Starting phenix.real_space_refine on Sun May 11 13:23:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozn_17315/05_2025/8ozn_17315.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozn_17315/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ozn_17315/05_2025/8ozn_17315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozn_17315/05_2025/8ozn_17315.map" model { file = "/net/cci-nas-00/data/ceres_data/8ozn_17315/05_2025/8ozn_17315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozn_17315/05_2025/8ozn_17315.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.56, per 1000 atoms: 0.94 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: 1.82 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.80 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: 1.94 Time building geometry restraints manager: 2.15 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: 2.550 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.500 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.030 0.008 TRP K 327 HIS 0.015 0.005 HIS I 309 PHE 0.039 0.009 PHE L 379 TYR 0.055 0.010 TYR J 408 ARG 0.014 0.002 ARG I 472 Details of bonding type rmsd hydrogen bonds : bond 0.29908 ( 433) hydrogen bonds : angle 8.66489 ( 1296) covalent geometry : bond 0.01460 ( 8186) covalent geometry : angle 2.02109 (11168) *********************** 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 : 0.930 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: 0.3187 time to fit residues: 72.6762 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 : 0.837 ------------------------------------------------------------------------------- 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 86 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 389 HIS H 458 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.107237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.090504 restraints weight = 10981.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.092834 restraints weight = 7619.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.094570 restraints weight = 5829.502| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8186 Z= 0.165 Angle : 0.669 6.743 11168 Z= 0.354 Chirality : 0.042 0.132 1312 Planarity : 0.005 0.060 1466 Dihedral : 5.160 52.560 1140 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.73 % Allowed : 10.94 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.23), residues: 1036 helix: -0.61 (0.18), residues: 724 sheet: None (None), residues: 0 loop : -2.54 (0.29), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 327 HIS 0.006 0.001 HIS H 389 PHE 0.012 0.001 PHE J 386 TYR 0.013 0.001 TYR M 464 ARG 0.005 0.001 ARG K 381 Details of bonding type rmsd hydrogen bonds : bond 0.06113 ( 433) hydrogen bonds : angle 4.73146 ( 1296) covalent geometry : bond 0.00369 ( 8186) covalent geometry : angle 0.66924 (11168) *********************** 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 140 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.937 Fit side-chains REVERT: I 475 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8363 (p) REVERT: J 348 CYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7575 (p) REVERT: J 388 MET cc_start: 0.5767 (mmp) cc_final: 0.5557 (tpt) REVERT: J 427 ARG cc_start: 0.7366 (mtm110) cc_final: 0.7074 (ttm170) REVERT: J 452 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6783 (mtt-85) REVERT: K 370 THR cc_start: 0.8145 (m) cc_final: 0.7883 (p) REVERT: M 455 THR cc_start: 0.8620 (m) cc_final: 0.8103 (p) outliers start: 15 outliers final: 8 residues processed: 137 average time/residue: 0.2454 time to fit residues: 43.6236 Evaluate side-chains 119 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 J residue 348 CYS Chi-restraints excluded: chain J 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 74 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 43 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 420 GLN H 459 HIS L 352 ASN L 383 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.109609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.092716 restraints weight = 11121.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.095104 restraints weight = 7728.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.096864 restraints weight = 5881.837| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2962 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= 0.111 Angle : 0.543 6.041 11168 Z= 0.278 Chirality : 0.039 0.133 1312 Planarity : 0.005 0.053 1466 Dihedral : 4.147 16.709 1136 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.15 % Allowed : 13.71 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1036 helix: 0.57 (0.19), residues: 723 sheet: None (None), residues: 0 loop : -1.99 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 327 HIS 0.002 0.001 HIS K 309 PHE 0.005 0.001 PHE J 386 TYR 0.006 0.001 TYR L 419 ARG 0.003 0.000 ARG J 442 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 433) hydrogen bonds : angle 4.07031 ( 1296) covalent geometry : bond 0.00236 ( 8186) covalent geometry : angle 0.54266 (11168) *********************** 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 117 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: J 388 MET cc_start: 0.5745 (mmp) cc_final: 0.5496 (tpt) REVERT: J 427 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6775 (ttp-170) REVERT: K 472 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7690 (mtt-85) REVERT: L 308 GLN cc_start: 0.7751 (pm20) cc_final: 0.7365 (pp30) outliers start: 10 outliers final: 7 residues processed: 114 average time/residue: 0.2503 time to fit residues: 36.4345 Evaluate side-chains 106 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 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 M residue 381 ARG Chi-restraints excluded: chain M residue 400 ASP 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 26 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 22 optimal weight: 0.0370 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 0.0020 chunk 42 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 overall best weight: 0.4466 ------------------------------------------------------------------------------- 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 = 0.3134 r_free = 0.3134 target = 0.111551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.094758 restraints weight = 11114.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.097142 restraints weight = 7716.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.098905 restraints weight = 5879.616| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3318 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= 0.096 Angle : 0.502 5.617 11168 Z= 0.254 Chirality : 0.039 0.131 1312 Planarity : 0.005 0.059 1466 Dihedral : 3.803 15.084 1136 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.27 % Allowed : 14.63 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1036 helix: 1.05 (0.20), residues: 731 sheet: None (None), residues: 0 loop : -1.62 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 327 HIS 0.002 0.000 HIS J 383 PHE 0.008 0.001 PHE J 386 TYR 0.005 0.001 TYR M 419 ARG 0.003 0.000 ARG K 381 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 433) hydrogen bonds : angle 3.76139 ( 1296) covalent geometry : bond 0.00201 ( 8186) covalent geometry : angle 0.50231 (11168) *********************** 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 118 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: J 388 MET cc_start: 0.5745 (mmp) cc_final: 0.5477 (tpt) REVERT: J 427 ARG cc_start: 0.7245 (mtm110) cc_final: 0.6708 (ttp-170) REVERT: K 472 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7701 (mtt-85) outliers start: 11 outliers final: 6 residues processed: 116 average time/residue: 0.2459 time to fit residues: 36.9318 Evaluate side-chains 101 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain K residue 342 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 75 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 101 optimal weight: 0.0050 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 352 ASN L 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.111658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.094938 restraints weight = 10940.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.097277 restraints weight = 7641.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.098934 restraints weight = 5862.813| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8186 Z= 0.094 Angle : 0.491 6.319 11168 Z= 0.248 Chirality : 0.038 0.170 1312 Planarity : 0.005 0.059 1466 Dihedral : 3.699 15.534 1136 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.73 % Allowed : 14.52 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1036 helix: 1.26 (0.20), residues: 735 sheet: None (None), residues: 0 loop : -1.51 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 327 HIS 0.003 0.000 HIS K 459 PHE 0.006 0.001 PHE J 386 TYR 0.004 0.000 TYR M 464 ARG 0.003 0.000 ARG J 330 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 433) hydrogen bonds : angle 3.63769 ( 1296) covalent geometry : bond 0.00202 ( 8186) covalent geometry : angle 0.49147 (11168) *********************** 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 117 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: J 427 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6671 (ttp-170) REVERT: K 465 GLU cc_start: 0.8143 (tt0) cc_final: 0.7932 (tt0) REVERT: K 472 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7694 (mtt-85) outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 0.2391 time to fit residues: 35.1380 Evaluate side-chains 109 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain I residue 316 GLU 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 342 THR Chi-restraints excluded: chain L residue 313 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.0370 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.111987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.095276 restraints weight = 10987.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.097652 restraints weight = 7670.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.099347 restraints weight = 5864.452| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8186 Z= 0.093 Angle : 0.481 5.856 11168 Z= 0.242 Chirality : 0.038 0.128 1312 Planarity : 0.004 0.060 1466 Dihedral : 3.569 13.812 1136 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.19 % Allowed : 15.67 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1036 helix: 1.42 (0.20), residues: 733 sheet: None (None), residues: 0 loop : -1.37 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 327 HIS 0.004 0.001 HIS K 459 PHE 0.006 0.001 PHE K 456 TYR 0.004 0.001 TYR M 464 ARG 0.002 0.000 ARG K 381 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 433) hydrogen bonds : angle 3.56220 ( 1296) covalent geometry : bond 0.00206 ( 8186) covalent geometry : angle 0.48076 (11168) *********************** 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 118 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.897 Fit side-chains REVERT: J 402 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: J 412 MET cc_start: 0.7447 (mmm) cc_final: 0.7178 (mmm) REVERT: J 427 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6597 (ttp-170) REVERT: K 472 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7672 (mtt-85) REVERT: M 381 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7512 (ttm170) outliers start: 19 outliers final: 11 residues processed: 112 average time/residue: 0.2461 time to fit residues: 36.4776 Evaluate side-chains 107 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 316 GLU Chi-restraints excluded: chain I residue 362 SER 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 326 ILE Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 313 VAL 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: 0.8980 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3126 r_free = 0.3126 target = 0.110975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.094260 restraints weight = 11123.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.096650 restraints weight = 7775.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.098394 restraints weight = 5944.901| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3641 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= 0.101 Angle : 0.484 5.540 11168 Z= 0.244 Chirality : 0.039 0.129 1312 Planarity : 0.004 0.059 1466 Dihedral : 3.525 14.091 1136 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.07 % Allowed : 16.01 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1036 helix: 1.45 (0.20), residues: 735 sheet: None (None), residues: 0 loop : -1.29 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 327 HIS 0.005 0.001 HIS K 459 PHE 0.008 0.001 PHE K 456 TYR 0.006 0.001 TYR M 464 ARG 0.002 0.000 ARG J 311 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 433) hydrogen bonds : angle 3.54396 ( 1296) covalent geometry : bond 0.00236 ( 8186) covalent geometry : angle 0.48385 (11168) *********************** 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 114 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.858 Fit side-chains REVERT: H 330 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7150 (ptt180) REVERT: J 412 MET cc_start: 0.7567 (mmm) cc_final: 0.7266 (mmm) REVERT: J 427 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6727 (ttp-170) REVERT: L 319 ARG cc_start: 0.7904 (mtp180) cc_final: 0.7662 (mtp85) REVERT: M 381 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7545 (ttm170) outliers start: 18 outliers final: 10 residues processed: 108 average time/residue: 0.2340 time to fit residues: 33.0256 Evaluate side-chains 106 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 426 ILE Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 345 ASP Chi-restraints excluded: chain M residue 381 ARG Chi-restraints excluded: chain M residue 413 MET 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 64 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 5 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 93 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.112927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.096136 restraints weight = 11178.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.098515 restraints weight = 7807.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.100288 restraints weight = 5952.396| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8186 Z= 0.088 Angle : 0.471 6.028 11168 Z= 0.237 Chirality : 0.038 0.128 1312 Planarity : 0.004 0.060 1466 Dihedral : 3.419 13.907 1136 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.19 % Allowed : 16.13 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1036 helix: 1.61 (0.20), residues: 734 sheet: None (None), residues: 0 loop : -1.18 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 327 HIS 0.005 0.000 HIS K 459 PHE 0.008 0.001 PHE J 386 TYR 0.004 0.000 TYR M 408 ARG 0.002 0.000 ARG K 381 Details of bonding type rmsd hydrogen bonds : bond 0.03000 ( 433) hydrogen bonds : angle 3.46400 ( 1296) covalent geometry : bond 0.00196 ( 8186) covalent geometry : angle 0.47114 (11168) *********************** 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 119 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.897 Fit side-chains REVERT: H 330 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7106 (ptt180) REVERT: I 369 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8124 (mp) REVERT: J 427 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6636 (ttp-170) REVERT: L 415 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8421 (p) REVERT: M 381 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7512 (ttm170) outliers start: 19 outliers final: 10 residues processed: 112 average time/residue: 0.2287 time to fit residues: 33.8224 Evaluate side-chains 112 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 330 ARG Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain I residue 362 SER 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 326 ILE Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 313 VAL 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 413 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 0.0670 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 0.0970 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 459 HIS L 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.113270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.096434 restraints weight = 11256.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.098905 restraints weight = 7766.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.100583 restraints weight = 5889.415| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8186 Z= 0.088 Angle : 0.469 6.585 11168 Z= 0.233 Chirality : 0.038 0.126 1312 Planarity : 0.004 0.059 1466 Dihedral : 3.344 13.902 1136 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.73 % Allowed : 16.71 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.27), residues: 1036 helix: 1.73 (0.20), residues: 732 sheet: None (None), residues: 0 loop : -1.14 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 327 HIS 0.005 0.000 HIS K 459 PHE 0.009 0.001 PHE J 386 TYR 0.003 0.000 TYR M 464 ARG 0.004 0.000 ARG L 319 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 433) hydrogen bonds : angle 3.41608 ( 1296) covalent geometry : bond 0.00196 ( 8186) covalent geometry : angle 0.46927 (11168) *********************** 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 123 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.823 Fit side-chains REVERT: I 369 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8125 (mp) REVERT: J 427 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6586 (ttp-170) REVERT: K 305 ILE cc_start: 0.8880 (mm) cc_final: 0.8619 (mt) REVERT: K 419 TYR cc_start: 0.8826 (t80) cc_final: 0.8549 (t80) REVERT: K 472 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7780 (mtt-85) REVERT: L 415 SER cc_start: 0.9206 (OUTLIER) cc_final: 0.8453 (p) REVERT: M 381 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7517 (ttm170) outliers start: 15 outliers final: 9 residues processed: 116 average time/residue: 0.2258 time to fit residues: 34.3759 Evaluate side-chains 116 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 400 ASP 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 326 ILE Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 415 SER Chi-restraints excluded: chain M residue 381 ARG Chi-restraints excluded: chain M residue 413 MET Chi-restraints excluded: chain M residue 426 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 0.0040 chunk 98 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 = 0.112301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.095591 restraints weight = 11144.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.097987 restraints weight = 7761.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.099746 restraints weight = 5909.308| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8186 Z= 0.093 Angle : 0.472 6.173 11168 Z= 0.235 Chirality : 0.038 0.128 1312 Planarity : 0.004 0.059 1466 Dihedral : 3.334 13.959 1136 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.61 % Allowed : 16.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.27), residues: 1036 helix: 1.78 (0.20), residues: 732 sheet: None (None), residues: 0 loop : -1.08 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 327 HIS 0.004 0.001 HIS K 309 PHE 0.009 0.001 PHE J 386 TYR 0.005 0.001 TYR M 464 ARG 0.002 0.000 ARG K 381 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 433) hydrogen bonds : angle 3.41077 ( 1296) covalent geometry : bond 0.00213 ( 8186) covalent geometry : angle 0.47197 (11168) ********************** 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 120 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.888 Fit side-chains REVERT: I 308 GLN cc_start: 0.7403 (pm20) cc_final: 0.7177 (pm20) REVERT: I 369 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8155 (mp) REVERT: I 465 GLU cc_start: 0.7457 (tt0) cc_final: 0.7074 (tt0) REVERT: J 342 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7760 (p) REVERT: J 427 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6589 (ttp-170) REVERT: K 305 ILE cc_start: 0.8896 (mm) cc_final: 0.8629 (mt) REVERT: K 419 TYR cc_start: 0.8831 (t80) cc_final: 0.8528 (t80) REVERT: K 472 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7776 (mtt-85) REVERT: L 415 SER cc_start: 0.9184 (OUTLIER) cc_final: 0.8452 (p) REVERT: M 381 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7534 (ttm170) outliers start: 14 outliers final: 8 residues processed: 114 average time/residue: 0.2559 time to fit residues: 37.5923 Evaluate side-chains 115 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 400 ASP 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 326 ILE Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 415 SER Chi-restraints excluded: chain M residue 381 ARG Chi-restraints excluded: chain M residue 413 MET Chi-restraints excluded: chain M residue 426 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 0.0370 chunk 4 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3150 r_free = 0.3150 target = 0.113046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.096336 restraints weight = 11155.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.098710 restraints weight = 7810.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.100367 restraints weight = 5985.265| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8186 Z= 0.088 Angle : 0.478 8.682 11168 Z= 0.234 Chirality : 0.038 0.127 1312 Planarity : 0.004 0.059 1466 Dihedral : 3.305 13.797 1136 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.50 % Allowed : 17.28 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1036 helix: 1.84 (0.20), residues: 733 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 327 HIS 0.005 0.001 HIS K 309 PHE 0.007 0.001 PHE J 386 TYR 0.004 0.000 TYR M 464 ARG 0.002 0.000 ARG K 381 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 433) hydrogen bonds : angle 3.39170 ( 1296) covalent geometry : bond 0.00199 ( 8186) covalent geometry : angle 0.47805 (11168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2651.72 seconds wall clock time: 46 minutes 54.16 seconds (2814.16 seconds total)