Starting phenix.real_space_refine on Fri Oct 10 11:46:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtx_36655/10_2025/8jtx_36655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtx_36655/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jtx_36655/10_2025/8jtx_36655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtx_36655/10_2025/8jtx_36655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jtx_36655/10_2025/8jtx_36655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtx_36655/10_2025/8jtx_36655.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1} 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, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 1.28, per 1000 atoms: 0.30 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: 0.33 Conformation dependent library (CDL) restraints added in 151.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.14 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: 0.73 Time building geometry restraints manager: 0.46 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: 1.220 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.190 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.290 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG A 486 TYR 0.019 0.001 TYR A 91 PHE 0.010 0.001 PHE A 355 TRP 0.021 0.001 TRP A 217 HIS 0.001 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4360) covalent geometry : angle 0.70073 ( 5949) SS BOND : bond 0.00108 ( 4) SS BOND : angle 0.56184 ( 8) hydrogen bonds : bond 0.18225 ( 181) hydrogen bonds : angle 6.84280 ( 537) *********************** 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 : 0.152 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: 0.1019 time to fit residues: 7.5868 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 : 0.161 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.0770 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.209945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.154929 restraints weight = 4607.187| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.55 r_work: 0.3498 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.0936 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= 0.107 Angle : 0.535 11.486 5957 Z= 0.268 Chirality : 0.039 0.136 687 Planarity : 0.004 0.063 746 Dihedral : 4.924 58.512 612 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.08 % Allowed : 24.77 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.36), residues: 560 helix: 0.47 (0.33), residues: 281 sheet: -0.65 (0.69), residues: 57 loop : -1.66 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 342 TYR 0.012 0.001 TYR A 91 PHE 0.008 0.001 PHE A 244 TRP 0.012 0.001 TRP A 217 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 4360) covalent geometry : angle 0.53457 ( 5949) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.93184 ( 8) hydrogen bonds : bond 0.04352 ( 181) hydrogen bonds : angle 4.74940 ( 537) *********************** 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: 9 poor density : 56 time to evaluate : 0.121 Fit side-chains REVERT: A 240 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.6954 (m-80) REVERT: A 277 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.6046 (tp) REVERT: B 81 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6876 (tp40) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 0.0826 time to fit residues: 6.3819 Evaluate side-chains 61 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 A residue 385 VAL 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 25 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.204395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156362 restraints weight = 4547.383| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.97 r_work: 0.3433 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4364 Z= 0.125 Angle : 0.539 11.168 5957 Z= 0.274 Chirality : 0.040 0.144 687 Planarity : 0.004 0.067 746 Dihedral : 4.839 57.705 612 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.24 % Allowed : 23.61 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.36), residues: 560 helix: 0.57 (0.33), residues: 282 sheet: -0.50 (0.70), residues: 57 loop : -1.67 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 342 TYR 0.010 0.001 TYR A 352 PHE 0.009 0.001 PHE A 355 TRP 0.020 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4360) covalent geometry : angle 0.53806 ( 5949) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.90511 ( 8) hydrogen bonds : bond 0.04988 ( 181) hydrogen bonds : angle 4.58387 ( 537) *********************** 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 70 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.161 Fit side-chains REVERT: A 240 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7107 (m-80) REVERT: A 277 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5932 (tp) REVERT: B 81 GLN cc_start: 0.7341 (mm-40) cc_final: 0.7098 (tp40) outliers start: 14 outliers final: 7 residues processed: 65 average time/residue: 0.0799 time to fit residues: 6.4618 Evaluate side-chains 65 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 356 THR 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 14 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 492 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.198815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150250 restraints weight = 4555.372| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.92 r_work: 0.3411 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4364 Z= 0.158 Angle : 0.576 10.496 5957 Z= 0.298 Chirality : 0.041 0.154 687 Planarity : 0.004 0.070 746 Dihedral : 5.002 55.576 612 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.35), residues: 560 helix: 0.22 (0.32), residues: 292 sheet: -0.40 (0.73), residues: 57 loop : -1.96 (0.37), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.010 0.001 TYR A 352 PHE 0.009 0.001 PHE A 355 TRP 0.022 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4360) covalent geometry : angle 0.57503 ( 5949) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.95302 ( 8) hydrogen bonds : bond 0.05681 ( 181) hydrogen bonds : angle 4.70102 ( 537) *********************** 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 77 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.154 Fit side-chains REVERT: A 277 LEU cc_start: 0.6145 (OUTLIER) cc_final: 0.5793 (tp) outliers start: 17 outliers final: 12 residues processed: 68 average time/residue: 0.0840 time to fit residues: 7.1352 Evaluate side-chains 71 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 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 82 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 1 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.203316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153857 restraints weight = 4559.106| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.12 r_work: 0.3433 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1652 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= 0.121 Angle : 0.541 11.228 5957 Z= 0.273 Chirality : 0.040 0.147 687 Planarity : 0.004 0.071 746 Dihedral : 4.832 54.397 612 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.36), residues: 560 helix: 0.39 (0.33), residues: 290 sheet: -0.37 (0.72), residues: 57 loop : -1.73 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.010 0.001 TYR A 352 PHE 0.010 0.001 PHE A 355 TRP 0.022 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4360) covalent geometry : angle 0.54064 ( 5949) SS BOND : bond 0.00138 ( 4) SS BOND : angle 0.76786 ( 8) hydrogen bonds : bond 0.04733 ( 181) hydrogen bonds : angle 4.45406 ( 537) *********************** 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 75 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.109 Fit side-chains REVERT: A 240 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: A 277 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5822 (tp) outliers start: 17 outliers final: 12 residues processed: 69 average time/residue: 0.0799 time to fit residues: 6.8720 Evaluate side-chains 70 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 169 PHE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 THR 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 B residue 18 LEU Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 82 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.0770 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.200916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158133 restraints weight = 4683.187| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.90 r_work: 0.3420 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4364 Z= 0.128 Angle : 0.561 11.051 5957 Z= 0.284 Chirality : 0.040 0.151 687 Planarity : 0.004 0.070 746 Dihedral : 4.819 53.661 612 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.86 % Allowed : 23.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.36), residues: 560 helix: 0.45 (0.33), residues: 289 sheet: -0.33 (0.73), residues: 57 loop : -1.72 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.010 0.001 TYR A 352 PHE 0.010 0.001 PHE A 355 TRP 0.027 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4360) covalent geometry : angle 0.55163 ( 5949) SS BOND : bond 0.00153 ( 4) SS BOND : angle 2.89836 ( 8) hydrogen bonds : bond 0.04864 ( 181) hydrogen bonds : angle 4.44195 ( 537) *********************** 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 79 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.152 Fit side-chains REVERT: A 240 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: A 277 LEU cc_start: 0.5964 (OUTLIER) cc_final: 0.5746 (tp) REVERT: A 519 VAL cc_start: 0.4222 (OUTLIER) cc_final: 0.3715 (t) outliers start: 21 outliers final: 15 residues processed: 72 average time/residue: 0.0803 time to fit residues: 7.2318 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 : 0.151 ------------------------------------------------------------------------------- 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 169 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 THR 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 69 ILE Chi-restraints excluded: chain B residue 82 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 26 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 0.0670 chunk 36 optimal weight: 0.7980 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.206871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.161411 restraints weight = 4597.182| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.79 r_work: 0.3524 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4364 Z= 0.098 Angle : 0.520 11.705 5957 Z= 0.260 Chirality : 0.038 0.139 687 Planarity : 0.004 0.069 746 Dihedral : 4.560 52.688 612 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.94 % Allowed : 25.46 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.36), residues: 560 helix: 0.73 (0.33), residues: 289 sheet: -0.31 (0.72), residues: 57 loop : -1.63 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 90 TYR 0.008 0.001 TYR A 352 PHE 0.008 0.001 PHE A 355 TRP 0.028 0.001 TRP A 217 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 4360) covalent geometry : angle 0.51419 ( 5949) SS BOND : bond 0.00079 ( 4) SS BOND : angle 2.18863 ( 8) hydrogen bonds : bond 0.03674 ( 181) hydrogen bonds : angle 4.12339 ( 537) *********************** 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 76 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.146 Fit side-chains REVERT: A 84 PHE cc_start: 0.4576 (OUTLIER) cc_final: 0.4296 (m-80) REVERT: A 240 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: A 519 VAL cc_start: 0.4335 (OUTLIER) cc_final: 0.3752 (t) outliers start: 17 outliers final: 9 residues processed: 71 average time/residue: 0.0798 time to fit residues: 7.0950 Evaluate side-chains 71 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS 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 394 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 18 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.0030 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 0.0000 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.207198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.159279 restraints weight = 4563.245| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.97 r_work: 0.3486 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1900 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= 0.098 Angle : 0.511 11.164 5957 Z= 0.254 Chirality : 0.038 0.142 687 Planarity : 0.004 0.069 746 Dihedral : 4.449 51.897 612 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.94 % Allowed : 25.23 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.37), residues: 560 helix: 0.82 (0.33), residues: 290 sheet: -0.29 (0.72), residues: 57 loop : -1.61 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.010 0.001 TYR A 361 PHE 0.009 0.001 PHE A 355 TRP 0.031 0.001 TRP A 217 HIS 0.001 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 4360) covalent geometry : angle 0.50683 ( 5949) SS BOND : bond 0.00060 ( 4) SS BOND : angle 1.77358 ( 8) hydrogen bonds : bond 0.03720 ( 181) hydrogen bonds : angle 4.02088 ( 537) *********************** 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: 17 poor density : 61 time to evaluate : 0.158 Fit side-chains REVERT: A 84 PHE cc_start: 0.4483 (OUTLIER) cc_final: 0.4224 (m-80) REVERT: A 240 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6920 (m-80) REVERT: A 519 VAL cc_start: 0.4221 (OUTLIER) cc_final: 0.3694 (t) outliers start: 17 outliers final: 10 residues processed: 74 average time/residue: 0.0836 time to fit residues: 7.7243 Evaluate side-chains 72 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS 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 340 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 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.0170 chunk 51 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.209877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162300 restraints weight = 4572.400| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.95 r_work: 0.3509 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1955 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= 0.096 Angle : 0.503 11.119 5957 Z= 0.251 Chirality : 0.038 0.141 687 Planarity : 0.004 0.068 746 Dihedral : 4.363 51.323 612 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.70 % Allowed : 25.46 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.37), residues: 560 helix: 0.90 (0.33), residues: 290 sheet: -0.21 (0.73), residues: 57 loop : -1.60 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.008 0.001 TYR A 352 PHE 0.008 0.001 PHE A 355 TRP 0.035 0.001 TRP A 217 HIS 0.001 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 4360) covalent geometry : angle 0.50021 ( 5949) SS BOND : bond 0.00070 ( 4) SS BOND : angle 1.57254 ( 8) hydrogen bonds : bond 0.03530 ( 181) hydrogen bonds : angle 3.95857 ( 537) *********************** 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 76 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.152 Fit side-chains REVERT: A 84 PHE cc_start: 0.4648 (OUTLIER) cc_final: 0.4400 (m-80) REVERT: A 240 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.6851 (m-80) REVERT: A 519 VAL cc_start: 0.4293 (OUTLIER) cc_final: 0.3720 (t) outliers start: 16 outliers final: 12 residues processed: 71 average time/residue: 0.0864 time to fit residues: 7.5135 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 : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 91 TYR 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 273 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 386 GLU 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 62 SER Chi-restraints excluded: chain B residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.200821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.158259 restraints weight = 4593.808| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.91 r_work: 0.3419 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4364 Z= 0.150 Angle : 0.561 9.925 5957 Z= 0.287 Chirality : 0.041 0.156 687 Planarity : 0.004 0.067 746 Dihedral : 4.619 51.076 612 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.94 % Allowed : 25.93 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.36), residues: 560 helix: 0.69 (0.33), residues: 287 sheet: -0.24 (0.73), residues: 57 loop : -1.72 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.011 0.001 TYR A 352 PHE 0.009 0.001 PHE A 355 TRP 0.036 0.002 TRP A 217 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4360) covalent geometry : angle 0.55809 ( 5949) SS BOND : bond 0.00138 ( 4) SS BOND : angle 1.58001 ( 8) hydrogen bonds : bond 0.05196 ( 181) hydrogen bonds : angle 4.34573 ( 537) ********************** 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 79 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.156 Fit side-chains REVERT: A 519 VAL cc_start: 0.4400 (OUTLIER) cc_final: 0.3819 (t) outliers start: 17 outliers final: 13 residues processed: 73 average time/residue: 0.0781 time to fit residues: 7.0481 Evaluate side-chains 75 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 TYR 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 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 386 GLU 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 62 SER Chi-restraints excluded: chain B residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.206019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.158870 restraints weight = 4507.349| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.96 r_work: 0.3492 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4364 Z= 0.117 Angle : 0.530 10.594 5957 Z= 0.269 Chirality : 0.040 0.148 687 Planarity : 0.004 0.067 746 Dihedral : 4.565 50.920 612 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.40 % Allowed : 25.23 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.36), residues: 560 helix: 0.67 (0.33), residues: 290 sheet: -0.17 (0.73), residues: 57 loop : -1.65 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.009 0.001 TYR A 352 PHE 0.009 0.001 PHE A 355 TRP 0.033 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4360) covalent geometry : angle 0.52774 ( 5949) SS BOND : bond 0.00114 ( 4) SS BOND : angle 1.43849 ( 8) hydrogen bonds : bond 0.04402 ( 181) hydrogen bonds : angle 4.21502 ( 537) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1374.35 seconds wall clock time: 24 minutes 6.37 seconds (1446.37 seconds total)