Starting phenix.real_space_refine on Thu Oct 10 15:39:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozn_17315/10_2024/8ozn_17315.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozn_17315/10_2024/8ozn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozn_17315/10_2024/8ozn_17315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozn_17315/10_2024/8ozn_17315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozn_17315/10_2024/8ozn_17315.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozn_17315/10_2024/8ozn_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 6.08, per 1000 atoms: 0.76 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: 2.11 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: 0.78 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: 2.10 Time building geometry restraints manager: 2.37 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: 0.00 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: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.320 Find NCS groups from input model: 0.380 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.560 ------------------------------------------------------------------------------- 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= 0.967 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.950 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: 0.3249 time to fit residues: 73.8668 Evaluate side-chains 133 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 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= 0.245 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 *********************** 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 fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 0.911 Fit side-chains REVERT: I 475 SER cc_start: 0.7641 (OUTLIER) cc_final: 0.7363 (p) REVERT: J 348 CYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6169 (p) REVERT: J 388 MET cc_start: 0.5375 (mmp) cc_final: 0.5033 (tpt) REVERT: J 452 ARG cc_start: 0.6004 (mtt180) cc_final: 0.5696 (mtt-85) REVERT: K 370 THR cc_start: 0.6787 (m) cc_final: 0.6427 (p) REVERT: M 319 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6874 (ttt180) REVERT: M 455 THR cc_start: 0.7144 (m) cc_final: 0.6671 (p) outliers start: 15 outliers final: 8 residues processed: 137 average time/residue: 0.2533 time to fit residues: 44.7601 Evaluate side-chains 122 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 319 ARG 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 51 optimal weight: 0.0770 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- 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 L 417 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8186 Z= 0.237 Angle : 0.575 5.817 11168 Z= 0.296 Chirality : 0.041 0.137 1312 Planarity : 0.005 0.055 1466 Dihedral : 4.287 17.401 1136 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.61 % Allowed : 13.48 % Favored : 84.91 % 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: -0.59 (0.25), residues: 1036 helix: 0.36 (0.19), residues: 724 sheet: None (None), residues: 0 loop : -2.11 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 327 HIS 0.004 0.001 HIS M 309 PHE 0.011 0.001 PHE K 456 TYR 0.008 0.001 TYR M 464 ARG 0.003 0.000 ARG K 381 *********************** 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 128 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: I 450 GLN cc_start: 0.6667 (tt0) cc_final: 0.6244 (tp-100) REVERT: J 348 CYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6283 (p) REVERT: J 388 MET cc_start: 0.5342 (mmp) cc_final: 0.4931 (tpt) REVERT: J 412 MET cc_start: 0.7605 (mtp) cc_final: 0.7388 (ttm) REVERT: J 417 GLN cc_start: 0.6691 (mm-40) cc_final: 0.6188 (mm110) REVERT: J 452 ARG cc_start: 0.6065 (mtt180) cc_final: 0.5710 (mtt-85) REVERT: L 352 ASN cc_start: 0.6776 (m-40) cc_final: 0.6424 (m110) REVERT: L 415 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7277 (p) REVERT: M 455 THR cc_start: 0.7149 (m) cc_final: 0.6708 (p) outliers start: 14 outliers final: 8 residues processed: 127 average time/residue: 0.2926 time to fit residues: 47.4004 Evaluate side-chains 113 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 348 CYS 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 395 ILE 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 69 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 chunk 62 optimal weight: 0.2980 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3226 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= 0.145 Angle : 0.514 5.929 11168 Z= 0.261 Chirality : 0.039 0.131 1312 Planarity : 0.005 0.060 1466 Dihedral : 3.952 15.634 1136 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.96 % Allowed : 14.63 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.26), residues: 1036 helix: 0.85 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.75 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 327 HIS 0.002 0.000 HIS K 309 PHE 0.007 0.001 PHE J 386 TYR 0.005 0.001 TYR L 419 ARG 0.003 0.000 ARG K 381 *********************** 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 119 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: I 450 GLN cc_start: 0.6663 (tt0) cc_final: 0.6259 (tp-100) REVERT: J 388 MET cc_start: 0.5353 (mmp) cc_final: 0.4923 (tpt) REVERT: J 412 MET cc_start: 0.7591 (mtp) cc_final: 0.7260 (ttt) REVERT: J 417 GLN cc_start: 0.6980 (mm-40) cc_final: 0.6309 (mm110) REVERT: L 352 ASN cc_start: 0.6740 (m-40) cc_final: 0.6540 (m110) REVERT: M 319 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6555 (tmm160) outliers start: 17 outliers final: 9 residues processed: 114 average time/residue: 0.2666 time to fit residues: 39.0350 Evaluate side-chains 104 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain K residue 342 THR 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 319 ARG 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 1 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8186 Z= 0.255 Angle : 0.547 5.727 11168 Z= 0.279 Chirality : 0.041 0.185 1312 Planarity : 0.005 0.062 1466 Dihedral : 4.002 17.647 1136 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.07 % Allowed : 15.55 % 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 (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: 0.11 (0.26), residues: 1036 helix: 0.82 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -1.71 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 327 HIS 0.004 0.001 HIS I 309 PHE 0.010 0.001 PHE K 456 TYR 0.011 0.001 TYR M 464 ARG 0.002 0.000 ARG K 349 *********************** 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 122 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: I 450 GLN cc_start: 0.6675 (tt0) cc_final: 0.6290 (tp-100) REVERT: J 348 CYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6328 (p) REVERT: J 417 GLN cc_start: 0.6975 (mm-40) cc_final: 0.6633 (mm110) REVERT: L 352 ASN cc_start: 0.6726 (m-40) cc_final: 0.6509 (m110) outliers start: 18 outliers final: 14 residues processed: 120 average time/residue: 0.2772 time to fit residues: 42.0168 Evaluate side-chains 115 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 348 CYS 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 426 ILE 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 57 optimal weight: 0.0030 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 51 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3522 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= 0.133 Angle : 0.490 5.581 11168 Z= 0.248 Chirality : 0.038 0.131 1312 Planarity : 0.005 0.062 1466 Dihedral : 3.732 14.946 1136 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.50 % Allowed : 17.17 % Favored : 81.34 % 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: 0.56 (0.26), residues: 1036 helix: 1.17 (0.20), residues: 726 sheet: None (None), residues: 0 loop : -1.52 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 327 HIS 0.002 0.000 HIS K 309 PHE 0.004 0.001 PHE K 456 TYR 0.005 0.001 TYR L 419 ARG 0.003 0.000 ARG K 381 *********************** 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 119 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.964 Fit side-chains REVERT: I 450 GLN cc_start: 0.6671 (tt0) cc_final: 0.6305 (tp-100) REVERT: J 412 MET cc_start: 0.7672 (mtp) cc_final: 0.7380 (ttt) REVERT: J 417 GLN cc_start: 0.7076 (mm-40) cc_final: 0.6412 (mm110) REVERT: M 319 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6464 (tmm160) outliers start: 13 outliers final: 7 residues processed: 117 average time/residue: 0.2690 time to fit residues: 40.5304 Evaluate side-chains 106 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 380 ILE Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain L residue 345 ASP Chi-restraints excluded: chain M residue 319 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 72 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8186 Z= 0.170 Angle : 0.498 5.994 11168 Z= 0.250 Chirality : 0.039 0.132 1312 Planarity : 0.005 0.061 1466 Dihedral : 3.655 14.617 1136 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.19 % Allowed : 17.40 % 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 (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: 0.64 (0.26), residues: 1036 helix: 1.22 (0.20), residues: 726 sheet: None (None), residues: 0 loop : -1.47 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 327 HIS 0.004 0.001 HIS K 459 PHE 0.006 0.001 PHE K 456 TYR 0.007 0.001 TYR M 464 ARG 0.002 0.000 ARG K 381 *********************** 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 118 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.976 Fit side-chains REVERT: I 450 GLN cc_start: 0.6852 (tt0) cc_final: 0.6453 (tp40) REVERT: J 348 CYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6376 (p) REVERT: J 417 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6649 (mm110) REVERT: M 319 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6533 (tmm160) outliers start: 19 outliers final: 13 residues processed: 115 average time/residue: 0.2675 time to fit residues: 39.4318 Evaluate side-chains 111 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 307 ILE Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 380 ILE Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain J residue 348 CYS 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 319 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 19 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.0570 overall best weight: 0.8300 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3685 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= 0.157 Angle : 0.488 5.742 11168 Z= 0.245 Chirality : 0.039 0.132 1312 Planarity : 0.005 0.061 1466 Dihedral : 3.576 14.532 1136 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.73 % Allowed : 18.32 % 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 (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: 0.78 (0.26), residues: 1036 helix: 1.31 (0.20), residues: 732 sheet: None (None), residues: 0 loop : -1.41 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 327 HIS 0.006 0.001 HIS K 459 PHE 0.009 0.001 PHE J 386 TYR 0.005 0.001 TYR M 464 ARG 0.002 0.000 ARG M 381 *********************** 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 115 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.940 Fit side-chains REVERT: I 450 GLN cc_start: 0.6815 (tt0) cc_final: 0.6446 (tp-100) REVERT: J 417 GLN cc_start: 0.7074 (mm-40) cc_final: 0.6656 (mm110) REVERT: K 419 TYR cc_start: 0.7468 (t80) cc_final: 0.7215 (t80) REVERT: L 415 SER cc_start: 0.7899 (OUTLIER) cc_final: 0.7293 (p) REVERT: M 319 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6522 (tmm160) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.2632 time to fit residues: 37.8708 Evaluate side-chains 108 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain I residue 380 ILE Chi-restraints excluded: chain J residue 342 THR 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 L residue 415 SER Chi-restraints excluded: chain M residue 319 ARG Chi-restraints excluded: chain M residue 426 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 0.0470 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3692 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= 0.185 Angle : 0.498 6.298 11168 Z= 0.250 Chirality : 0.039 0.134 1312 Planarity : 0.005 0.061 1466 Dihedral : 3.599 14.760 1136 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.84 % Allowed : 18.09 % 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 (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: 0.81 (0.26), residues: 1036 helix: 1.31 (0.20), residues: 729 sheet: None (None), residues: 0 loop : -1.32 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 327 HIS 0.005 0.001 HIS K 459 PHE 0.008 0.001 PHE K 456 TYR 0.007 0.001 TYR M 419 ARG 0.004 0.000 ARG L 319 *********************** 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 111 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.074 Fit side-chains REVERT: I 450 GLN cc_start: 0.6815 (tt0) cc_final: 0.6467 (tp-100) REVERT: J 348 CYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6368 (p) REVERT: L 415 SER cc_start: 0.7922 (OUTLIER) cc_final: 0.7316 (p) REVERT: M 319 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6557 (tmm160) outliers start: 16 outliers final: 12 residues processed: 109 average time/residue: 0.2442 time to fit residues: 34.7434 Evaluate side-chains 108 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 307 ILE Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain H residue 400 ASP Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 380 ILE Chi-restraints excluded: chain J residue 342 THR Chi-restraints excluded: chain J residue 348 CYS 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 415 SER Chi-restraints excluded: chain M residue 319 ARG 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 101 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8186 Z= 0.153 Angle : 0.483 6.545 11168 Z= 0.242 Chirality : 0.039 0.130 1312 Planarity : 0.004 0.061 1466 Dihedral : 3.526 14.646 1136 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.61 % Allowed : 18.32 % 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 (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 (0.27), residues: 1036 helix: 1.39 (0.20), residues: 735 sheet: None (None), residues: 0 loop : -1.28 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 327 HIS 0.005 0.001 HIS K 459 PHE 0.011 0.001 PHE J 386 TYR 0.005 0.001 TYR M 464 ARG 0.004 0.000 ARG L 319 ********************** 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 113 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.906 Fit side-chains REVERT: I 450 GLN cc_start: 0.6893 (tt0) cc_final: 0.6474 (tp-100) REVERT: J 342 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7759 (p) REVERT: J 417 GLN cc_start: 0.7035 (mm-40) cc_final: 0.6500 (mm-40) REVERT: L 415 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7415 (p) REVERT: M 319 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6569 (tmm160) outliers start: 14 outliers final: 11 residues processed: 110 average time/residue: 0.2538 time to fit residues: 36.3889 Evaluate side-chains 111 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 307 ILE 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 I residue 380 ILE Chi-restraints excluded: chain J residue 342 THR 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 415 SER Chi-restraints excluded: chain M residue 319 ARG 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 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.110289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.094745 restraints weight = 11102.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.096690 restraints weight = 8243.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.098159 restraints weight = 6547.820| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8186 Z= 0.163 Angle : 0.495 8.580 11168 Z= 0.245 Chirality : 0.039 0.130 1312 Planarity : 0.004 0.061 1466 Dihedral : 3.512 14.718 1136 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.84 % Allowed : 18.55 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.27), residues: 1036 helix: 1.38 (0.20), residues: 735 sheet: None (None), residues: 0 loop : -1.28 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 327 HIS 0.005 0.001 HIS K 459 PHE 0.008 0.001 PHE J 386 TYR 0.005 0.001 TYR M 464 ARG 0.001 0.000 ARG M 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1828.45 seconds wall clock time: 34 minutes 3.16 seconds (2043.16 seconds total)