Starting phenix.real_space_refine on Tue Jan 14 10:38:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jda_36076/01_2025/8jda_36076_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jda_36076/01_2025/8jda_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/cci-nas-00/data/ceres_data/8jda_36076/01_2025/8jda_36076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jda_36076/01_2025/8jda_36076.map" model { file = "/net/cci-nas-00/data/ceres_data/8jda_36076/01_2025/8jda_36076_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jda_36076/01_2025/8jda_36076_neut.cif" } 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. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 4.44, per 1000 atoms: 0.68 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 - 3.00 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: 1.69 Conformation dependent library (CDL) restraints added in 882.2 milliseconds 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: 0.71 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: 1.82 Time building geometry restraints manager: 1.95 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: 0.00 - 1.71: 8703 1.71 - 3.42: 291 3.42 - 5.12: 45 5.12 - 6.83: 17 6.83 - 8.54: 6 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 3.040 nonbonded pdb=" O LYS A 309 " pdb=" ND1 HIS A 313 " model vdw 2.203 3.120 nonbonded pdb=" OD1 ASP A 35 " pdb=" OH TYR B 274 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR B 77 " pdb=" ND2 ASN B 94 " model vdw 2.211 3.120 nonbonded pdb=" O GLY A 47 " pdb=" OG SER A 50 " model vdw 2.224 3.040 ... (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 Time spend for trying shortcut: 0.03 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: 1.250 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.570 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.864 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.1468 time to fit residues: 24.9107 Evaluate side-chains 99 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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: 0.7980 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN B 362 GLN ** B 414 ASN ** 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 = 0.4536 r_free = 0.4536 target = 0.214997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.198240 restraints weight = 7374.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.201677 restraints weight = 9079.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.201058 restraints weight = 5618.979| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6670 Z= 0.231 Angle : 0.680 8.729 9062 Z= 0.345 Chirality : 0.042 0.195 1094 Planarity : 0.004 0.053 1088 Dihedral : 5.124 28.510 899 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % 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: -0.91 (0.29), residues: 844 helix: -0.18 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -1.59 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 158 HIS 0.003 0.001 HIS B 88 PHE 0.027 0.002 PHE B 298 TYR 0.012 0.001 TYR B 273 ARG 0.002 0.000 ARG B 397 *********************** 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 133 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.694 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 124 average time/residue: 0.1377 time to fit residues: 24.6365 Evaluate side-chains 109 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 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 35 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 chunk 55 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN B 218 GLN B 362 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.215555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.198487 restraints weight = 7429.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.201620 restraints weight = 9255.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.201377 restraints weight = 6246.447| |-----------------------------------------------------------------------------| r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1727 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= 0.200 Angle : 0.633 8.448 9062 Z= 0.320 Chirality : 0.040 0.193 1094 Planarity : 0.004 0.047 1088 Dihedral : 4.827 23.470 896 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.43 % Allowed : 14.29 % Favored : 83.29 % 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: -0.68 (0.29), residues: 844 helix: -0.02 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.55 (0.43), residues: 196 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 0.027 0.001 PHE B 298 TYR 0.015 0.001 TYR A 273 ARG 0.002 0.000 ARG B 300 *********************** 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 137 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 256 ASN cc_start: 0.7198 (p0) cc_final: 0.6921 (p0) outliers start: 17 outliers final: 11 residues processed: 126 average time/residue: 0.1484 time to fit residues: 27.2948 Evaluate side-chains 114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 42 MET 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 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 17 optimal weight: 0.4980 chunk 23 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.215006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.197528 restraints weight = 7546.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.201084 restraints weight = 9613.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.200590 restraints weight = 5908.741| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2040 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= 0.198 Angle : 0.628 8.636 9062 Z= 0.315 Chirality : 0.040 0.200 1094 Planarity : 0.004 0.047 1088 Dihedral : 4.708 21.370 896 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.43 % Allowed : 18.00 % Favored : 79.57 % 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: -0.52 (0.30), residues: 844 helix: 0.09 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.46 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 156 HIS 0.003 0.001 HIS B 88 PHE 0.021 0.001 PHE B 298 TYR 0.011 0.001 TYR B 273 ARG 0.002 0.000 ARG B 300 *********************** 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 134 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.677 Fit side-chains REVERT: B 42 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7509 (ttp) outliers start: 17 outliers final: 8 residues processed: 123 average time/residue: 0.1507 time to fit residues: 26.8354 Evaluate side-chains 114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 318 VAL 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 131 LEU Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS B 218 GLN B 362 GLN B 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.214686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.195750 restraints weight = 7459.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.196254 restraints weight = 9165.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.197112 restraints weight = 7891.990| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6670 Z= 0.199 Angle : 0.635 8.574 9062 Z= 0.316 Chirality : 0.041 0.213 1094 Planarity : 0.004 0.050 1088 Dihedral : 4.666 20.411 896 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.00 % Allowed : 18.00 % Favored : 79.00 % 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: 0.11 (0.21), residues: 654 sheet: None (None), residues: 0 loop : -1.45 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 156 HIS 0.010 0.001 HIS A 313 PHE 0.015 0.001 PHE B 298 TYR 0.012 0.001 TYR B 273 ARG 0.001 0.000 ARG B 397 *********************** 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 132 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.748 Fit side-chains REVERT: B 42 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7526 (ttp) outliers start: 21 outliers final: 12 residues processed: 116 average time/residue: 0.1665 time to fit residues: 27.9768 Evaluate side-chains 115 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR 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 131 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 336 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 47 optimal weight: 0.0020 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.215798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.197108 restraints weight = 7365.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.197265 restraints weight = 9047.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.198316 restraints weight = 8048.791| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6670 Z= 0.184 Angle : 0.624 8.326 9062 Z= 0.311 Chirality : 0.041 0.218 1094 Planarity : 0.004 0.051 1088 Dihedral : 4.587 21.360 896 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.29 % Allowed : 19.71 % 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: -0.32 (0.30), residues: 844 helix: 0.20 (0.21), residues: 658 sheet: None (None), residues: 0 loop : -1.33 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 156 HIS 0.002 0.001 HIS B 88 PHE 0.025 0.001 PHE A 434 TYR 0.014 0.001 TYR B 273 ARG 0.001 0.000 ARG B 365 *********************** 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 136 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.719 Fit side-chains REVERT: A 351 TRP cc_start: 0.5770 (t-100) cc_final: 0.5391 (t60) REVERT: B 42 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7570 (ttp) outliers start: 23 outliers final: 13 residues processed: 124 average time/residue: 0.1484 time to fit residues: 26.6128 Evaluate side-chains 116 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR 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 131 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 336 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.0077 > 50: distance: 2 - 21: 32.890 distance: 6 - 30: 35.243 distance: 10 - 37: 37.588 distance: 16 - 21: 30.909 distance: 17 - 44: 17.631 distance: 21 - 22: 53.416 distance: 22 - 23: 41.560 distance: 22 - 25: 54.347 distance: 23 - 24: 18.850 distance: 23 - 30: 41.938 distance: 25 - 26: 45.178 distance: 26 - 27: 10.983 distance: 27 - 28: 19.157 distance: 28 - 29: 20.984 distance: 30 - 31: 39.461 distance: 31 - 32: 48.279 distance: 31 - 34: 13.922 distance: 32 - 33: 27.237 distance: 32 - 37: 48.539 distance: 34 - 35: 19.633 distance: 34 - 36: 43.554 distance: 37 - 38: 56.935 distance: 38 - 39: 4.147 distance: 38 - 41: 65.784 distance: 39 - 40: 23.880 distance: 39 - 44: 44.579 distance: 41 - 43: 20.637 distance: 44 - 45: 27.798 distance: 45 - 46: 33.055 distance: 45 - 48: 33.136 distance: 46 - 47: 40.611 distance: 46 - 55: 33.584 distance: 48 - 49: 20.002 distance: 49 - 50: 19.374 distance: 49 - 51: 10.056 distance: 50 - 52: 23.626 distance: 51 - 53: 7.463 distance: 52 - 54: 42.218 distance: 53 - 54: 46.830 distance: 55 - 56: 58.813 distance: 55 - 61: 49.486 distance: 56 - 57: 48.857 distance: 56 - 59: 42.081 distance: 57 - 58: 12.902 distance: 57 - 62: 48.788 distance: 59 - 60: 17.986 distance: 60 - 61: 57.086 distance: 62 - 63: 56.740 distance: 63 - 64: 7.524 distance: 63 - 66: 45.442 distance: 64 - 65: 18.252 distance: 64 - 74: 32.773 distance: 66 - 67: 29.810 distance: 67 - 68: 32.758 distance: 67 - 69: 29.949 distance: 68 - 70: 17.062 distance: 69 - 71: 27.374 distance: 70 - 72: 20.002 distance: 71 - 72: 17.091 distance: 72 - 73: 5.783 distance: 74 - 75: 9.225 distance: 75 - 76: 22.184 distance: 75 - 78: 31.237 distance: 76 - 77: 42.334 distance: 76 - 83: 20.835 distance: 78 - 79: 12.391 distance: 79 - 80: 14.356 distance: 80 - 81: 14.524 distance: 80 - 82: 25.796 distance: 83 - 84: 32.438 distance: 84 - 85: 28.784 distance: 84 - 87: 11.888 distance: 85 - 86: 26.089 distance: 85 - 97: 58.461 distance: 87 - 88: 25.715 distance: 88 - 89: 20.282 distance: 88 - 90: 15.039 distance: 89 - 91: 12.251 distance: 90 - 92: 7.681 distance: 90 - 93: 4.072 distance: 91 - 92: 3.890 distance: 92 - 94: 4.817 distance: 93 - 95: 9.154 distance: 94 - 96: 5.514 distance: 95 - 96: 5.093 distance: 97 - 98: 32.922 distance: 98 - 99: 30.183 distance: 98 - 101: 23.084 distance: 99 - 100: 5.351 distance: 99 - 105: 20.070 distance: 100 - 134: 37.091 distance: 101 - 102: 12.630 distance: 102 - 103: 17.663 distance: 102 - 104: 29.511 distance: 105 - 106: 39.931 distance: 106 - 107: 31.069 distance: 106 - 109: 40.465 distance: 107 - 108: 11.600 distance: 107 - 119: 34.625 distance: 108 - 140: 29.442 distance: 109 - 110: 33.572 distance: 110 - 111: 20.559 distance: 110 - 112: 23.595 distance: 112 - 114: 7.010 distance: 112 - 115: 12.392 distance: 113 - 114: 13.186 distance: 114 - 116: 20.527 distance: 115 - 117: 15.892 distance: 116 - 118: 12.058 distance: 117 - 118: 19.296