Starting phenix.real_space_refine on Thu Feb 13 08:39:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v1q_21015/02_2025/6v1q_21015.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v1q_21015/02_2025/6v1q_21015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v1q_21015/02_2025/6v1q_21015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v1q_21015/02_2025/6v1q_21015.map" model { file = "/net/cci-nas-00/data/ceres_data/6v1q_21015/02_2025/6v1q_21015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v1q_21015/02_2025/6v1q_21015.cif" } resolution = 3.11 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= -0.001 sd= 0.082 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 Na 1 4.78 5 C 5920 2.51 5 N 1402 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8825 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4412 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 17, 'TRANS': 520} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 8.18, per 1000 atoms: 0.93 Number of scatterers: 8825 At special positions: 0 Unit cell: (124.344, 116.808, 97.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 Na 1 11.00 O 1464 8.00 N 1402 7.00 C 5920 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 70.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 63 through 70 Processing helix chain 'A' and resid 71 through 88 removed outlier: 3.641A pdb=" N TYR A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 100 through 126 removed outlier: 3.696A pdb=" N ILE A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 154 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 171 through 179 removed outlier: 3.742A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 220 removed outlier: 3.524A pdb=" N ARG A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Proline residue: A 197 - end of helix removed outlier: 3.976A pdb=" N TYR A 201 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 removed outlier: 3.732A pdb=" N PHE A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.836A pdb=" N PHE A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 300 removed outlier: 3.812A pdb=" N LEU A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 4.862A pdb=" N LYS A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE A 318 " --> pdb=" O MET A 314 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A 319 " --> pdb=" O CYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 415 Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 441 through 457 removed outlier: 3.709A pdb=" N ALA A 447 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TRP A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 490 removed outlier: 3.544A pdb=" N THR A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 484 " --> pdb=" O TRP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.786A pdb=" N ILE A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 500 " --> pdb=" O ASN A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 522 removed outlier: 4.096A pdb=" N ILE A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU A 520 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 543 through 568 removed outlier: 4.197A pdb=" N LEU A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 609 through 622 removed outlier: 3.602A pdb=" N LEU A 616 " --> pdb=" O SER A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 634 removed outlier: 3.504A pdb=" N PHE A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 641 through 653 removed outlier: 3.820A pdb=" N PHE A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 removed outlier: 3.704A pdb=" N PHE A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 46 Processing helix chain 'B' and resid 63 through 70 Processing helix chain 'B' and resid 71 through 88 removed outlier: 3.641A pdb=" N TYR B 79 " --> pdb=" O GLN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 100 through 126 removed outlier: 3.697A pdb=" N ILE B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 154 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 171 through 179 removed outlier: 3.742A pdb=" N LEU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B 176 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 220 removed outlier: 3.524A pdb=" N ARG B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Proline residue: B 197 - end of helix removed outlier: 3.976A pdb=" N TYR B 201 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.733A pdb=" N PHE B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.835A pdb=" N PHE B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 300 removed outlier: 3.813A pdb=" N LEU B 288 " --> pdb=" O MET B 284 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 4.861A pdb=" N LYS B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE B 318 " --> pdb=" O MET B 314 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 319 " --> pdb=" O CYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 415 Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 441 through 457 removed outlier: 3.709A pdb=" N ALA B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TRP B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.544A pdb=" N THR B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 484 " --> pdb=" O TRP B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.787A pdb=" N ILE B 495 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B 500 " --> pdb=" O ASN B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 522 removed outlier: 4.096A pdb=" N ILE B 516 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 522 " --> pdb=" O ARG B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 530 Processing helix chain 'B' and resid 543 through 568 removed outlier: 4.197A pdb=" N LEU B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 567 " --> pdb=" O VAL B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 609 through 622 removed outlier: 3.602A pdb=" N LEU B 616 " --> pdb=" O SER B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 634 removed outlier: 3.504A pdb=" N PHE B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 641 through 653 removed outlier: 3.820A pdb=" N PHE B 645 " --> pdb=" O ALA B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 removed outlier: 3.704A pdb=" N PHE B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1302 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: 2.27 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1286 1.28 - 1.41: 2510 1.41 - 1.54: 5151 1.54 - 1.67: 43 1.67 - 1.81: 66 Bond restraints: 9056 Sorted by residual: bond pdb=" CA PRO A 135 " pdb=" C PRO A 135 " ideal model delta sigma weight residual 1.516 1.411 0.105 1.42e-02 4.96e+03 5.51e+01 bond pdb=" CA PRO B 135 " pdb=" C PRO B 135 " ideal model delta sigma weight residual 1.516 1.411 0.105 1.42e-02 4.96e+03 5.48e+01 bond pdb=" C ASP B 134 " pdb=" O ASP B 134 " ideal model delta sigma weight residual 1.237 1.142 0.095 1.29e-02 6.01e+03 5.43e+01 bond pdb=" C ASP A 134 " pdb=" O ASP A 134 " ideal model delta sigma weight residual 1.237 1.143 0.095 1.29e-02 6.01e+03 5.37e+01 bond pdb=" N LYS B 133 " pdb=" CA LYS B 133 " ideal model delta sigma weight residual 1.456 1.364 0.093 1.33e-02 5.65e+03 4.85e+01 ... (remaining 9051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 12070 3.00 - 5.99: 192 5.99 - 8.99: 32 8.99 - 11.99: 10 11.99 - 14.99: 6 Bond angle restraints: 12310 Sorted by residual: angle pdb=" C ILE A 459 " pdb=" N LEU A 460 " pdb=" CA LEU A 460 " ideal model delta sigma weight residual 121.83 135.59 -13.76 1.48e+00 4.57e-01 8.64e+01 angle pdb=" C ILE B 459 " pdb=" N LEU B 460 " pdb=" CA LEU B 460 " ideal model delta sigma weight residual 121.83 135.58 -13.75 1.48e+00 4.57e-01 8.63e+01 angle pdb=" N TYR B 262 " pdb=" CA TYR B 262 " pdb=" C TYR B 262 " ideal model delta sigma weight residual 114.75 105.22 9.53 1.26e+00 6.30e-01 5.72e+01 angle pdb=" N TYR A 262 " pdb=" CA TYR A 262 " pdb=" C TYR A 262 " ideal model delta sigma weight residual 114.75 105.25 9.50 1.26e+00 6.30e-01 5.68e+01 angle pdb=" CA ILE B 459 " pdb=" C ILE B 459 " pdb=" N LEU B 460 " ideal model delta sigma weight residual 116.60 105.71 10.89 1.45e+00 4.76e-01 5.64e+01 ... (remaining 12305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4513 17.64 - 35.29: 577 35.29 - 52.93: 152 52.93 - 70.57: 26 70.57 - 88.22: 10 Dihedral angle restraints: 5278 sinusoidal: 2072 harmonic: 3206 Sorted by residual: dihedral pdb=" CA LYS A 541 " pdb=" C LYS A 541 " pdb=" N ILE A 542 " pdb=" CA ILE A 542 " ideal model delta harmonic sigma weight residual -180.00 -131.46 -48.54 0 5.00e+00 4.00e-02 9.42e+01 dihedral pdb=" CA LYS B 541 " pdb=" C LYS B 541 " pdb=" N ILE B 542 " pdb=" CA ILE B 542 " ideal model delta harmonic sigma weight residual -180.00 -131.50 -48.50 0 5.00e+00 4.00e-02 9.41e+01 dihedral pdb=" C LEU A 457 " pdb=" N LEU A 457 " pdb=" CA LEU A 457 " pdb=" CB LEU A 457 " ideal model delta harmonic sigma weight residual -122.60 -143.97 21.37 0 2.50e+00 1.60e-01 7.31e+01 ... (remaining 5275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 1438 0.179 - 0.357: 6 0.357 - 0.536: 2 0.536 - 0.715: 2 0.715 - 0.893: 4 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CG LEU B 461 " pdb=" CB LEU B 461 " pdb=" CD1 LEU B 461 " pdb=" CD2 LEU B 461 " both_signs ideal model delta sigma weight residual False -2.59 -1.70 -0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CG LEU A 461 " pdb=" CB LEU A 461 " pdb=" CD1 LEU A 461 " pdb=" CD2 LEU A 461 " both_signs ideal model delta sigma weight residual False -2.59 -1.70 -0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA LEU A 457 " pdb=" N LEU A 457 " pdb=" C LEU A 457 " pdb=" CB LEU A 457 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.91e+01 ... (remaining 1449 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 224 " 1.051 9.50e-02 1.11e+02 4.71e-01 1.34e+02 pdb=" NE ARG A 224 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 224 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 224 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 224 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 224 " -1.051 9.50e-02 1.11e+02 4.71e-01 1.34e+02 pdb=" NE ARG B 224 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG B 224 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 224 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 224 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 456 " -0.038 2.00e-02 2.50e+03 7.23e-02 5.22e+01 pdb=" C MET A 456 " 0.125 2.00e-02 2.50e+03 pdb=" O MET A 456 " -0.046 2.00e-02 2.50e+03 pdb=" N LEU A 457 " -0.041 2.00e-02 2.50e+03 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 10 2.10 - 2.80: 2776 2.80 - 3.50: 12517 3.50 - 4.20: 21187 4.20 - 4.90: 36947 Nonbonded interactions: 73437 Sorted by model distance: nonbonded pdb=" NH2 ARG A 224 " pdb=" OE1 GLU B 440 " model vdw 1.396 3.120 nonbonded pdb=" OE1 GLU A 440 " pdb=" NH2 ARG B 224 " model vdw 1.396 3.120 nonbonded pdb=" NZ LYS A 219 " pdb=" OD2 ASP B 438 " model vdw 1.777 3.120 nonbonded pdb=" OD2 ASP A 438 " pdb=" NZ LYS B 219 " model vdw 1.786 3.120 nonbonded pdb=" NZ LYS A 223 " pdb=" OE2 GLU B 439 " model vdw 1.852 3.120 ... (remaining 73432 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 'A' and resid 34 through 672) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.040 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 : 0.008 0.105 9056 Z= 0.534 Angle : 1.007 14.986 12310 Z= 0.596 Chirality : 0.073 0.893 1452 Planarity : 0.018 0.471 1482 Dihedral : 17.131 88.216 3198 Min Nonbonded Distance : 1.396 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.40 % Favored : 90.23 % Rotamer: Outliers : 7.48 % Allowed : 18.14 % Favored : 74.39 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -4.86 (0.21), residues: 1064 helix: -2.97 (0.15), residues: 686 sheet: None (None), residues: 0 loop : -3.44 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 626 HIS 0.003 0.001 HIS B 121 PHE 0.010 0.001 PHE B 420 TYR 0.015 0.002 TYR B 163 ARG 0.004 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 77 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5619 (ttmt) REVERT: A 441 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8610 (p0) REVERT: A 541 LYS cc_start: 0.2714 (OUTLIER) cc_final: 0.2039 (mmtt) REVERT: A 546 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8202 (tp) REVERT: B 223 LYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5662 (ttmt) REVERT: B 441 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8481 (p0) REVERT: B 541 LYS cc_start: 0.2774 (OUTLIER) cc_final: 0.2056 (mmtt) REVERT: B 546 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8294 (tp) outliers start: 73 outliers final: 35 residues processed: 146 average time/residue: 0.2102 time to fit residues: 42.8331 Evaluate side-chains 100 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 57 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 532 PHE Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 587 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 263 ASN A 279 ASN A 649 HIS A 658 ASN B 194 ASN B 263 ASN B 279 ASN ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 HIS B 658 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.064492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.055858 restraints weight = 44772.725| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.62 r_work: 0.3168 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9056 Z= 0.195 Angle : 0.705 10.625 12310 Z= 0.369 Chirality : 0.044 0.153 1452 Planarity : 0.005 0.043 1482 Dihedral : 9.704 57.018 1274 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 5.74 % Allowed : 19.88 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.81 (0.25), residues: 1064 helix: -1.31 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -2.74 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 478 HIS 0.003 0.001 HIS B 71 PHE 0.020 0.001 PHE A 560 TYR 0.014 0.001 TYR A 424 ARG 0.005 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 70 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.9131 (ttp) cc_final: 0.8902 (ttp) REVERT: A 647 ILE cc_start: 0.9720 (mt) cc_final: 0.9510 (pt) REVERT: B 461 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.4906 (tp) REVERT: B 565 MET cc_start: 0.8860 (ptp) cc_final: 0.8559 (ptp) REVERT: B 647 ILE cc_start: 0.9731 (mt) cc_final: 0.9479 (pt) outliers start: 56 outliers final: 20 residues processed: 118 average time/residue: 0.1937 time to fit residues: 32.8001 Evaluate side-chains 84 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.063034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.054055 restraints weight = 46466.775| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.62 r_work: 0.3120 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9056 Z= 0.329 Angle : 0.722 9.654 12310 Z= 0.382 Chirality : 0.046 0.285 1452 Planarity : 0.004 0.024 1482 Dihedral : 7.505 54.836 1200 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.48 % Allowed : 21.31 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.97 (0.26), residues: 1064 helix: -0.61 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -2.54 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 626 HIS 0.002 0.001 HIS A 121 PHE 0.015 0.001 PHE B 560 TYR 0.030 0.002 TYR B 201 ARG 0.005 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 59 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 22 residues processed: 89 average time/residue: 0.1903 time to fit residues: 25.0488 Evaluate side-chains 75 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 101 optimal weight: 0.0370 chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.064701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.056119 restraints weight = 46436.246| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.67 r_work: 0.3196 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9056 Z= 0.161 Angle : 0.631 7.902 12310 Z= 0.328 Chirality : 0.043 0.224 1452 Planarity : 0.003 0.022 1482 Dihedral : 6.625 48.338 1190 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.38 % Allowed : 21.00 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.78 (0.26), residues: 1064 helix: -0.37 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.70 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 626 HIS 0.002 0.001 HIS B 501 PHE 0.016 0.001 PHE A 560 TYR 0.018 0.001 TYR A 201 ARG 0.003 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8253 (t0) REVERT: A 151 MET cc_start: 0.9063 (ttp) cc_final: 0.8837 (ttp) REVERT: A 201 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: A 562 MET cc_start: 0.9542 (mmp) cc_final: 0.9148 (mmp) REVERT: A 573 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.9009 (pm20) REVERT: B 70 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8299 (t0) REVERT: B 201 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.7130 (m-80) REVERT: B 562 MET cc_start: 0.9526 (mmp) cc_final: 0.9150 (mmp) REVERT: B 573 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.9018 (pm20) outliers start: 33 outliers final: 11 residues processed: 94 average time/residue: 0.1627 time to fit residues: 23.3460 Evaluate side-chains 71 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 0.0000 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN B 70 ASN ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.065154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.056775 restraints weight = 45865.226| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.65 r_work: 0.3214 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9056 Z= 0.159 Angle : 0.629 7.659 12310 Z= 0.322 Chirality : 0.043 0.228 1452 Planarity : 0.003 0.021 1482 Dihedral : 6.070 46.104 1180 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.38 % Allowed : 22.03 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.62 (0.26), residues: 1064 helix: -0.23 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -2.72 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 626 HIS 0.005 0.001 HIS A 71 PHE 0.017 0.001 PHE B 560 TYR 0.016 0.001 TYR A 424 ARG 0.003 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 1.074 Fit side-chains REVERT: A 70 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8186 (t0) REVERT: A 108 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8664 (pt0) REVERT: A 151 MET cc_start: 0.9043 (ttp) cc_final: 0.8692 (ttp) REVERT: A 201 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: A 461 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.5696 (tt) REVERT: A 573 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.9063 (pm20) REVERT: B 70 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8279 (t0) REVERT: B 201 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.7141 (m-80) REVERT: B 461 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.5870 (tt) REVERT: B 565 MET cc_start: 0.9290 (mtp) cc_final: 0.9043 (mtp) REVERT: B 573 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.9051 (pm20) outliers start: 33 outliers final: 9 residues processed: 94 average time/residue: 0.1773 time to fit residues: 24.4794 Evaluate side-chains 72 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 99 optimal weight: 0.0770 chunk 44 optimal weight: 8.9990 chunk 93 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.064948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.056508 restraints weight = 45594.017| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.69 r_work: 0.3203 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9056 Z= 0.180 Angle : 0.629 7.998 12310 Z= 0.324 Chirality : 0.043 0.217 1452 Planarity : 0.003 0.020 1482 Dihedral : 5.623 45.372 1176 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.28 % Allowed : 23.05 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.33 (0.27), residues: 1064 helix: 0.03 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -2.65 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 478 HIS 0.003 0.001 HIS A 649 PHE 0.014 0.001 PHE B 560 TYR 0.017 0.001 TYR A 201 ARG 0.003 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 1.011 Fit side-chains REVERT: A 70 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8188 (t0) REVERT: A 151 MET cc_start: 0.9091 (ttp) cc_final: 0.8856 (ttp) REVERT: A 201 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.7016 (m-10) REVERT: A 461 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.5804 (tt) REVERT: A 573 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.9035 (pm20) REVERT: B 70 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8161 (t0) REVERT: B 201 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: B 461 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6441 (tt) REVERT: B 565 MET cc_start: 0.9294 (mtp) cc_final: 0.9065 (mtp) REVERT: B 573 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.9029 (pm20) outliers start: 32 outliers final: 11 residues processed: 86 average time/residue: 0.1747 time to fit residues: 22.7616 Evaluate side-chains 74 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 0.0270 chunk 37 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 70 ASN ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.065049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.056321 restraints weight = 46282.836| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.74 r_work: 0.3196 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9056 Z= 0.189 Angle : 0.627 8.289 12310 Z= 0.324 Chirality : 0.043 0.226 1452 Planarity : 0.003 0.028 1482 Dihedral : 5.558 44.294 1176 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.38 % Allowed : 24.18 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.16 (0.27), residues: 1064 helix: 0.13 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.55 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 478 HIS 0.004 0.001 HIS B 71 PHE 0.014 0.001 PHE B 560 TYR 0.017 0.001 TYR A 201 ARG 0.002 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.967 Fit side-chains REVERT: A 70 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8251 (t0) REVERT: A 74 MET cc_start: 0.8681 (mmm) cc_final: 0.8188 (mpp) REVERT: A 151 MET cc_start: 0.9104 (ttp) cc_final: 0.8862 (ttp) REVERT: A 201 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.7196 (m-10) REVERT: A 461 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6163 (tt) REVERT: A 573 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.9012 (pm20) REVERT: B 70 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8241 (t0) REVERT: B 201 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.7200 (m-10) REVERT: B 461 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6401 (tt) REVERT: B 565 MET cc_start: 0.9260 (mtp) cc_final: 0.9029 (mtp) REVERT: B 573 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.9006 (pm20) outliers start: 33 outliers final: 14 residues processed: 91 average time/residue: 0.1863 time to fit residues: 24.9258 Evaluate side-chains 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 0.0060 chunk 81 optimal weight: 3.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 70 ASN ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.065211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.056621 restraints weight = 46097.363| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.74 r_work: 0.3205 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9056 Z= 0.165 Angle : 0.622 8.343 12310 Z= 0.318 Chirality : 0.043 0.199 1452 Planarity : 0.003 0.028 1482 Dihedral : 5.494 43.238 1176 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.66 % Allowed : 24.39 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.08 (0.27), residues: 1064 helix: 0.20 (0.21), residues: 700 sheet: None (None), residues: 0 loop : -2.53 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 478 HIS 0.004 0.001 HIS A 71 PHE 0.014 0.001 PHE B 560 TYR 0.016 0.001 TYR A 201 ARG 0.007 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 1.077 Fit side-chains REVERT: A 70 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8230 (t0) REVERT: A 108 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8601 (pt0) REVERT: A 151 MET cc_start: 0.9065 (ttp) cc_final: 0.8746 (ttp) REVERT: A 186 ARG cc_start: 0.8573 (ptt90) cc_final: 0.7844 (tpt170) REVERT: A 201 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.7206 (m-10) REVERT: A 461 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6040 (tt) REVERT: A 573 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.9006 (pm20) REVERT: B 70 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8204 (t0) REVERT: B 201 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.7233 (m-10) REVERT: B 461 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6186 (tt) REVERT: B 573 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.9004 (pm20) outliers start: 26 outliers final: 12 residues processed: 88 average time/residue: 0.1648 time to fit residues: 22.5013 Evaluate side-chains 79 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 625 GLN B 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.065479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.056684 restraints weight = 45808.943| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.76 r_work: 0.3205 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9056 Z= 0.175 Angle : 0.631 8.855 12310 Z= 0.321 Chirality : 0.043 0.196 1452 Planarity : 0.003 0.027 1482 Dihedral : 5.453 42.580 1176 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.87 % Allowed : 24.90 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.03 (0.27), residues: 1064 helix: 0.23 (0.21), residues: 700 sheet: None (None), residues: 0 loop : -2.49 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 72 HIS 0.003 0.001 HIS A 649 PHE 0.013 0.001 PHE B 560 TYR 0.016 0.001 TYR B 201 ARG 0.006 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 1.027 Fit side-chains REVERT: A 70 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8323 (t0) REVERT: A 108 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8592 (pt0) REVERT: A 151 MET cc_start: 0.9052 (ttp) cc_final: 0.8748 (ttp) REVERT: A 186 ARG cc_start: 0.8552 (ptt90) cc_final: 0.7846 (tpt170) REVERT: A 201 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.7265 (m-10) REVERT: A 461 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6002 (tt) REVERT: A 573 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.9005 (pm20) REVERT: B 70 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8311 (t0) REVERT: B 186 ARG cc_start: 0.8572 (ptt90) cc_final: 0.7830 (tpt170) REVERT: B 201 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7313 (m-10) REVERT: B 461 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6030 (tt) REVERT: B 573 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.9002 (pm20) outliers start: 28 outliers final: 16 residues processed: 83 average time/residue: 0.1801 time to fit residues: 22.6240 Evaluate side-chains 84 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 90 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 73 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.065349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.056627 restraints weight = 45787.496| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.72 r_work: 0.3206 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9056 Z= 0.172 Angle : 0.639 9.149 12310 Z= 0.324 Chirality : 0.043 0.189 1452 Planarity : 0.003 0.026 1482 Dihedral : 5.429 42.150 1176 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.77 % Allowed : 25.00 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.06 (0.27), residues: 1064 helix: 0.18 (0.21), residues: 712 sheet: None (None), residues: 0 loop : -2.51 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 626 HIS 0.003 0.001 HIS A 649 PHE 0.013 0.001 PHE B 560 TYR 0.016 0.001 TYR B 201 ARG 0.005 0.000 ARG B 518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.987 Fit side-chains REVERT: A 70 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8346 (t0) REVERT: A 108 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8611 (pt0) REVERT: A 151 MET cc_start: 0.9035 (ttp) cc_final: 0.8735 (ttp) REVERT: A 201 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7199 (m-10) REVERT: A 461 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.5971 (tt) REVERT: A 573 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8994 (pm20) REVERT: B 70 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8329 (t0) REVERT: B 201 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.7242 (m-10) REVERT: B 461 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6066 (tt) REVERT: B 573 GLN cc_start: 0.9326 (OUTLIER) cc_final: 0.9036 (pm20) REVERT: B 655 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.9274 (mp) REVERT: B 670 VAL cc_start: 0.9255 (t) cc_final: 0.9048 (m) outliers start: 27 outliers final: 15 residues processed: 80 average time/residue: 0.1543 time to fit residues: 19.7226 Evaluate side-chains 79 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 1 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN B 70 ASN ** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.066015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.057180 restraints weight = 46115.215| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.75 r_work: 0.3230 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9056 Z= 0.150 Angle : 0.631 9.108 12310 Z= 0.318 Chirality : 0.042 0.169 1452 Planarity : 0.003 0.026 1482 Dihedral : 5.339 41.362 1176 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.46 % Allowed : 25.41 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.08 (0.27), residues: 1064 helix: 0.19 (0.21), residues: 710 sheet: None (None), residues: 0 loop : -2.58 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 72 HIS 0.003 0.001 HIS A 649 PHE 0.013 0.001 PHE B 560 TYR 0.015 0.001 TYR A 201 ARG 0.005 0.000 ARG B 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3945.01 seconds wall clock time: 70 minutes 54.81 seconds (4254.81 seconds total)