Starting phenix.real_space_refine on Wed Jul 23 20:26:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtx_36655/07_2025/8jtx_36655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtx_36655/07_2025/8jtx_36655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jtx_36655/07_2025/8jtx_36655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtx_36655/07_2025/8jtx_36655.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtx_36655/07_2025/8jtx_36655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtx_36655/07_2025/8jtx_36655.cif" } resolution = 3.28 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= -0.004 sd= 0.174 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 34 5.16 5 C 2777 2.51 5 N 699 2.21 5 O 743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4253 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3360 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 3.20, per 1000 atoms: 0.75 Number of scatterers: 4253 At special positions: 0 Unit cell: (60.2, 79.12, 126.42, 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 34 16.00 O 743 8.00 N 699 7.00 C 2777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 919.0 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 3 sheets defined 61.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 removed outlier: 4.288A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 37 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 63 removed outlier: 3.721A pdb=" N LEU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.902A pdb=" N TYR A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 73' Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 105 through 110 removed outlier: 4.117A pdb=" N LEU A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 110' Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 182 removed outlier: 4.208A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG A 172 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N LYS A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.764A pdb=" N GLY A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.713A pdb=" N MET A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 231 through 258 removed outlier: 4.012A pdb=" N ILE A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 277 removed outlier: 3.749A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.884A pdb=" N PHE A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 369 removed outlier: 3.742A pdb=" N PHE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE A 355 " --> pdb=" O MET A 351 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 366 " --> pdb=" O GLN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.606A pdb=" N ASP A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 4.391A pdb=" N ALA A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.543A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 457 removed outlier: 3.707A pdb=" N LEU A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 447 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 487 removed outlier: 3.756A pdb=" N ILE A 479 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.877A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'B' and resid 26 through 32 removed outlier: 4.151A pdb=" N TYR B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.540A pdb=" N GLN B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 18 " --> pdb=" O MET B 82 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B 82 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 80 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 70 " --> pdb=" O TYR B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.836A pdb=" N ASN B 58 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 50 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 51 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 96 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 116 " --> pdb=" O TYR B 93 " (cutoff:3.500A) 181 hydrogen bonds defined for protein. 537 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: 1.01 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 658 1.32 - 1.44: 1235 1.44 - 1.57: 2416 1.57 - 1.69: 0 1.69 - 1.82: 51 Bond restraints: 4360 Sorted by residual: bond pdb=" CA TYR A 240 " pdb=" CB TYR A 240 " ideal model delta sigma weight residual 1.529 1.473 0.057 1.78e-02 3.16e+03 1.01e+01 bond pdb=" C TYR A 240 " pdb=" O TYR A 240 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.29e-02 6.01e+03 9.59e+00 bond pdb=" C SER A 424 " pdb=" N PRO A 425 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.04e+00 bond pdb=" C TYR A 240 " pdb=" N GLN A 241 " ideal model delta sigma weight residual 1.333 1.313 0.020 1.45e-02 4.76e+03 1.92e+00 bond pdb=" C MET A 239 " pdb=" N TYR A 240 " ideal model delta sigma weight residual 1.334 1.349 -0.015 1.38e-02 5.25e+03 1.19e+00 ... (remaining 4355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 5816 1.99 - 3.98: 112 3.98 - 5.97: 13 5.97 - 7.96: 6 7.96 - 9.96: 2 Bond angle restraints: 5949 Sorted by residual: angle pdb=" N ILE B 110 " pdb=" CA ILE B 110 " pdb=" C ILE B 110 " ideal model delta sigma weight residual 113.20 109.38 3.82 9.60e-01 1.09e+00 1.58e+01 angle pdb=" CA TYR A 240 " pdb=" C TYR A 240 " pdb=" N GLN A 241 " ideal model delta sigma weight residual 118.43 123.55 -5.12 1.33e+00 5.65e-01 1.48e+01 angle pdb=" N VAL A 37 " pdb=" CA VAL A 37 " pdb=" C VAL A 37 " ideal model delta sigma weight residual 113.53 109.87 3.66 9.80e-01 1.04e+00 1.39e+01 angle pdb=" C TYR A 240 " pdb=" N GLN A 241 " pdb=" CA GLN A 241 " ideal model delta sigma weight residual 121.64 129.53 -7.89 2.13e+00 2.20e-01 1.37e+01 angle pdb=" C GLY B 113 " pdb=" N GLN B 114 " pdb=" CA GLN B 114 " ideal model delta sigma weight residual 121.54 128.30 -6.76 1.91e+00 2.74e-01 1.25e+01 ... (remaining 5944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 2175 17.55 - 35.10: 264 35.10 - 52.65: 66 52.65 - 70.20: 12 70.20 - 87.75: 1 Dihedral angle restraints: 2518 sinusoidal: 908 harmonic: 1610 Sorted by residual: dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 159.06 -66.06 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 102 " pdb=" CB CYS A 102 " ideal model delta sinusoidal sigma weight residual -86.00 -145.88 59.88 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -44.62 -41.38 1 1.00e+01 1.00e-02 2.40e+01 ... (remaining 2515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 382 0.026 - 0.053: 192 0.053 - 0.079: 69 0.079 - 0.105: 29 0.105 - 0.131: 15 Chirality restraints: 687 Sorted by residual: chirality pdb=" CA THR A 480 " pdb=" N THR A 480 " pdb=" C THR A 480 " pdb=" CB THR A 480 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA PRO A 425 " pdb=" N PRO A 425 " pdb=" C PRO A 425 " pdb=" CB PRO A 425 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA THR A 111 " pdb=" N THR A 111 " pdb=" C THR A 111 " pdb=" CB THR A 111 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 684 not shown) Planarity restraints: 746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 240 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C TYR A 240 " -0.057 2.00e-02 2.50e+03 pdb=" O TYR A 240 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN A 241 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 271 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 74 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 75 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.023 5.00e-02 4.00e+02 ... (remaining 743 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1245 2.82 - 3.34: 3700 3.34 - 3.86: 6236 3.86 - 4.38: 6683 4.38 - 4.90: 12377 Nonbonded interactions: 30241 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O TRP B 106 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR A 127 " pdb=" OD1 ASN A 139 " model vdw 2.318 3.040 nonbonded pdb=" O PRO A 405 " pdb=" OG SER A 409 " model vdw 2.322 3.040 nonbonded pdb=" O MET A 368 " pdb=" OG SER A 372 " model vdw 2.360 3.040 nonbonded pdb=" OG1 THR A 182 " pdb=" OD1 ASN A 216 " model vdw 2.373 3.040 ... (remaining 30236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.230 Find NCS groups from input model: 0.040 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4364 Z= 0.167 Angle : 0.701 9.956 5957 Z= 0.391 Chirality : 0.040 0.131 687 Planarity : 0.004 0.047 746 Dihedral : 15.904 87.752 1482 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.46 % Allowed : 22.92 % Favored : 76.62 % 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: -1.20 (0.35), residues: 560 helix: 0.03 (0.33), residues: 280 sheet: -0.64 (0.78), residues: 53 loop : -1.84 (0.35), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 217 HIS 0.001 0.001 HIS A 48 PHE 0.010 0.001 PHE A 355 TYR 0.019 0.001 TYR A 91 ARG 0.006 0.000 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.18225 ( 181) hydrogen bonds : angle 6.84280 ( 537) SS BOND : bond 0.00108 ( 4) SS BOND : angle 0.56184 ( 8) covalent geometry : bond 0.00296 ( 4360) covalent geometry : angle 0.70073 ( 5949) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.462 Fit side-chains REVERT: A 240 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6797 (m-80) outliers start: 2 outliers final: 0 residues processed: 62 average time/residue: 0.2096 time to fit residues: 15.7907 Evaluate side-chains 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.0050 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.0170 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 overall best weight: 0.3432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.210660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163248 restraints weight = 4540.010| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.92 r_work: 0.3532 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4364 Z= 0.104 Angle : 0.529 11.277 5957 Z= 0.264 Chirality : 0.038 0.131 687 Planarity : 0.004 0.064 746 Dihedral : 4.920 58.704 612 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.62 % Allowed : 25.00 % Favored : 73.38 % 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 (0.36), residues: 560 helix: 0.51 (0.33), residues: 281 sheet: -0.56 (0.70), residues: 57 loop : -1.64 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 217 HIS 0.004 0.001 HIS A 48 PHE 0.008 0.001 PHE A 244 TYR 0.012 0.001 TYR A 91 ARG 0.002 0.000 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 181) hydrogen bonds : angle 4.79073 ( 537) SS BOND : bond 0.00213 ( 4) SS BOND : angle 0.93222 ( 8) covalent geometry : bond 0.00206 ( 4360) covalent geometry : angle 0.52817 ( 5949) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.510 Fit side-chains REVERT: A 240 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.7011 (m-80) REVERT: A 277 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.6084 (tp) REVERT: B 81 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6937 (tp40) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 0.2351 time to fit residues: 19.1105 Evaluate side-chains 62 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 81 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.2980 chunk 13 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 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.204332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158732 restraints weight = 4470.209| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.78 r_work: 0.3485 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 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 0.034 4364 Z= 0.116 Angle : 0.528 11.360 5957 Z= 0.267 Chirality : 0.039 0.143 687 Planarity : 0.004 0.067 746 Dihedral : 4.794 58.103 612 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.78 % Allowed : 23.61 % Favored : 73.61 % 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: -0.53 (0.36), residues: 560 helix: 0.65 (0.33), residues: 283 sheet: -0.36 (0.72), residues: 57 loop : -1.65 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.010 0.001 TYR A 352 ARG 0.004 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.04678 ( 181) hydrogen bonds : angle 4.52527 ( 537) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.86464 ( 8) covalent geometry : bond 0.00255 ( 4360) covalent geometry : angle 0.52778 ( 5949) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.413 Fit side-chains REVERT: A 240 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: A 277 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5899 (tp) REVERT: B 81 GLN cc_start: 0.7283 (mm-40) cc_final: 0.7026 (tp40) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 0.2047 time to fit residues: 16.8060 Evaluate side-chains 62 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 2 optimal weight: 0.8980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.203851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150576 restraints weight = 4565.950| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.26 r_work: 0.3388 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4364 Z= 0.139 Angle : 0.552 10.775 5957 Z= 0.283 Chirality : 0.041 0.148 687 Planarity : 0.004 0.069 746 Dihedral : 4.880 55.843 612 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.17 % Allowed : 23.15 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.36), residues: 560 helix: 0.36 (0.32), residues: 294 sheet: -0.35 (0.73), residues: 57 loop : -1.90 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.010 0.001 TYR A 352 ARG 0.003 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 181) hydrogen bonds : angle 4.56825 ( 537) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.88733 ( 8) covalent geometry : bond 0.00327 ( 4360) covalent geometry : angle 0.55171 ( 5949) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.428 Fit side-chains REVERT: A 240 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: A 277 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5798 (tp) REVERT: B 81 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.7000 (tp40) outliers start: 18 outliers final: 11 residues processed: 68 average time/residue: 0.1738 time to fit residues: 14.8322 Evaluate side-chains 71 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 81 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.202536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.156570 restraints weight = 4637.589| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.89 r_work: 0.3434 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4364 Z= 0.136 Angle : 0.554 10.947 5957 Z= 0.281 Chirality : 0.040 0.151 687 Planarity : 0.004 0.070 746 Dihedral : 4.845 54.744 612 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.24 % Allowed : 25.23 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.36), residues: 560 helix: 0.41 (0.33), residues: 289 sheet: -0.34 (0.73), residues: 57 loop : -1.76 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.05076 ( 181) hydrogen bonds : angle 4.51271 ( 537) SS BOND : bond 0.00158 ( 4) SS BOND : angle 0.84826 ( 8) covalent geometry : bond 0.00319 ( 4360) covalent geometry : angle 0.55303 ( 5949) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.401 Fit side-chains REVERT: A 240 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: A 277 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5774 (tp) outliers start: 14 outliers final: 7 residues processed: 65 average time/residue: 0.1745 time to fit residues: 14.2096 Evaluate side-chains 66 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 7 optimal weight: 0.0470 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.208624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159373 restraints weight = 4522.949| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.96 r_work: 0.3485 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4364 Z= 0.099 Angle : 0.510 11.717 5957 Z= 0.254 Chirality : 0.039 0.140 687 Planarity : 0.004 0.069 746 Dihedral : 4.584 53.696 612 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.94 % Allowed : 24.54 % Favored : 71.53 % 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: -0.35 (0.36), residues: 560 helix: 0.80 (0.34), residues: 283 sheet: -0.30 (0.72), residues: 57 loop : -1.56 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 217 HIS 0.001 0.001 HIS A 48 PHE 0.008 0.001 PHE A 355 TYR 0.008 0.001 TYR A 352 ARG 0.002 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 181) hydrogen bonds : angle 4.13756 ( 537) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.65855 ( 8) covalent geometry : bond 0.00205 ( 4360) covalent geometry : angle 0.50986 ( 5949) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.462 Fit side-chains REVERT: A 240 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.6834 (m-80) REVERT: A 519 VAL cc_start: 0.4139 (OUTLIER) cc_final: 0.3622 (t) REVERT: B 81 GLN cc_start: 0.7544 (tp40) cc_final: 0.7187 (mm-40) outliers start: 17 outliers final: 10 residues processed: 72 average time/residue: 0.1843 time to fit residues: 16.7041 Evaluate side-chains 72 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.0170 chunk 0 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.201469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152508 restraints weight = 4563.068| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.21 r_work: 0.3402 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4364 Z= 0.131 Angle : 0.565 10.752 5957 Z= 0.285 Chirality : 0.040 0.152 687 Planarity : 0.004 0.069 746 Dihedral : 4.687 52.956 612 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.94 % Allowed : 24.54 % Favored : 71.53 % 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: -0.54 (0.36), residues: 560 helix: 0.64 (0.33), residues: 287 sheet: -0.34 (0.73), residues: 57 loop : -1.71 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.011 0.001 TYR A 361 ARG 0.002 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 181) hydrogen bonds : angle 4.33645 ( 537) SS BOND : bond 0.00246 ( 4) SS BOND : angle 3.21200 ( 8) covalent geometry : bond 0.00306 ( 4360) covalent geometry : angle 0.55316 ( 5949) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.403 Fit side-chains REVERT: A 240 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7056 (m-80) REVERT: A 519 VAL cc_start: 0.4272 (OUTLIER) cc_final: 0.3721 (t) outliers start: 17 outliers final: 13 residues processed: 71 average time/residue: 0.1730 time to fit residues: 15.4696 Evaluate side-chains 74 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.200563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.156305 restraints weight = 4525.887| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.81 r_work: 0.3432 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4364 Z= 0.136 Angle : 0.564 10.708 5957 Z= 0.287 Chirality : 0.041 0.152 687 Planarity : 0.004 0.068 746 Dihedral : 4.769 52.174 612 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.17 % Allowed : 24.31 % Favored : 71.53 % 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: -0.50 (0.36), residues: 560 helix: 0.60 (0.33), residues: 283 sheet: -0.35 (0.73), residues: 57 loop : -1.53 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 217 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.010 0.001 TYR A 361 ARG 0.002 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.05019 ( 181) hydrogen bonds : angle 4.42233 ( 537) SS BOND : bond 0.00148 ( 4) SS BOND : angle 2.36670 ( 8) covalent geometry : bond 0.00321 ( 4360) covalent geometry : angle 0.55807 ( 5949) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.414 Fit side-chains REVERT: A 84 PHE cc_start: 0.4808 (OUTLIER) cc_final: 0.4530 (m-80) REVERT: A 519 VAL cc_start: 0.4367 (OUTLIER) cc_final: 0.3822 (t) outliers start: 18 outliers final: 14 residues processed: 71 average time/residue: 0.1801 time to fit residues: 16.1184 Evaluate side-chains 75 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 38 optimal weight: 7.9990 chunk 9 optimal weight: 0.0570 chunk 1 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.202859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153649 restraints weight = 4599.785| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.43 r_work: 0.3443 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4364 Z= 0.126 Angle : 0.550 10.534 5957 Z= 0.279 Chirality : 0.040 0.152 687 Planarity : 0.004 0.068 746 Dihedral : 4.714 51.706 612 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.94 % Allowed : 25.00 % Favored : 71.06 % 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: -0.45 (0.36), residues: 560 helix: 0.65 (0.33), residues: 283 sheet: -0.38 (0.73), residues: 57 loop : -1.49 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 355 TYR 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 181) hydrogen bonds : angle 4.31810 ( 537) SS BOND : bond 0.00148 ( 4) SS BOND : angle 1.86089 ( 8) covalent geometry : bond 0.00290 ( 4360) covalent geometry : angle 0.54624 ( 5949) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.489 Fit side-chains REVERT: A 84 PHE cc_start: 0.4908 (OUTLIER) cc_final: 0.4695 (m-80) REVERT: A 519 VAL cc_start: 0.4332 (OUTLIER) cc_final: 0.3750 (t) outliers start: 17 outliers final: 14 residues processed: 69 average time/residue: 0.1685 time to fit residues: 14.5538 Evaluate side-chains 73 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 30 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.208072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.159879 restraints weight = 4516.694| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.91 r_work: 0.3477 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4364 Z= 0.100 Angle : 0.520 11.012 5957 Z= 0.260 Chirality : 0.039 0.145 687 Planarity : 0.004 0.069 746 Dihedral : 4.511 50.939 612 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.24 % Allowed : 25.69 % Favored : 71.06 % 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: -0.27 (0.37), residues: 560 helix: 0.80 (0.33), residues: 284 sheet: -0.35 (0.73), residues: 57 loop : -1.41 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 217 HIS 0.001 0.001 HIS A 48 PHE 0.008 0.001 PHE A 355 TYR 0.008 0.001 TYR A 361 ARG 0.002 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 181) hydrogen bonds : angle 4.06626 ( 537) SS BOND : bond 0.00113 ( 4) SS BOND : angle 1.48706 ( 8) covalent geometry : bond 0.00210 ( 4360) covalent geometry : angle 0.51711 ( 5949) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.447 Fit side-chains REVERT: A 240 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.6878 (m-80) REVERT: A 519 VAL cc_start: 0.4311 (OUTLIER) cc_final: 0.3727 (t) outliers start: 14 outliers final: 8 residues processed: 70 average time/residue: 0.1792 time to fit residues: 15.7661 Evaluate side-chains 70 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.206324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159912 restraints weight = 4540.139| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.87 r_work: 0.3468 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4364 Z= 0.103 Angle : 0.516 10.960 5957 Z= 0.258 Chirality : 0.039 0.145 687 Planarity : 0.004 0.069 746 Dihedral : 4.437 50.527 612 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.55 % Allowed : 26.16 % Favored : 71.30 % 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: -0.31 (0.36), residues: 560 helix: 0.78 (0.33), residues: 289 sheet: -0.28 (0.73), residues: 57 loop : -1.53 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 217 HIS 0.002 0.001 HIS A 48 PHE 0.009 0.001 PHE A 355 TYR 0.009 0.001 TYR A 361 ARG 0.002 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 181) hydrogen bonds : angle 4.02078 ( 537) SS BOND : bond 0.00095 ( 4) SS BOND : angle 1.28531 ( 8) covalent geometry : bond 0.00221 ( 4360) covalent geometry : angle 0.51456 ( 5949) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2954.01 seconds wall clock time: 51 minutes 57.32 seconds (3117.32 seconds total)