Starting phenix.real_space_refine on Fri Aug 22 21:30:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozn_17315/08_2025/8ozn_17315.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozn_17315/08_2025/8ozn_17315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ozn_17315/08_2025/8ozn_17315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozn_17315/08_2025/8ozn_17315.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ozn_17315/08_2025/8ozn_17315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozn_17315/08_2025/8ozn_17315.map" } resolution = 3.5 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= 0.000 sd= 0.003 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 30 5.16 5 C 5076 2.51 5 N 1444 2.21 5 O 1480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8030 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "I" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "J" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1331 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "K" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "L" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1331 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 11, 'TRANS': 163} Time building chain proxies: 2.30, per 1000 atoms: 0.29 Number of scatterers: 8030 At special positions: 0 Unit cell: (115.56, 126.36, 93.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1480 8.00 N 1444 7.00 C 5076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 457.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 0 sheets defined 72.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'H' and resid 306 through 315 removed outlier: 3.503A pdb=" N SER H 312 " --> pdb=" O GLN H 308 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 313 " --> pdb=" O HIS H 309 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY H 315 " --> pdb=" O ARG H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 339 Proline residue: H 333 - end of helix Processing helix chain 'H' and resid 343 through 356 removed outlier: 3.501A pdb=" N ARG H 347 " --> pdb=" O THR H 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 369 removed outlier: 3.676A pdb=" N LEU H 369 " --> pdb=" O GLY H 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 384 Processing helix chain 'H' and resid 386 through 389 removed outlier: 3.620A pdb=" N HIS H 389 " --> pdb=" O PHE H 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 386 through 389' Processing helix chain 'H' and resid 390 through 400 removed outlier: 3.546A pdb=" N VAL H 394 " --> pdb=" O GLN H 390 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS H 396 " --> pdb=" O GLY H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 414 Processing helix chain 'H' and resid 418 through 428 removed outlier: 3.651A pdb=" N VAL H 422 " --> pdb=" O ASN H 418 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY H 424 " --> pdb=" O GLN H 420 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY H 428 " --> pdb=" O GLY H 424 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 443 removed outlier: 3.705A pdb=" N VAL H 436 " --> pdb=" O GLY H 432 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR H 437 " --> pdb=" O GLN H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 468 removed outlier: 6.010A pdb=" N ILE H 457 " --> pdb=" O ALA H 453 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN H 458 " --> pdb=" O GLU H 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU H 465 " --> pdb=" O ASN H 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 314 removed outlier: 3.724A pdb=" N SER I 312 " --> pdb=" O GLN I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 322 No H-bonds generated for 'chain 'I' and resid 320 through 322' Processing helix chain 'I' and resid 323 through 330 Processing helix chain 'I' and resid 331 through 339 Processing helix chain 'I' and resid 343 through 356 Processing helix chain 'I' and resid 370 through 384 Processing helix chain 'I' and resid 387 through 389 No H-bonds generated for 'chain 'I' and resid 387 through 389' Processing helix chain 'I' and resid 390 through 400 Processing helix chain 'I' and resid 403 through 414 Processing helix chain 'I' and resid 418 through 428 removed outlier: 3.680A pdb=" N VAL I 422 " --> pdb=" O ASN I 418 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY I 428 " --> pdb=" O GLY I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 445 Processing helix chain 'I' and resid 455 through 466 Processing helix chain 'J' and resid 306 through 315 removed outlier: 3.599A pdb=" N SER J 312 " --> pdb=" O GLN J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 323 through 331 removed outlier: 3.522A pdb=" N TRP J 327 " --> pdb=" O GLU J 323 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 339 removed outlier: 3.817A pdb=" N ILE J 335 " --> pdb=" O ASN J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 355 Processing helix chain 'J' and resid 370 through 384 Processing helix chain 'J' and resid 387 through 400 removed outlier: 3.623A pdb=" N ASP J 400 " --> pdb=" O LYS J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 403 through 415 removed outlier: 3.637A pdb=" N ALA J 407 " --> pdb=" O GLY J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 418 through 427 removed outlier: 3.596A pdb=" N VAL J 422 " --> pdb=" O ASN J 418 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY J 424 " --> pdb=" O GLN J 420 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG J 427 " --> pdb=" O SER J 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 446 removed outlier: 3.731A pdb=" N THR J 437 " --> pdb=" O GLN J 433 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU J 446 " --> pdb=" O ARG J 442 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 455 Processing helix chain 'J' and resid 455 through 466 removed outlier: 3.624A pdb=" N ALA J 462 " --> pdb=" O GLN J 458 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL J 463 " --> pdb=" O HIS J 459 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 315 removed outlier: 3.662A pdb=" N ILE K 310 " --> pdb=" O PRO K 306 " (cutoff:3.500A) Processing helix chain 'K' and resid 323 through 331 removed outlier: 3.511A pdb=" N TRP K 327 " --> pdb=" O GLU K 323 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY K 329 " --> pdb=" O PRO K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 339 Processing helix chain 'K' and resid 343 through 356 Processing helix chain 'K' and resid 370 through 384 removed outlier: 3.563A pdb=" N LEU K 378 " --> pdb=" O ALA K 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 400 Processing helix chain 'K' and resid 403 through 415 Processing helix chain 'K' and resid 418 through 427 removed outlier: 3.674A pdb=" N GLY K 424 " --> pdb=" O GLN K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 444 removed outlier: 3.758A pdb=" N THR K 437 " --> pdb=" O GLN K 433 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG K 442 " --> pdb=" O ALA K 438 " (cutoff:3.500A) Processing helix chain 'K' and resid 448 through 455 Processing helix chain 'K' and resid 455 through 467 removed outlier: 3.571A pdb=" N VAL K 463 " --> pdb=" O HIS K 459 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 314 removed outlier: 3.793A pdb=" N SER L 312 " --> pdb=" O GLN L 308 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL L 313 " --> pdb=" O HIS L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 323 through 331 removed outlier: 3.564A pdb=" N ASN L 331 " --> pdb=" O TRP L 327 " (cutoff:3.500A) Processing helix chain 'L' and resid 331 through 339 Processing helix chain 'L' and resid 343 through 356 Processing helix chain 'L' and resid 370 through 383 removed outlier: 4.037A pdb=" N ALA L 374 " --> pdb=" O THR L 370 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL L 375 " --> pdb=" O TRP L 371 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG L 381 " --> pdb=" O THR L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 389 No H-bonds generated for 'chain 'L' and resid 387 through 389' Processing helix chain 'L' and resid 390 through 402 Processing helix chain 'L' and resid 403 through 414 removed outlier: 3.639A pdb=" N THR L 409 " --> pdb=" O ALA L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 418 through 427 Processing helix chain 'L' and resid 432 through 445 removed outlier: 3.571A pdb=" N THR L 437 " --> pdb=" O GLN L 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 450 through 455 Processing helix chain 'L' and resid 455 through 468 removed outlier: 3.961A pdb=" N HIS L 459 " --> pdb=" O THR L 455 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU L 467 " --> pdb=" O VAL L 463 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 315 removed outlier: 3.766A pdb=" N THR M 314 " --> pdb=" O ILE M 310 " (cutoff:3.500A) Processing helix chain 'M' and resid 323 through 330 Processing helix chain 'M' and resid 331 through 339 Processing helix chain 'M' and resid 343 through 356 removed outlier: 3.516A pdb=" N GLY M 356 " --> pdb=" O ASN M 352 " (cutoff:3.500A) Processing helix chain 'M' and resid 370 through 384 removed outlier: 3.590A pdb=" N ALA M 374 " --> pdb=" O THR M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 389 through 403 Processing helix chain 'M' and resid 403 through 415 removed outlier: 3.806A pdb=" N LEU M 410 " --> pdb=" O THR M 406 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 428 removed outlier: 4.072A pdb=" N GLY M 424 " --> pdb=" O GLN M 420 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY M 428 " --> pdb=" O GLY M 424 " (cutoff:3.500A) Processing helix chain 'M' and resid 432 through 446 removed outlier: 3.544A pdb=" N THR M 437 " --> pdb=" O GLN M 433 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA M 438 " --> pdb=" O ALA M 434 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG M 442 " --> pdb=" O ALA M 438 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU M 446 " --> pdb=" O ARG M 442 " (cutoff:3.500A) Processing helix chain 'M' and resid 448 through 455 Processing helix chain 'M' and resid 456 through 468 433 hydrogen bonds defined for protein. 1296 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: 1.14 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1344 1.31 - 1.44: 2040 1.44 - 1.57: 4754 1.57 - 1.71: 0 1.71 - 1.84: 48 Bond restraints: 8186 Sorted by residual: bond pdb=" CA SER L 415 " pdb=" CB SER L 415 " ideal model delta sigma weight residual 1.537 1.471 0.066 1.41e-02 5.03e+03 2.20e+01 bond pdb=" N MET K 413 " pdb=" CA MET K 413 " ideal model delta sigma weight residual 1.463 1.513 -0.050 1.08e-02 8.57e+03 2.14e+01 bond pdb=" C THR K 406 " pdb=" O THR K 406 " ideal model delta sigma weight residual 1.236 1.289 -0.053 1.15e-02 7.56e+03 2.11e+01 bond pdb=" C VAL M 436 " pdb=" O VAL M 436 " ideal model delta sigma weight residual 1.236 1.287 -0.050 1.11e-02 8.12e+03 2.06e+01 bond pdb=" C CYS L 348 " pdb=" O CYS L 348 " ideal model delta sigma weight residual 1.236 1.286 -0.049 1.15e-02 7.56e+03 1.85e+01 ... (remaining 8181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 9555 2.94 - 5.88: 1554 5.88 - 8.82: 56 8.82 - 11.76: 2 11.76 - 14.69: 1 Bond angle restraints: 11168 Sorted by residual: angle pdb=" CA ARG I 477 " pdb=" C ARG I 477 " pdb=" O ARG I 477 " ideal model delta sigma weight residual 120.80 135.49 -14.69 1.70e+00 3.46e-01 7.47e+01 angle pdb=" CA GLY L 384 " pdb=" C GLY L 384 " pdb=" O GLY L 384 " ideal model delta sigma weight residual 122.45 117.63 4.82 7.20e-01 1.93e+00 4.49e+01 angle pdb=" N PRO J 387 " pdb=" CA PRO J 387 " pdb=" CB PRO J 387 " ideal model delta sigma weight residual 102.81 98.36 4.45 6.70e-01 2.23e+00 4.41e+01 angle pdb=" N PRO J 317 " pdb=" CA PRO J 317 " pdb=" CB PRO J 317 " ideal model delta sigma weight residual 103.19 106.66 -3.47 5.60e-01 3.19e+00 3.84e+01 angle pdb=" CA GLY I 432 " pdb=" C GLY I 432 " pdb=" O GLY I 432 " ideal model delta sigma weight residual 122.52 117.88 4.64 7.90e-01 1.60e+00 3.46e+01 ... (remaining 11163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4365 17.65 - 35.30: 391 35.30 - 52.96: 98 52.96 - 70.61: 30 70.61 - 88.26: 8 Dihedral angle restraints: 4892 sinusoidal: 1946 harmonic: 2946 Sorted by residual: dihedral pdb=" CA LEU H 355 " pdb=" C LEU H 355 " pdb=" N GLY H 356 " pdb=" CA GLY H 356 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA GLY L 403 " pdb=" C GLY L 403 " pdb=" N VAL L 404 " pdb=" CA VAL L 404 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ASP I 444 " pdb=" C ASP I 444 " pdb=" N GLN I 445 " pdb=" CA GLN I 445 " ideal model delta harmonic sigma weight residual 180.00 153.76 26.24 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 4889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 620 0.061 - 0.122: 460 0.122 - 0.183: 184 0.183 - 0.243: 43 0.243 - 0.304: 5 Chirality restraints: 1312 Sorted by residual: chirality pdb=" CA PRO K 325 " pdb=" N PRO K 325 " pdb=" C PRO K 325 " pdb=" CB PRO K 325 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA VAL L 313 " pdb=" N VAL L 313 " pdb=" C VAL L 313 " pdb=" CB VAL L 313 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA VAL K 341 " pdb=" N VAL K 341 " pdb=" C VAL K 341 " pdb=" CB VAL K 341 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1309 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 408 " -0.055 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR J 408 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR J 408 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR J 408 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR J 408 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR J 408 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR J 408 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR J 408 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE M 305 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ILE M 305 " 0.063 2.00e-02 2.50e+03 pdb=" O ILE M 305 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO M 306 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 419 " -0.046 2.00e-02 2.50e+03 2.36e-02 1.12e+01 pdb=" CG TYR K 419 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR K 419 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR K 419 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR K 419 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR K 419 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR K 419 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR K 419 " -0.018 2.00e-02 2.50e+03 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 967 2.78 - 3.31: 8128 3.31 - 3.84: 11610 3.84 - 4.37: 15531 4.37 - 4.90: 24307 Nonbonded interactions: 60543 Sorted by model distance: nonbonded pdb=" OD1 ASN L 470 " pdb=" O GLN L 474 " model vdw 2.254 3.040 nonbonded pdb=" O PRO H 321 " pdb=" OG1 THR H 382 " model vdw 2.406 3.040 nonbonded pdb=" N GLU I 446 " pdb=" O GLU I 446 " model vdw 2.430 2.496 nonbonded pdb=" OD1 ASP L 448 " pdb=" N ASP L 449 " model vdw 2.456 3.120 nonbonded pdb=" OG1 THR M 370 " pdb=" OD1 ASP M 372 " model vdw 2.462 3.040 ... (remaining 60538 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'H' and resid 303 through 476) selection = (chain 'I' and resid 303 through 476) selection = chain 'J' selection = (chain 'K' and resid 303 through 476) selection = chain 'L' selection = (chain 'M' and resid 303 through 476) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.090 Find NCS groups from input model: 0.170 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 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 : 0.015 0.067 8186 Z= 1.071 Angle : 2.021 14.694 11168 Z= 1.485 Chirality : 0.090 0.304 1312 Planarity : 0.008 0.044 1466 Dihedral : 15.491 88.257 3012 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.12 % Allowed : 8.29 % Favored : 91.59 % 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: -4.62 (0.19), residues: 1036 helix: -2.80 (0.14), residues: 704 sheet: None (None), residues: 0 loop : -3.27 (0.27), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG I 472 TYR 0.055 0.010 TYR J 408 PHE 0.039 0.009 PHE L 379 TRP 0.030 0.008 TRP K 327 HIS 0.015 0.005 HIS I 309 Details of bonding type rmsd covalent geometry : bond 0.01460 ( 8186) covalent geometry : angle 2.02109 (11168) hydrogen bonds : bond 0.29908 ( 433) hydrogen bonds : angle 8.66489 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.318 Fit side-chains REVERT: H 420 GLN cc_start: 0.7646 (mt0) cc_final: 0.7360 (mm-40) REVERT: I 312 SER cc_start: 0.7740 (m) cc_final: 0.7503 (p) REVERT: J 312 SER cc_start: 0.7804 (t) cc_final: 0.7595 (p) REVERT: J 388 MET cc_start: 0.5564 (mmp) cc_final: 0.5265 (mmm) REVERT: J 402 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7873 (mt-10) REVERT: J 417 GLN cc_start: 0.6179 (mm-40) cc_final: 0.5141 (mm110) REVERT: J 420 GLN cc_start: 0.8664 (mt0) cc_final: 0.8110 (tm-30) REVERT: J 427 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6759 (ttp-170) REVERT: J 452 ARG cc_start: 0.6277 (mtt180) cc_final: 0.5973 (mtt-85) REVERT: K 359 ILE cc_start: 0.6638 (mt) cc_final: 0.6420 (tp) REVERT: K 370 THR cc_start: 0.7548 (m) cc_final: 0.7149 (p) REVERT: K 419 TYR cc_start: 0.7639 (t80) cc_final: 0.7406 (t80) REVERT: M 319 ARG cc_start: 0.6910 (mtt180) cc_final: 0.6381 (tmm160) REVERT: M 455 THR cc_start: 0.7550 (m) cc_final: 0.7130 (p) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1606 time to fit residues: 36.5024 Evaluate side-chains 133 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 427 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 389 HIS H 390 GLN H 458 GLN H 459 HIS I 320 ASN I 440 GLN J 352 ASN J 401 GLN J 433 GLN K 433 GLN L 309 HIS L 331 ASN L 474 GLN M 309 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.108794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.092068 restraints weight = 10973.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.094385 restraints weight = 7598.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.096250 restraints weight = 5798.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.097550 restraints weight = 4680.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.098511 restraints weight = 3935.116| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8186 Z= 0.152 Angle : 0.658 6.839 11168 Z= 0.347 Chirality : 0.042 0.132 1312 Planarity : 0.005 0.061 1466 Dihedral : 5.103 52.460 1140 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.84 % Allowed : 10.71 % Favored : 87.44 % 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: -1.75 (0.24), residues: 1036 helix: -0.54 (0.18), residues: 724 sheet: None (None), residues: 0 loop : -2.45 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 381 TYR 0.012 0.001 TYR M 464 PHE 0.011 0.001 PHE J 386 TRP 0.019 0.001 TRP K 327 HIS 0.005 0.001 HIS H 389 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8186) covalent geometry : angle 0.65840 (11168) hydrogen bonds : bond 0.05491 ( 433) hydrogen bonds : angle 4.64415 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.319 Fit side-chains REVERT: I 475 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8382 (p) REVERT: J 427 ARG cc_start: 0.7321 (mtm110) cc_final: 0.6753 (ttp-170) REVERT: J 452 ARG cc_start: 0.7174 (mtt180) cc_final: 0.6811 (mtt-85) REVERT: K 472 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7681 (mtt-85) REVERT: M 455 THR cc_start: 0.8606 (m) cc_final: 0.8089 (p) outliers start: 16 outliers final: 7 residues processed: 132 average time/residue: 0.1229 time to fit residues: 20.8214 Evaluate side-chains 115 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain I residue 475 SER Chi-restraints excluded: chain K residue 348 CYS Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 345 ASP Chi-restraints excluded: chain L residue 415 SER Chi-restraints excluded: chain M residue 426 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 352 ASN L 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.107240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.090385 restraints weight = 11141.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.092737 restraints weight = 7766.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.094485 restraints weight = 5931.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.095719 restraints weight = 4822.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.096657 restraints weight = 4094.006| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8186 Z= 0.137 Angle : 0.568 5.747 11168 Z= 0.292 Chirality : 0.040 0.134 1312 Planarity : 0.005 0.055 1466 Dihedral : 4.190 17.111 1136 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.15 % Allowed : 14.06 % Favored : 84.79 % 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 (0.25), residues: 1036 helix: 0.43 (0.19), residues: 723 sheet: None (None), residues: 0 loop : -2.04 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 442 TYR 0.008 0.001 TYR M 464 PHE 0.009 0.001 PHE K 386 TRP 0.015 0.001 TRP K 327 HIS 0.004 0.001 HIS I 309 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8186) covalent geometry : angle 0.56844 (11168) hydrogen bonds : bond 0.05031 ( 433) hydrogen bonds : angle 4.12951 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: J 427 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6736 (ttp-170) REVERT: L 415 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8430 (p) outliers start: 10 outliers final: 7 residues processed: 122 average time/residue: 0.1274 time to fit residues: 19.9513 Evaluate side-chains 113 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain J residue 427 ARG Chi-restraints excluded: chain K residue 342 THR Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 345 ASP Chi-restraints excluded: chain L residue 415 SER Chi-restraints excluded: chain M residue 381 ARG Chi-restraints excluded: chain M residue 426 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 352 ASN L 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.108968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.092021 restraints weight = 11316.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.094412 restraints weight = 7896.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.096107 restraints weight = 6034.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.097412 restraints weight = 4919.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.098323 restraints weight = 4159.693| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8186 Z= 0.112 Angle : 0.523 5.649 11168 Z= 0.265 Chirality : 0.039 0.133 1312 Planarity : 0.005 0.058 1466 Dihedral : 3.939 15.566 1136 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.73 % Allowed : 15.44 % Favored : 82.83 % 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: 0.09 (0.26), residues: 1036 helix: 0.82 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -1.71 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 381 TYR 0.007 0.001 TYR M 464 PHE 0.007 0.001 PHE K 456 TRP 0.013 0.001 TRP J 327 HIS 0.002 0.001 HIS I 309 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8186) covalent geometry : angle 0.52345 (11168) hydrogen bonds : bond 0.04036 ( 433) hydrogen bonds : angle 3.86967 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: J 427 ARG cc_start: 0.7240 (mtm110) cc_final: 0.6654 (ttp-170) REVERT: L 415 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8394 (p) REVERT: M 419 TYR cc_start: 0.8520 (t80) cc_final: 0.8292 (t80) outliers start: 15 outliers final: 9 residues processed: 118 average time/residue: 0.1257 time to fit residues: 19.0034 Evaluate side-chains 107 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 345 ASP Chi-restraints excluded: chain L residue 415 SER Chi-restraints excluded: chain M residue 381 ARG Chi-restraints excluded: chain M residue 382 THR Chi-restraints excluded: chain M residue 395 ILE Chi-restraints excluded: chain M residue 426 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.107794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.090991 restraints weight = 11287.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.093297 restraints weight = 7910.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.094944 restraints weight = 6075.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.096225 restraints weight = 4973.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.097141 restraints weight = 4230.931| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8186 Z= 0.128 Angle : 0.525 5.665 11168 Z= 0.266 Chirality : 0.040 0.138 1312 Planarity : 0.005 0.062 1466 Dihedral : 3.861 15.395 1136 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.30 % Allowed : 15.32 % Favored : 82.37 % 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: 0.26 (0.26), residues: 1036 helix: 0.92 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 442 TYR 0.008 0.001 TYR M 464 PHE 0.009 0.001 PHE K 456 TRP 0.012 0.001 TRP K 327 HIS 0.003 0.001 HIS K 459 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8186) covalent geometry : angle 0.52520 (11168) hydrogen bonds : bond 0.04335 ( 433) hydrogen bonds : angle 3.80864 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: J 427 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6749 (ttp-170) REVERT: L 415 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8401 (p) REVERT: M 419 TYR cc_start: 0.8559 (t80) cc_final: 0.8327 (t80) outliers start: 20 outliers final: 15 residues processed: 114 average time/residue: 0.1339 time to fit residues: 19.3409 Evaluate side-chains 110 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 380 ILE Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 427 ARG Chi-restraints excluded: chain K residue 342 THR Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain K residue 458 GLN Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 345 ASP Chi-restraints excluded: chain L residue 415 SER Chi-restraints excluded: chain M residue 381 ARG Chi-restraints excluded: chain M residue 395 ILE Chi-restraints excluded: chain M residue 426 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 75 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.110047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.093432 restraints weight = 11122.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.095729 restraints weight = 7784.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.097439 restraints weight = 5958.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.098693 restraints weight = 4850.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.099644 restraints weight = 4114.933| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8186 Z= 0.097 Angle : 0.491 5.546 11168 Z= 0.247 Chirality : 0.038 0.130 1312 Planarity : 0.004 0.062 1466 Dihedral : 3.679 14.480 1136 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.07 % Allowed : 16.47 % Favored : 81.45 % 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: 0.62 (0.26), residues: 1036 helix: 1.17 (0.20), residues: 728 sheet: None (None), residues: 0 loop : -1.39 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 381 TYR 0.004 0.001 TYR J 408 PHE 0.006 0.001 PHE K 456 TRP 0.011 0.001 TRP J 327 HIS 0.002 0.001 HIS K 459 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8186) covalent geometry : angle 0.49055 (11168) hydrogen bonds : bond 0.03493 ( 433) hydrogen bonds : angle 3.67100 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.320 Fit side-chains REVERT: J 427 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6699 (ttp-170) REVERT: K 461 ASN cc_start: 0.8881 (m-40) cc_final: 0.8650 (m-40) REVERT: M 381 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7479 (ttm170) outliers start: 18 outliers final: 11 residues processed: 115 average time/residue: 0.1097 time to fit residues: 16.4654 Evaluate side-chains 104 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 380 ILE Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 427 ARG Chi-restraints excluded: chain K residue 326 ILE Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 345 ASP Chi-restraints excluded: chain M residue 381 ARG Chi-restraints excluded: chain M residue 426 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 0.0980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 45 optimal weight: 0.3980 chunk 67 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.109689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.093026 restraints weight = 11180.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.095273 restraints weight = 7870.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.096992 restraints weight = 6046.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.098250 restraints weight = 4916.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.099172 restraints weight = 4182.222| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8186 Z= 0.104 Angle : 0.495 6.168 11168 Z= 0.247 Chirality : 0.039 0.132 1312 Planarity : 0.005 0.061 1466 Dihedral : 3.590 14.067 1136 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.73 % Allowed : 17.74 % Favored : 80.53 % 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: 0.75 (0.26), residues: 1036 helix: 1.25 (0.20), residues: 734 sheet: None (None), residues: 0 loop : -1.34 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 381 TYR 0.006 0.001 TYR M 464 PHE 0.006 0.001 PHE K 456 TRP 0.009 0.001 TRP J 327 HIS 0.004 0.001 HIS K 459 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8186) covalent geometry : angle 0.49509 (11168) hydrogen bonds : bond 0.03649 ( 433) hydrogen bonds : angle 3.63139 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.289 Fit side-chains REVERT: I 369 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8219 (mp) REVERT: J 427 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6671 (ttp-170) REVERT: L 319 ARG cc_start: 0.7855 (mtp180) cc_final: 0.7606 (mtp85) REVERT: L 415 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8417 (p) REVERT: L 472 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.7945 (mtt90) REVERT: M 381 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7500 (ttm170) outliers start: 15 outliers final: 11 residues processed: 116 average time/residue: 0.1246 time to fit residues: 18.4720 Evaluate side-chains 115 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 380 ILE Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 427 ARG Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 345 ASP Chi-restraints excluded: chain L residue 415 SER Chi-restraints excluded: chain M residue 381 ARG Chi-restraints excluded: chain M residue 426 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 0.0060 chunk 80 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 95 optimal weight: 4.9990 chunk 68 optimal weight: 0.0000 chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.113010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.096461 restraints weight = 11117.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.098781 restraints weight = 7762.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.100531 restraints weight = 5935.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.101743 restraints weight = 4799.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.102794 restraints weight = 4077.927| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8186 Z= 0.086 Angle : 0.473 7.071 11168 Z= 0.235 Chirality : 0.038 0.128 1312 Planarity : 0.004 0.061 1466 Dihedral : 3.449 13.926 1136 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.50 % Allowed : 18.09 % Favored : 80.41 % 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: 1.14 (0.27), residues: 1036 helix: 1.54 (0.20), residues: 735 sheet: None (None), residues: 0 loop : -1.20 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 347 TYR 0.004 0.000 TYR J 419 PHE 0.004 0.001 PHE J 386 TRP 0.011 0.001 TRP J 327 HIS 0.005 0.000 HIS K 459 Details of bonding type rmsd covalent geometry : bond 0.00183 ( 8186) covalent geometry : angle 0.47343 (11168) hydrogen bonds : bond 0.02799 ( 433) hydrogen bonds : angle 3.50130 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.320 Fit side-chains REVERT: J 415 SER cc_start: 0.7768 (m) cc_final: 0.7559 (t) REVERT: J 427 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6642 (ttp-170) REVERT: L 319 ARG cc_start: 0.7815 (mtp180) cc_final: 0.7614 (mtp85) REVERT: L 472 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7902 (mtt90) REVERT: M 381 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7569 (ttm170) outliers start: 13 outliers final: 9 residues processed: 121 average time/residue: 0.1172 time to fit residues: 18.3483 Evaluate side-chains 114 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 427 ARG Chi-restraints excluded: chain K residue 326 ILE Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 345 ASP Chi-restraints excluded: chain M residue 381 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 chunk 38 optimal weight: 0.0070 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 86 optimal weight: 0.0570 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 352 ASN M 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.113326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.096600 restraints weight = 11180.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.098921 restraints weight = 7845.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.100633 restraints weight = 6004.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.101918 restraints weight = 4889.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.102750 restraints weight = 4154.423| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8186 Z= 0.086 Angle : 0.483 7.657 11168 Z= 0.235 Chirality : 0.038 0.127 1312 Planarity : 0.004 0.061 1466 Dihedral : 3.361 13.855 1136 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.04 % Allowed : 18.89 % Favored : 80.07 % 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: 1.27 (0.27), residues: 1036 helix: 1.65 (0.20), residues: 736 sheet: None (None), residues: 0 loop : -1.20 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 330 TYR 0.004 0.000 TYR L 419 PHE 0.005 0.001 PHE J 386 TRP 0.010 0.001 TRP J 327 HIS 0.005 0.001 HIS K 459 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 8186) covalent geometry : angle 0.48288 (11168) hydrogen bonds : bond 0.02881 ( 433) hydrogen bonds : angle 3.47647 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.251 Fit side-chains REVERT: J 342 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7751 (p) REVERT: J 427 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6609 (ttp-170) REVERT: K 419 TYR cc_start: 0.8832 (t80) cc_final: 0.8551 (t80) REVERT: K 472 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7759 (mtt-85) REVERT: L 472 ARG cc_start: 0.8214 (mtp-110) cc_final: 0.7960 (mtt90) REVERT: M 381 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7612 (ttm170) outliers start: 9 outliers final: 4 residues processed: 114 average time/residue: 0.1230 time to fit residues: 17.8751 Evaluate side-chains 108 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 427 ARG Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain M residue 381 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.0060 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.112453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.095637 restraints weight = 11163.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.097988 restraints weight = 7855.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.099692 restraints weight = 6043.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.100926 restraints weight = 4921.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.101852 restraints weight = 4192.328| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8186 Z= 0.092 Angle : 0.486 8.094 11168 Z= 0.237 Chirality : 0.038 0.128 1312 Planarity : 0.004 0.061 1466 Dihedral : 3.365 14.032 1136 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.04 % Allowed : 19.01 % Favored : 79.95 % 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: 1.31 (0.27), residues: 1036 helix: 1.69 (0.20), residues: 734 sheet: None (None), residues: 0 loop : -1.21 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 319 TYR 0.004 0.000 TYR M 464 PHE 0.006 0.001 PHE K 456 TRP 0.008 0.001 TRP J 327 HIS 0.005 0.001 HIS K 459 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 8186) covalent geometry : angle 0.48642 (11168) hydrogen bonds : bond 0.03059 ( 433) hydrogen bonds : angle 3.46347 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.332 Fit side-chains REVERT: I 308 GLN cc_start: 0.7416 (pm20) cc_final: 0.7106 (pm20) REVERT: I 369 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8179 (mp) REVERT: J 342 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7749 (p) REVERT: J 427 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6626 (ttp-170) REVERT: K 419 TYR cc_start: 0.8816 (t80) cc_final: 0.8525 (t80) REVERT: K 472 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7715 (mtt-85) REVERT: L 472 ARG cc_start: 0.8233 (mtp-110) cc_final: 0.7956 (mtt90) REVERT: M 381 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7622 (ttm170) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 0.1104 time to fit residues: 15.3740 Evaluate side-chains 106 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 330 ARG Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 427 ARG Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain M residue 381 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 17 optimal weight: 0.0050 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.112187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.095479 restraints weight = 11141.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.097772 restraints weight = 7816.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.099464 restraints weight = 6005.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.100641 restraints weight = 4900.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.101605 restraints weight = 4186.329| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8186 Z= 0.091 Angle : 0.485 8.012 11168 Z= 0.236 Chirality : 0.038 0.128 1312 Planarity : 0.004 0.060 1466 Dihedral : 3.350 13.998 1136 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.27 % Allowed : 18.89 % Favored : 79.84 % 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: 1.33 (0.27), residues: 1036 helix: 1.68 (0.20), residues: 737 sheet: None (None), residues: 0 loop : -1.15 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 330 TYR 0.004 0.000 TYR M 464 PHE 0.006 0.001 PHE K 456 TRP 0.008 0.001 TRP J 327 HIS 0.005 0.001 HIS K 459 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 8186) covalent geometry : angle 0.48476 (11168) hydrogen bonds : bond 0.03110 ( 433) hydrogen bonds : angle 3.47433 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1468.38 seconds wall clock time: 25 minutes 57.10 seconds (1557.10 seconds total)