C 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3621.66 seconds wall clock time: 65 minutes 29.80 seconds (3929.80 seconds total)