Starting phenix.real_space_refine on Fri Nov 15 11:03:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlr_36405/11_2024/8jlr_36405_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlr_36405/11_2024/8jlr_36405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlr_36405/11_2024/8jlr_36405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlr_36405/11_2024/8jlr_36405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlr_36405/11_2024/8jlr_36405_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlr_36405/11_2024/8jlr_36405_neut.cif" } resolution = 3.0 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= -0.005 sd= 0.100 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 67 5.16 5 C 5695 2.51 5 N 1522 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8934 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1928 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2160 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 11, 'TRANS': 256} Chain breaks: 2 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1784 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'VRK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.20, per 1000 atoms: 0.58 Number of scatterers: 8934 At special positions: 0 Unit cell: (109.2, 102.96, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1650 8.00 N 1522 7.00 C 5695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 37.9% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.555A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.628A pdb=" N PHE A 282 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.606A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.782A pdb=" N ARG A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'R' and resid 20 through 51 Processing helix chain 'R' and resid 56 through 84 removed outlier: 4.482A pdb=" N MET R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) Proline residue: R 78 - end of helix removed outlier: 3.844A pdb=" N VAL R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG R 83 " --> pdb=" O TYR R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 127 removed outlier: 3.802A pdb=" N ILE R 98 " --> pdb=" O VAL R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 187 through 199 removed outlier: 3.637A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 228 removed outlier: 4.269A pdb=" N MET R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 277 removed outlier: 3.935A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS R 265 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 4.194A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP R 287 " --> pdb=" O PRO R 283 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 319 Processing helix chain 'Y' and resid 7 through 24 Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 Processing helix chain 'S' and resid 28 through 32 removed outlier: 4.212A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.544A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 3.813A pdb=" N ASP A 200 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.726A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.692A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.710A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.607A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.442A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.913A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.680A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 3.829A pdb=" N VAL S 48 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.585A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1236 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: 2.81 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1428 1.31 - 1.44: 2583 1.44 - 1.56: 5024 1.56 - 1.69: 0 1.69 - 1.81: 101 Bond restraints: 9136 Sorted by residual: bond pdb=" CA THR R 194 " pdb=" C THR R 194 " ideal model delta sigma weight residual 1.523 1.440 0.083 1.35e-02 5.49e+03 3.76e+01 bond pdb=" C THR R 194 " pdb=" O THR R 194 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.26e-02 6.30e+03 1.51e+01 bond pdb=" N TRP B 332 " pdb=" CA TRP B 332 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.32e-02 5.74e+03 5.54e+00 bond pdb=" N ASP R 103 " pdb=" CA ASP R 103 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.47e+00 bond pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.40e-02 5.10e+03 5.18e+00 ... (remaining 9131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 12064 1.67 - 3.33: 257 3.33 - 5.00: 38 5.00 - 6.67: 15 6.67 - 8.34: 3 Bond angle restraints: 12377 Sorted by residual: angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 113.15 108.97 4.18 1.19e+00 7.06e-01 1.24e+01 angle pdb=" N SER S 193 " pdb=" CA SER S 193 " pdb=" C SER S 193 " ideal model delta sigma weight residual 114.56 110.81 3.75 1.27e+00 6.20e-01 8.71e+00 angle pdb=" N TRP B 332 " pdb=" CA TRP B 332 " pdb=" C TRP B 332 " ideal model delta sigma weight residual 113.16 109.69 3.47 1.24e+00 6.50e-01 7.85e+00 angle pdb=" CB MET R 273 " pdb=" CG MET R 273 " pdb=" SD MET R 273 " ideal model delta sigma weight residual 112.70 121.04 -8.34 3.00e+00 1.11e-01 7.72e+00 angle pdb=" N ILE R 201 " pdb=" CA ILE R 201 " pdb=" C ILE R 201 " ideal model delta sigma weight residual 112.35 109.18 3.17 1.20e+00 6.94e-01 6.96e+00 ... (remaining 12372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 4803 16.19 - 32.39: 484 32.39 - 48.58: 137 48.58 - 64.78: 16 64.78 - 80.97: 11 Dihedral angle restraints: 5451 sinusoidal: 2165 harmonic: 3286 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual -86.00 -161.05 75.05 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1281 0.082 - 0.164: 102 0.164 - 0.246: 1 0.246 - 0.329: 0 0.329 - 0.411: 1 Chirality restraints: 1385 Sorted by residual: chirality pdb=" C3 VRK R 401 " pdb=" C14 VRK R 401 " pdb=" C4 VRK R 401 " pdb=" O1 VRK R 401 " both_signs ideal model delta sigma weight residual False 2.41 2.00 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C2 VRK R 401 " pdb=" C1 VRK R 401 " pdb=" C16 VRK R 401 " pdb=" O1 VRK R 401 " both_signs ideal model delta sigma weight residual False 2.45 2.20 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ILE A 255 " pdb=" N ILE A 255 " pdb=" C ILE A 255 " pdb=" CB ILE A 255 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1382 not shown) Planarity restraints: 1561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 298 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO A 299 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 292 " -0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 293 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 308 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO R 309 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO R 309 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 309 " -0.035 5.00e-02 4.00e+02 ... (remaining 1558 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 710 2.74 - 3.28: 9244 3.28 - 3.82: 15591 3.82 - 4.36: 18651 4.36 - 4.90: 32163 Nonbonded interactions: 76359 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.200 3.040 nonbonded pdb=" O ARG A 250 " pdb=" OG1 THR A 251 " model vdw 2.226 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.250 3.040 nonbonded pdb=" O PHE R 186 " pdb=" OH TYR R 279 " model vdw 2.261 3.040 ... (remaining 76354 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.450 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.140 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 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 : 0.003 0.083 9136 Z= 0.197 Angle : 0.613 8.335 12377 Z= 0.333 Chirality : 0.044 0.411 1385 Planarity : 0.005 0.069 1561 Dihedral : 14.183 80.969 3322 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.21 % Allowed : 0.31 % Favored : 99.49 % 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: -0.20 (0.25), residues: 1112 helix: 1.60 (0.26), residues: 385 sheet: -0.84 (0.30), residues: 265 loop : -1.15 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 339 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE S 29 TYR 0.016 0.001 TYR S 228 ARG 0.003 0.000 ARG R 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 212 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7378 (m-80) cc_final: 0.7044 (m-10) REVERT: A 274 LYS cc_start: 0.7765 (mmpt) cc_final: 0.7504 (mmtt) REVERT: R 123 TYR cc_start: 0.7732 (m-80) cc_final: 0.7403 (m-80) REVERT: R 211 TYR cc_start: 0.7978 (t80) cc_final: 0.7480 (t80) REVERT: S 228 TYR cc_start: 0.7710 (m-80) cc_final: 0.7034 (m-80) REVERT: S 237 LEU cc_start: 0.5182 (mp) cc_final: 0.4929 (mp) outliers start: 2 outliers final: 1 residues processed: 213 average time/residue: 0.8605 time to fit residues: 200.8921 Evaluate side-chains 165 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 194 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9136 Z= 0.229 Angle : 0.602 7.747 12377 Z= 0.317 Chirality : 0.044 0.205 1385 Planarity : 0.005 0.057 1561 Dihedral : 5.382 40.198 1279 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.16 % Allowed : 10.57 % Favored : 87.27 % 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: -0.13 (0.25), residues: 1112 helix: 1.52 (0.25), residues: 397 sheet: -0.73 (0.31), residues: 258 loop : -1.08 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.003 0.001 HIS A 324 PHE 0.015 0.001 PHE R 299 TYR 0.018 0.002 TYR S 190 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7478 (m-80) cc_final: 0.7192 (m-10) REVERT: A 274 LYS cc_start: 0.7482 (mmpt) cc_final: 0.7249 (mmtt) REVERT: B 163 ASP cc_start: 0.6555 (t0) cc_final: 0.6323 (t0) REVERT: R 97 LYS cc_start: 0.8244 (tppt) cc_final: 0.7916 (mttm) REVERT: R 123 TYR cc_start: 0.7920 (m-80) cc_final: 0.7579 (m-80) REVERT: R 211 TYR cc_start: 0.7946 (t80) cc_final: 0.7517 (t80) REVERT: S 228 TYR cc_start: 0.7812 (m-80) cc_final: 0.7032 (m-80) outliers start: 21 outliers final: 8 residues processed: 185 average time/residue: 0.7956 time to fit residues: 162.7944 Evaluate side-chains 178 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.5980 chunk 31 optimal weight: 0.0040 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 0.0370 overall best weight: 0.9274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9136 Z= 0.220 Angle : 0.581 7.720 12377 Z= 0.305 Chirality : 0.044 0.184 1385 Planarity : 0.005 0.055 1561 Dihedral : 5.173 36.280 1279 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.95 % Allowed : 14.78 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1112 helix: 1.55 (0.25), residues: 394 sheet: -0.80 (0.31), residues: 258 loop : -1.11 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.003 0.001 HIS A 324 PHE 0.012 0.001 PHE A 189 TYR 0.016 0.002 TYR S 190 ARG 0.006 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7432 (m-80) cc_final: 0.7196 (m-10) REVERT: B 163 ASP cc_start: 0.6587 (t0) cc_final: 0.6365 (t0) REVERT: R 97 LYS cc_start: 0.8289 (tppt) cc_final: 0.7973 (mttm) REVERT: R 123 TYR cc_start: 0.7967 (m-80) cc_final: 0.7634 (m-80) REVERT: R 194 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8449 (p) REVERT: R 211 TYR cc_start: 0.7960 (t80) cc_final: 0.7582 (t80) REVERT: S 188 LEU cc_start: 0.8000 (mt) cc_final: 0.7612 (mt) REVERT: S 228 TYR cc_start: 0.7783 (m-80) cc_final: 0.7152 (m-80) outliers start: 19 outliers final: 8 residues processed: 193 average time/residue: 0.7879 time to fit residues: 167.6415 Evaluate side-chains 174 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9136 Z= 0.267 Angle : 0.605 11.047 12377 Z= 0.313 Chirality : 0.044 0.187 1385 Planarity : 0.005 0.055 1561 Dihedral : 5.145 35.711 1279 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.36 % Allowed : 16.63 % Favored : 81.01 % 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: -0.15 (0.25), residues: 1112 helix: 1.55 (0.25), residues: 396 sheet: -0.87 (0.31), residues: 262 loop : -1.05 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 324 PHE 0.015 0.001 PHE A 189 TYR 0.020 0.002 TYR B 85 ARG 0.007 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 290 ASP cc_start: 0.6666 (p0) cc_final: 0.6452 (t0) REVERT: R 97 LYS cc_start: 0.8288 (tppt) cc_final: 0.8014 (mttm) REVERT: R 123 TYR cc_start: 0.7955 (m-80) cc_final: 0.7726 (m-80) REVERT: R 158 MET cc_start: 0.6215 (tmm) cc_final: 0.5958 (ttm) REVERT: R 194 THR cc_start: 0.8645 (m) cc_final: 0.8365 (p) REVERT: R 211 TYR cc_start: 0.7993 (t80) cc_final: 0.7592 (t80) REVERT: S 188 LEU cc_start: 0.8019 (mt) cc_final: 0.7651 (mt) REVERT: S 228 TYR cc_start: 0.7810 (m-80) cc_final: 0.7294 (m-80) outliers start: 23 outliers final: 13 residues processed: 191 average time/residue: 0.8108 time to fit residues: 170.5700 Evaluate side-chains 173 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9136 Z= 0.195 Angle : 0.579 8.496 12377 Z= 0.299 Chirality : 0.043 0.187 1385 Planarity : 0.005 0.055 1561 Dihedral : 4.991 32.769 1278 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.50 % Favored : 95.41 % Rotamer: Outliers : 2.67 % Allowed : 18.17 % Favored : 79.16 % 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: -0.10 (0.25), residues: 1112 helix: 1.54 (0.25), residues: 399 sheet: -0.82 (0.31), residues: 260 loop : -0.99 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS A 324 PHE 0.016 0.001 PHE R 91 TYR 0.018 0.002 TYR R 214 ARG 0.007 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 1.051 Fit side-chains REVERT: A 197 HIS cc_start: 0.7535 (m170) cc_final: 0.7197 (m-70) REVERT: A 290 ASP cc_start: 0.6667 (p0) cc_final: 0.6442 (t0) REVERT: B 239 ASN cc_start: 0.7337 (m-40) cc_final: 0.7012 (m110) REVERT: R 97 LYS cc_start: 0.8244 (tppt) cc_final: 0.7971 (mttm) REVERT: R 123 TYR cc_start: 0.7926 (m-80) cc_final: 0.7553 (m-80) REVERT: R 158 MET cc_start: 0.6258 (tmm) cc_final: 0.6018 (ttm) REVERT: R 194 THR cc_start: 0.8600 (m) cc_final: 0.8307 (p) REVERT: R 211 TYR cc_start: 0.7973 (t80) cc_final: 0.7607 (t80) REVERT: S 188 LEU cc_start: 0.8062 (mt) cc_final: 0.7709 (mt) REVERT: S 228 TYR cc_start: 0.7817 (m-80) cc_final: 0.7406 (m-80) outliers start: 26 outliers final: 14 residues processed: 189 average time/residue: 0.8231 time to fit residues: 171.0532 Evaluate side-chains 174 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 0.2980 chunk 8 optimal weight: 0.0060 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN R 63 HIS ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9136 Z= 0.224 Angle : 0.590 10.412 12377 Z= 0.304 Chirality : 0.043 0.200 1385 Planarity : 0.005 0.054 1561 Dihedral : 4.896 31.585 1278 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.77 % Allowed : 19.10 % Favored : 78.13 % 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: -0.13 (0.25), residues: 1112 helix: 1.51 (0.25), residues: 400 sheet: -0.91 (0.30), residues: 260 loop : -0.96 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS A 324 PHE 0.015 0.001 PHE A 189 TYR 0.016 0.002 TYR R 214 ARG 0.007 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.104 Fit side-chains REVERT: A 274 LYS cc_start: 0.7479 (mmtt) cc_final: 0.7164 (mmmt) REVERT: A 290 ASP cc_start: 0.6661 (p0) cc_final: 0.6416 (t0) REVERT: R 97 LYS cc_start: 0.8253 (tppt) cc_final: 0.7979 (mttm) REVERT: R 123 TYR cc_start: 0.7942 (m-80) cc_final: 0.7583 (m-80) REVERT: R 194 THR cc_start: 0.8608 (m) cc_final: 0.8192 (p) REVERT: R 211 TYR cc_start: 0.7989 (t80) cc_final: 0.7618 (t80) REVERT: S 188 LEU cc_start: 0.8066 (mt) cc_final: 0.7776 (mt) REVERT: S 228 TYR cc_start: 0.7745 (m-80) cc_final: 0.7435 (m-80) outliers start: 27 outliers final: 13 residues processed: 185 average time/residue: 0.8673 time to fit residues: 176.0987 Evaluate side-chains 173 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9136 Z= 0.220 Angle : 0.607 9.124 12377 Z= 0.312 Chirality : 0.043 0.190 1385 Planarity : 0.005 0.054 1561 Dihedral : 4.871 30.915 1278 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.36 % Allowed : 20.53 % Favored : 77.10 % 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: -0.10 (0.25), residues: 1112 helix: 1.54 (0.25), residues: 398 sheet: -0.78 (0.31), residues: 267 loop : -1.02 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS A 324 PHE 0.017 0.001 PHE R 91 TYR 0.017 0.002 TYR B 59 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.509 Fit side-chains REVERT: A 53 MET cc_start: 0.4935 (OUTLIER) cc_final: 0.4660 (mtm) REVERT: A 197 HIS cc_start: 0.7476 (m170) cc_final: 0.7159 (m-70) REVERT: A 274 LYS cc_start: 0.7458 (mmtt) cc_final: 0.7171 (mmmt) REVERT: A 290 ASP cc_start: 0.6701 (p0) cc_final: 0.6365 (t0) REVERT: B 57 LYS cc_start: 0.8577 (pttm) cc_final: 0.8275 (pttp) REVERT: R 97 LYS cc_start: 0.8244 (tppt) cc_final: 0.8040 (mttm) REVERT: R 123 TYR cc_start: 0.7946 (m-80) cc_final: 0.7715 (m-80) REVERT: R 158 MET cc_start: 0.6197 (ttt) cc_final: 0.5927 (ttt) REVERT: R 194 THR cc_start: 0.8594 (m) cc_final: 0.8314 (p) REVERT: R 211 TYR cc_start: 0.7992 (t80) cc_final: 0.7612 (t80) REVERT: S 188 LEU cc_start: 0.8054 (mt) cc_final: 0.7775 (mt) REVERT: S 228 TYR cc_start: 0.7759 (m-80) cc_final: 0.7458 (m-80) outliers start: 23 outliers final: 13 residues processed: 181 average time/residue: 0.8659 time to fit residues: 171.6718 Evaluate side-chains 178 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.0370 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9136 Z= 0.200 Angle : 0.600 10.413 12377 Z= 0.308 Chirality : 0.043 0.191 1385 Planarity : 0.005 0.056 1561 Dihedral : 4.797 29.091 1278 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.16 % Allowed : 20.84 % Favored : 77.00 % 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: -0.04 (0.25), residues: 1112 helix: 1.67 (0.25), residues: 393 sheet: -0.72 (0.31), residues: 265 loop : -1.06 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.003 0.001 HIS B 142 PHE 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR S 190 ARG 0.007 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 1.129 Fit side-chains REVERT: A 197 HIS cc_start: 0.7476 (m170) cc_final: 0.7140 (m-70) REVERT: A 290 ASP cc_start: 0.6648 (p0) cc_final: 0.6293 (t0) REVERT: R 97 LYS cc_start: 0.8243 (tppt) cc_final: 0.7971 (mttm) REVERT: R 123 TYR cc_start: 0.7932 (m-80) cc_final: 0.7571 (m-80) REVERT: R 194 THR cc_start: 0.8596 (m) cc_final: 0.8316 (p) REVERT: R 211 TYR cc_start: 0.7981 (t80) cc_final: 0.7553 (t80) REVERT: S 188 LEU cc_start: 0.8042 (mt) cc_final: 0.7777 (mt) REVERT: S 228 TYR cc_start: 0.7738 (m-80) cc_final: 0.7460 (m-80) outliers start: 21 outliers final: 15 residues processed: 179 average time/residue: 0.8506 time to fit residues: 166.9055 Evaluate side-chains 175 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9136 Z= 0.202 Angle : 0.617 9.566 12377 Z= 0.317 Chirality : 0.044 0.235 1385 Planarity : 0.005 0.057 1561 Dihedral : 4.768 28.086 1278 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.16 % Allowed : 21.46 % Favored : 76.39 % 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: -0.04 (0.25), residues: 1112 helix: 1.68 (0.26), residues: 393 sheet: -0.70 (0.31), residues: 265 loop : -1.09 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.003 0.001 HIS B 142 PHE 0.014 0.001 PHE A 189 TYR 0.040 0.002 TYR B 59 ARG 0.007 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.958 Fit side-chains REVERT: A 197 HIS cc_start: 0.7472 (m170) cc_final: 0.7095 (m-70) REVERT: A 290 ASP cc_start: 0.6648 (p0) cc_final: 0.6292 (t0) REVERT: R 97 LYS cc_start: 0.8237 (tppt) cc_final: 0.7959 (mttm) REVERT: R 123 TYR cc_start: 0.7927 (m-80) cc_final: 0.7572 (m-80) REVERT: R 194 THR cc_start: 0.8593 (m) cc_final: 0.8293 (p) REVERT: R 211 TYR cc_start: 0.7981 (t80) cc_final: 0.7559 (t80) REVERT: S 188 LEU cc_start: 0.8015 (mt) cc_final: 0.7750 (mt) REVERT: S 228 TYR cc_start: 0.7714 (m-80) cc_final: 0.7490 (m-80) outliers start: 21 outliers final: 15 residues processed: 178 average time/residue: 0.8816 time to fit residues: 171.6835 Evaluate side-chains 173 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.0040 chunk 109 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 87 optimal weight: 0.0570 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.7514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9136 Z= 0.209 Angle : 0.623 10.434 12377 Z= 0.318 Chirality : 0.044 0.213 1385 Planarity : 0.005 0.058 1561 Dihedral : 4.769 27.038 1278 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.95 % Allowed : 21.77 % Favored : 76.28 % 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: -0.06 (0.25), residues: 1112 helix: 1.67 (0.25), residues: 393 sheet: -0.79 (0.31), residues: 269 loop : -1.06 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.001 PHE A 189 TYR 0.034 0.002 TYR B 59 ARG 0.010 0.000 ARG A 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.140 Fit side-chains REVERT: A 197 HIS cc_start: 0.7438 (m170) cc_final: 0.7069 (m-70) REVERT: R 97 LYS cc_start: 0.8244 (tppt) cc_final: 0.8032 (mttm) REVERT: R 123 TYR cc_start: 0.7912 (m-80) cc_final: 0.7568 (m-80) REVERT: R 194 THR cc_start: 0.8613 (m) cc_final: 0.8348 (p) REVERT: R 211 TYR cc_start: 0.7985 (t80) cc_final: 0.7562 (t80) REVERT: S 188 LEU cc_start: 0.7980 (mt) cc_final: 0.7758 (mt) REVERT: S 228 TYR cc_start: 0.7815 (m-80) cc_final: 0.7589 (m-80) outliers start: 19 outliers final: 15 residues processed: 171 average time/residue: 0.8934 time to fit residues: 167.7438 Evaluate side-chains 173 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 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 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.206595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157795 restraints weight = 10223.212| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.59 r_work: 0.3657 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9136 Z= 0.227 Angle : 0.635 11.186 12377 Z= 0.325 Chirality : 0.044 0.200 1385 Planarity : 0.005 0.058 1561 Dihedral : 4.776 26.337 1278 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.05 % Allowed : 21.97 % Favored : 75.98 % 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: -0.07 (0.25), residues: 1112 helix: 1.64 (0.25), residues: 393 sheet: -0.72 (0.31), residues: 267 loop : -1.08 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.001 PHE A 189 TYR 0.022 0.002 TYR B 59 ARG 0.010 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3496.12 seconds wall clock time: 63 minutes 39.02 seconds (3819.02 seconds total)