Starting phenix.real_space_refine on Mon Mar 11 02:12:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jda_36076/03_2024/8jda_36076_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jda_36076/03_2024/8jda_36076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jda_36076/03_2024/8jda_36076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jda_36076/03_2024/8jda_36076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jda_36076/03_2024/8jda_36076_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jda_36076/03_2024/8jda_36076_neut.pdb" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.065 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 26 5.16 5 C 4322 2.51 5 N 1042 2.21 5 O 1136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6526 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3263 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 8, 'TRANS': 415} Chain: "B" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3263 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 8, 'TRANS': 415} Time building chain proxies: 4.10, per 1000 atoms: 0.63 Number of scatterers: 6526 At special positions: 0 Unit cell: (68.04, 106.92, 66.96, 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 26 16.00 O 1136 8.00 N 1042 7.00 C 4322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.3 seconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 80.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 33 through 54 removed outlier: 4.161A pdb=" N VAL A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 77 removed outlier: 3.938A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.783A pdb=" N GLU A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 116 removed outlier: 4.059A pdb=" N LEU A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Proline residue: A 107 - end of helix removed outlier: 4.339A pdb=" N GLU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.649A pdb=" N LEU A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 139 through 152 removed outlier: 3.594A pdb=" N VAL A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 169 removed outlier: 4.123A pdb=" N LEU A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 188 through 204 removed outlier: 3.971A pdb=" N SER A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET A 199 " --> pdb=" O GLY A 195 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLY A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 4.595A pdb=" N PHE A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 257 through 278 removed outlier: 3.533A pdb=" N ILE A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 298 removed outlier: 3.685A pdb=" N THR A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 339 removed outlier: 4.218A pdb=" N LYS A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A 316 " --> pdb=" O HIS A 312 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 4.130A pdb=" N TRP A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 352' Processing helix chain 'A' and resid 353 through 378 removed outlier: 3.651A pdb=" N VAL A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 372 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Proline residue: A 374 - end of helix removed outlier: 3.924A pdb=" N ARG A 378 " --> pdb=" O PRO A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 398 through 410 Processing helix chain 'A' and resid 418 through 451 removed outlier: 3.561A pdb=" N THR A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 54 removed outlier: 3.789A pdb=" N LEU B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 77 removed outlier: 4.122A pdb=" N ALA B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.653A pdb=" N ALA B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 110 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 125 through 138 Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 139 through 152 removed outlier: 3.744A pdb=" N LEU B 147 " --> pdb=" O CYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.830A pdb=" N LEU B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 183 removed outlier: 3.707A pdb=" N VAL B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.591A pdb=" N LEU B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLY B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 removed outlier: 4.307A pdb=" N PHE B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.620A pdb=" N ILE B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE B 226 " --> pdb=" O TRP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 254 Processing helix chain 'B' and resid 257 through 281 removed outlier: 4.011A pdb=" N PHE B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 274 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 299 Processing helix chain 'B' and resid 304 through 339 removed outlier: 4.077A pdb=" N LYS B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 316 " --> pdb=" O HIS B 312 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET B 317 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 377 removed outlier: 3.786A pdb=" N VAL B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 372 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 398 through 411 removed outlier: 3.584A pdb=" N LEU B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 439 Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.683A pdb=" N ARG B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1290 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: 1.77 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1972 1.34 - 1.46: 1133 1.46 - 1.57: 3519 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 6670 Sorted by residual: bond pdb=" C VAL A 134 " pdb=" N PRO A 135 " ideal model delta sigma weight residual 1.335 1.354 -0.019 9.40e-03 1.13e+04 4.23e+00 bond pdb=" C VAL B 134 " pdb=" N PRO B 135 " ideal model delta sigma weight residual 1.335 1.354 -0.019 9.40e-03 1.13e+04 4.05e+00 bond pdb=" C TYR A 373 " pdb=" N PRO A 374 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.38e-02 5.25e+03 1.87e+00 bond pdb=" CA ILE A 438 " pdb=" C ILE A 438 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.27e-02 6.20e+03 1.66e+00 bond pdb=" CG1 ILE B 193 " pdb=" CD1 ILE B 193 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.58e+00 ... (remaining 6665 not shown) Histogram of bond angle deviations from ideal: 97.02 - 104.46: 60 104.46 - 111.89: 3310 111.89 - 119.32: 2319 119.32 - 126.75: 3276 126.75 - 134.19: 97 Bond angle restraints: 9062 Sorted by residual: angle pdb=" N LEU A 132 " pdb=" CA LEU A 132 " pdb=" C LEU A 132 " ideal model delta sigma weight residual 114.75 107.72 7.03 1.26e+00 6.30e-01 3.11e+01 angle pdb=" N VAL B 207 " pdb=" CA VAL B 207 " pdb=" C VAL B 207 " ideal model delta sigma weight residual 112.80 107.59 5.21 1.15e+00 7.56e-01 2.05e+01 angle pdb=" N ILE B 139 " pdb=" CA ILE B 139 " pdb=" C ILE B 139 " ideal model delta sigma weight residual 111.90 108.56 3.34 8.10e-01 1.52e+00 1.71e+01 angle pdb=" C VAL B 232 " pdb=" N ALA B 233 " pdb=" CA ALA B 233 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 angle pdb=" N GLY A 84 " pdb=" CA GLY A 84 " pdb=" C GLY A 84 " ideal model delta sigma weight residual 111.21 114.91 -3.70 1.04e+00 9.25e-01 1.26e+01 ... (remaining 9057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 3364 14.40 - 28.81: 313 28.81 - 43.21: 136 43.21 - 57.61: 17 57.61 - 72.01: 10 Dihedral angle restraints: 3840 sinusoidal: 1428 harmonic: 2412 Sorted by residual: dihedral pdb=" CA LEU A 198 " pdb=" C LEU A 198 " pdb=" N MET A 199 " pdb=" CA MET A 199 " ideal model delta harmonic sigma weight residual 180.00 151.80 28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA GLU B 99 " pdb=" C GLU B 99 " pdb=" N LEU B 100 " pdb=" CA LEU B 100 " ideal model delta harmonic sigma weight residual 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LEU B 131 " pdb=" C LEU B 131 " pdb=" N LEU B 132 " pdb=" CA LEU B 132 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 3837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 958 0.064 - 0.128: 129 0.128 - 0.192: 6 0.192 - 0.255: 0 0.255 - 0.319: 1 Chirality restraints: 1094 Sorted by residual: chirality pdb=" CB ILE A 438 " pdb=" CA ILE A 438 " pdb=" CG1 ILE A 438 " pdb=" CG2 ILE A 438 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB ILE A 417 " pdb=" CA ILE A 417 " pdb=" CG1 ILE A 417 " pdb=" CG2 ILE A 417 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ASN A 256 " pdb=" N ASN A 256 " pdb=" C ASN A 256 " pdb=" CB ASN A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 1091 not shown) Planarity restraints: 1088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 233 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ALA B 233 " -0.073 2.00e-02 2.50e+03 pdb=" O ALA B 233 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU B 234 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 97 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO B 98 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 373 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO A 374 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 374 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 374 " 0.026 5.00e-02 4.00e+02 ... (remaining 1085 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 288 2.72 - 3.27: 7176 3.27 - 3.81: 10998 3.81 - 4.36: 13750 4.36 - 4.90: 22530 Nonbonded interactions: 54742 Sorted by model distance: nonbonded pdb=" OH TYR A 274 " pdb=" OD1 ASP B 35 " model vdw 2.176 2.440 nonbonded pdb=" O LYS A 309 " pdb=" ND1 HIS A 313 " model vdw 2.203 2.520 nonbonded pdb=" OD1 ASP A 35 " pdb=" OH TYR B 274 " model vdw 2.206 2.440 nonbonded pdb=" OH TYR B 77 " pdb=" ND2 ASN B 94 " model vdw 2.211 2.520 nonbonded pdb=" O GLY A 47 " pdb=" OG SER A 50 " model vdw 2.224 2.440 ... (remaining 54737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 0.970 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: 0.000 Extract box with map and model: 4.280 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 21.990 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 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 0.049 6670 Z= 0.240 Angle : 0.779 8.539 9062 Z= 0.441 Chirality : 0.043 0.319 1094 Planarity : 0.005 0.056 1088 Dihedral : 14.021 72.012 2300 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer: Outliers : 0.14 % Allowed : 1.14 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.29), residues: 844 helix: -0.57 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -1.67 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 156 HIS 0.003 0.001 HIS B 416 PHE 0.021 0.002 PHE A 425 TYR 0.025 0.002 TYR A 273 ARG 0.003 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.740 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.1467 time to fit residues: 24.7385 Evaluate side-chains 99 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 0.0050 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6670 Z= 0.208 Angle : 0.657 8.374 9062 Z= 0.331 Chirality : 0.041 0.194 1094 Planarity : 0.004 0.053 1088 Dihedral : 5.084 27.180 899 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.00 % Allowed : 9.71 % Favored : 88.29 % 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: -0.88 (0.29), residues: 844 helix: -0.15 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -1.67 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 158 HIS 0.003 0.001 HIS B 88 PHE 0.026 0.002 PHE B 298 TYR 0.011 0.001 TYR B 273 ARG 0.002 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.791 Fit side-chains REVERT: A 256 ASN cc_start: 0.7393 (p0) cc_final: 0.7176 (p0) outliers start: 14 outliers final: 10 residues processed: 116 average time/residue: 0.1462 time to fit residues: 24.2480 Evaluate side-chains 106 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 362 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6670 Z= 0.207 Angle : 0.627 7.959 9062 Z= 0.316 Chirality : 0.040 0.195 1094 Planarity : 0.004 0.053 1088 Dihedral : 4.844 23.087 896 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.29 % Allowed : 13.71 % Favored : 84.00 % 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: -0.63 (0.30), residues: 844 helix: 0.03 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -1.62 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 158 HIS 0.003 0.001 HIS B 88 PHE 0.028 0.001 PHE B 298 TYR 0.014 0.001 TYR A 273 ARG 0.001 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.749 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 118 average time/residue: 0.1569 time to fit residues: 26.8060 Evaluate side-chains 110 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 394 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 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 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6670 Z= 0.230 Angle : 0.637 9.044 9062 Z= 0.319 Chirality : 0.041 0.207 1094 Planarity : 0.004 0.047 1088 Dihedral : 4.823 20.715 896 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.00 % Allowed : 16.71 % Favored : 80.29 % 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: -0.58 (0.30), residues: 844 helix: 0.10 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.63 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 156 HIS 0.002 0.001 HIS B 88 PHE 0.021 0.001 PHE B 298 TYR 0.014 0.001 TYR B 273 ARG 0.001 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.702 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 119 average time/residue: 0.1673 time to fit residues: 28.0497 Evaluate side-chains 107 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 394 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6670 Z= 0.205 Angle : 0.623 8.735 9062 Z= 0.310 Chirality : 0.040 0.212 1094 Planarity : 0.004 0.046 1088 Dihedral : 4.741 20.608 896 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.14 % Allowed : 18.86 % Favored : 78.00 % 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: -0.48 (0.30), residues: 844 helix: 0.17 (0.21), residues: 654 sheet: None (None), residues: 0 loop : -1.70 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 156 HIS 0.002 0.001 HIS B 88 PHE 0.014 0.001 PHE B 298 TYR 0.013 0.001 TYR B 273 ARG 0.001 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.721 Fit side-chains REVERT: B 158 TRP cc_start: 0.4725 (m100) cc_final: 0.4311 (t60) outliers start: 22 outliers final: 13 residues processed: 121 average time/residue: 0.1545 time to fit residues: 26.2550 Evaluate side-chains 113 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 394 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.0050 chunk 20 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6670 Z= 0.168 Angle : 0.610 8.890 9062 Z= 0.301 Chirality : 0.040 0.214 1094 Planarity : 0.004 0.050 1088 Dihedral : 4.600 21.561 896 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.86 % Allowed : 21.43 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.30), residues: 844 helix: 0.30 (0.21), residues: 656 sheet: None (None), residues: 0 loop : -1.41 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 156 HIS 0.003 0.000 HIS B 88 PHE 0.034 0.001 PHE B 298 TYR 0.015 0.001 TYR B 273 ARG 0.001 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.5917 (t-100) cc_final: 0.5433 (t60) REVERT: B 99 GLU cc_start: 0.7451 (pm20) cc_final: 0.7235 (pm20) outliers start: 20 outliers final: 15 residues processed: 123 average time/residue: 0.1449 time to fit residues: 25.3767 Evaluate side-chains 122 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 394 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 362 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6670 Z= 0.227 Angle : 0.645 8.560 9062 Z= 0.317 Chirality : 0.042 0.231 1094 Planarity : 0.004 0.050 1088 Dihedral : 4.693 20.831 896 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.57 % Allowed : 21.57 % Favored : 74.86 % 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: -0.26 (0.30), residues: 844 helix: 0.28 (0.21), residues: 654 sheet: None (None), residues: 0 loop : -1.45 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 156 HIS 0.003 0.001 HIS A 52 PHE 0.029 0.001 PHE B 228 TYR 0.016 0.001 TYR B 273 ARG 0.001 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.724 Fit side-chains REVERT: A 351 TRP cc_start: 0.5703 (t-100) cc_final: 0.5301 (t60) outliers start: 25 outliers final: 18 residues processed: 121 average time/residue: 0.1497 time to fit residues: 25.4717 Evaluate side-chains 118 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 394 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 0.0270 chunk 77 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 362 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6670 Z= 0.189 Angle : 0.641 9.632 9062 Z= 0.313 Chirality : 0.043 0.260 1094 Planarity : 0.004 0.050 1088 Dihedral : 4.637 21.660 896 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.71 % Allowed : 22.43 % Favored : 73.86 % 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: -0.19 (0.30), residues: 844 helix: 0.33 (0.21), residues: 654 sheet: None (None), residues: 0 loop : -1.41 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 156 HIS 0.002 0.001 HIS A 52 PHE 0.023 0.001 PHE B 228 TYR 0.013 0.001 TYR B 273 ARG 0.001 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 0.735 Fit side-chains REVERT: A 256 ASN cc_start: 0.7122 (p0) cc_final: 0.6871 (p0) REVERT: A 351 TRP cc_start: 0.5673 (t-100) cc_final: 0.5277 (t60) outliers start: 26 outliers final: 18 residues processed: 116 average time/residue: 0.1635 time to fit residues: 26.9434 Evaluate side-chains 117 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 394 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 362 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6670 Z= 0.244 Angle : 0.681 10.791 9062 Z= 0.332 Chirality : 0.044 0.240 1094 Planarity : 0.004 0.050 1088 Dihedral : 4.759 21.032 896 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.29 % Allowed : 23.71 % Favored : 73.00 % 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: -0.28 (0.30), residues: 844 helix: 0.29 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -1.53 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 156 HIS 0.003 0.001 HIS A 52 PHE 0.020 0.001 PHE B 228 TYR 0.022 0.001 TYR B 273 ARG 0.002 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.787 Fit side-chains REVERT: A 351 TRP cc_start: 0.5739 (t-100) cc_final: 0.5314 (t60) REVERT: B 158 TRP cc_start: 0.5154 (m100) cc_final: 0.4933 (t60) outliers start: 23 outliers final: 19 residues processed: 116 average time/residue: 0.1560 time to fit residues: 25.3788 Evaluate side-chains 120 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 394 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6670 Z= 0.216 Angle : 0.670 10.084 9062 Z= 0.326 Chirality : 0.043 0.230 1094 Planarity : 0.004 0.050 1088 Dihedral : 4.701 21.593 896 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.00 % Allowed : 23.86 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.30), residues: 844 helix: 0.32 (0.21), residues: 656 sheet: None (None), residues: 0 loop : -1.45 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 156 HIS 0.002 0.001 HIS A 52 PHE 0.020 0.001 PHE B 298 TYR 0.020 0.002 TYR B 273 ARG 0.001 0.000 ARG A 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.727 Fit side-chains REVERT: A 351 TRP cc_start: 0.5721 (t-100) cc_final: 0.5296 (t60) outliers start: 21 outliers final: 20 residues processed: 115 average time/residue: 0.1498 time to fit residues: 24.2078 Evaluate side-chains 123 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 394 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 414 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 = 0.4285 r_free = 0.4285 target = 0.195946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.170018 restraints weight = 7407.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.172634 restraints weight = 7404.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174020 restraints weight = 6654.296| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6670 Z= 0.213 Angle : 0.662 9.540 9062 Z= 0.323 Chirality : 0.043 0.225 1094 Planarity : 0.004 0.050 1088 Dihedral : 4.677 21.606 896 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.00 % Allowed : 24.14 % Favored : 72.86 % 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: -0.18 (0.30), residues: 844 helix: 0.34 (0.21), residues: 656 sheet: None (None), residues: 0 loop : -1.45 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 156 HIS 0.002 0.001 HIS B 88 PHE 0.020 0.001 PHE B 298 TYR 0.019 0.001 TYR B 273 ARG 0.001 0.000 ARG A 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1458.78 seconds wall clock time: 27 minutes 34.40 seconds (1654.40 seconds total)