Starting phenix.real_space_refine on Fri Jul 19 18:01:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/07_2024/8t57_41044.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/07_2024/8t57_41044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/07_2024/8t57_41044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/07_2024/8t57_41044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/07_2024/8t57_41044.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t57_41044/07_2024/8t57_41044.cif" } resolution = 2.7 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= 0.004 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 26 5.16 5 C 5752 2.51 5 N 1270 2.21 5 O 1418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8466 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4033 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 29, 'TRANS': 474} Chain breaks: 5 Chain: "B" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4033 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 29, 'TRANS': 474} Chain breaks: 5 Chain: "A" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Unusual residues: {'CLR': 2, 'PLM': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Unusual residues: {'CLR': 2, 'PLM': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 5.00, per 1000 atoms: 0.59 Number of scatterers: 8466 At special positions: 0 Unit cell: (85.49, 120.51, 85.49, 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 26 16.00 O 1418 8.00 N 1270 7.00 C 5752 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 - 3.50 Amino acid : False - 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: 3.39 Conformation dependent library (CDL) restraints added in 1.4 seconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 80.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 2 through 25 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 73 through 81 Processing helix chain 'A' and resid 82 through 109 Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 130 through 139 removed outlier: 6.746A pdb=" N ILE A 136 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A 137 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 182 removed outlier: 3.611A pdb=" N HIS A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 310 through 320 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.783A pdb=" N VAL A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 347 removed outlier: 3.614A pdb=" N ALA A 347 " --> pdb=" O PHE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 368 Processing helix chain 'A' and resid 411 through 420 removed outlier: 3.502A pdb=" N PHE A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 437 through 457 Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 475 through 478 removed outlier: 6.597A pdb=" N LYS A 478 " --> pdb=" O LEU A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 491 through 512 Processing helix chain 'A' and resid 540 through 562 Proline residue: A 546 - end of helix removed outlier: 3.908A pdb=" N PHE A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 587 Processing helix chain 'A' and resid 598 through 624 Processing helix chain 'A' and resid 626 through 633 Processing helix chain 'A' and resid 634 through 651 removed outlier: 3.565A pdb=" N VAL A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 656 Processing helix chain 'A' and resid 659 through 674 removed outlier: 3.671A pdb=" N ARG A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 removed outlier: 4.083A pdb=" N SER A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 82 through 109 Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 130 through 139 removed outlier: 6.746A pdb=" N ILE B 136 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER B 137 " --> pdb=" O PHE B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 182 removed outlier: 3.611A pdb=" N HIS B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.782A pdb=" N VAL B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 347 removed outlier: 3.614A pdb=" N ALA B 347 " --> pdb=" O PHE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 368 Processing helix chain 'B' and resid 411 through 420 removed outlier: 3.502A pdb=" N PHE B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 431 Processing helix chain 'B' and resid 437 through 457 Processing helix chain 'B' and resid 457 through 463 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 475 through 478 removed outlier: 6.598A pdb=" N LYS B 478 " --> pdb=" O LEU B 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 475 through 478' Processing helix chain 'B' and resid 479 through 486 Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 491 through 512 Processing helix chain 'B' and resid 540 through 562 Proline residue: B 546 - end of helix removed outlier: 3.909A pdb=" N PHE B 560 " --> pdb=" O ILE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 587 Processing helix chain 'B' and resid 598 through 624 Processing helix chain 'B' and resid 626 through 633 Processing helix chain 'B' and resid 634 through 651 removed outlier: 3.565A pdb=" N VAL B 638 " --> pdb=" O ILE B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 656 Processing helix chain 'B' and resid 659 through 674 removed outlier: 3.670A pdb=" N ARG B 672 " --> pdb=" O LYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 684 removed outlier: 4.083A pdb=" N SER B 681 " --> pdb=" O SER B 677 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 224 removed outlier: 3.897A pdb=" N SER A 222 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 220 through 224 removed outlier: 3.897A pdb=" N SER B 222 " --> pdb=" O SER B 307 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1671 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: 2.38 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1283 1.30 - 1.43: 2361 1.43 - 1.55: 4707 1.55 - 1.67: 301 1.67 - 1.80: 40 Bond restraints: 8692 Sorted by residual: bond pdb=" C10 CLR B 802 " pdb=" C9 CLR B 802 " ideal model delta sigma weight residual 1.551 1.715 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" C10 CLR A 802 " pdb=" C9 CLR A 802 " ideal model delta sigma weight residual 1.551 1.715 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" C4 CLR B 802 " pdb=" C5 CLR B 802 " ideal model delta sigma weight residual 1.506 1.660 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C4 CLR A 802 " pdb=" C5 CLR A 802 " ideal model delta sigma weight residual 1.506 1.659 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C10 CLR A 801 " pdb=" C9 CLR A 801 " ideal model delta sigma weight residual 1.551 1.704 -0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 8687 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.41: 260 105.41 - 112.58: 4273 112.58 - 119.76: 3518 119.76 - 126.93: 3639 126.93 - 134.10: 90 Bond angle restraints: 11780 Sorted by residual: angle pdb=" C SER B 562 " pdb=" N PRO B 563 " pdb=" CA PRO B 563 " ideal model delta sigma weight residual 119.56 128.55 -8.99 1.02e+00 9.61e-01 7.77e+01 angle pdb=" C SER A 562 " pdb=" N PRO A 563 " pdb=" CA PRO A 563 " ideal model delta sigma weight residual 119.56 128.53 -8.97 1.02e+00 9.61e-01 7.74e+01 angle pdb=" C TYR A 658 " pdb=" N PRO A 659 " pdb=" CA PRO A 659 " ideal model delta sigma weight residual 120.21 127.68 -7.47 9.60e-01 1.09e+00 6.06e+01 angle pdb=" C TYR B 658 " pdb=" N PRO B 659 " pdb=" CA PRO B 659 " ideal model delta sigma weight residual 120.21 127.65 -7.44 9.60e-01 1.09e+00 6.01e+01 angle pdb=" C LEU A 410 " pdb=" N PRO A 411 " pdb=" CA PRO A 411 " ideal model delta sigma weight residual 119.82 127.26 -7.44 9.80e-01 1.04e+00 5.76e+01 ... (remaining 11775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 4982 15.82 - 31.64: 250 31.64 - 47.46: 46 47.46 - 63.28: 34 63.28 - 79.09: 4 Dihedral angle restraints: 5316 sinusoidal: 2338 harmonic: 2978 Sorted by residual: dihedral pdb=" N LEU A 652 " pdb=" C LEU A 652 " pdb=" CA LEU A 652 " pdb=" CB LEU A 652 " ideal model delta harmonic sigma weight residual 122.80 131.22 -8.42 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" N LEU B 652 " pdb=" C LEU B 652 " pdb=" CA LEU B 652 " pdb=" CB LEU B 652 " ideal model delta harmonic sigma weight residual 122.80 131.16 -8.36 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" C TRP B 599 " pdb=" N TRP B 599 " pdb=" CA TRP B 599 " pdb=" CB TRP B 599 " ideal model delta harmonic sigma weight residual -122.60 -130.71 8.11 0 2.50e+00 1.60e-01 1.05e+01 ... (remaining 5313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 912 0.102 - 0.203: 338 0.203 - 0.304: 80 0.304 - 0.406: 16 0.406 - 0.507: 16 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CB ILE B 26 " pdb=" CA ILE B 26 " pdb=" CG1 ILE B 26 " pdb=" CG2 ILE B 26 " both_signs ideal model delta sigma weight residual False 2.64 3.15 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" CB ILE A 26 " pdb=" CA ILE A 26 " pdb=" CG1 ILE A 26 " pdb=" CG2 ILE A 26 " both_signs ideal model delta sigma weight residual False 2.64 3.15 -0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" CB ILE B 368 " pdb=" CA ILE B 368 " pdb=" CG1 ILE B 368 " pdb=" CG2 ILE B 368 " both_signs ideal model delta sigma weight residual False 2.64 3.13 -0.49 2.00e-01 2.50e+01 5.97e+00 ... (remaining 1359 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 24 " -0.052 2.00e-02 2.50e+03 3.15e-02 1.98e+01 pdb=" CG TYR B 24 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 24 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 24 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 24 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 24 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR B 24 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 24 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 24 " 0.052 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR A 24 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR A 24 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 24 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 24 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 24 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 24 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 24 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 215 " -0.059 2.00e-02 2.50e+03 2.98e-02 1.78e+01 pdb=" CG TYR B 215 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 215 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 215 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR B 215 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 215 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 215 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 215 " -0.037 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3280 2.89 - 3.39: 8658 3.39 - 3.89: 14173 3.89 - 4.40: 18020 4.40 - 4.90: 27840 Nonbonded interactions: 71971 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" NZ LYS A 174 " model vdw 2.385 2.520 nonbonded pdb=" OD1 ASP B 75 " pdb=" NZ LYS B 174 " model vdw 2.385 2.520 nonbonded pdb=" CB GLU A 510 " pdb=" OE1 GLU A 510 " model vdw 2.412 2.752 nonbonded pdb=" CB GLU B 510 " pdb=" OE1 GLU B 510 " model vdw 2.412 2.752 nonbonded pdb=" N PRO A 335 " pdb=" O PRO A 335 " model vdw 2.508 2.496 ... (remaining 71966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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: 0.450 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.510 Find NCS groups from input model: 0.320 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:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.027 0.164 8692 Z= 1.715 Angle : 1.654 11.819 11780 Z= 1.110 Chirality : 0.120 0.507 1362 Planarity : 0.008 0.031 1398 Dihedral : 11.192 79.094 3380 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.77 (0.25), residues: 984 helix: 0.45 (0.18), residues: 706 sheet: 2.58 (0.99), residues: 24 loop : 0.92 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.007 TRP A 599 HIS 0.007 0.003 HIS A 614 PHE 0.039 0.006 PHE A 99 TYR 0.059 0.009 TYR B 215 ARG 0.005 0.001 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.026 Fit side-chains REVERT: A 426 MET cc_start: 0.8327 (mmt) cc_final: 0.7787 (mmt) REVERT: B 426 MET cc_start: 0.8314 (mmt) cc_final: 0.7575 (mmt) outliers start: 0 outliers final: 2 residues processed: 151 average time/residue: 0.9667 time to fit residues: 158.3127 Evaluate side-chains 68 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 109 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 543 GLN B 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8692 Z= 0.246 Angle : 0.620 6.461 11780 Z= 0.321 Chirality : 0.046 0.151 1362 Planarity : 0.005 0.037 1398 Dihedral : 9.754 57.938 1566 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.43 % Allowed : 8.30 % Favored : 89.27 % 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: 1.97 (0.26), residues: 984 helix: 1.66 (0.19), residues: 694 sheet: 1.38 (1.09), residues: 24 loop : 0.55 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 599 HIS 0.008 0.002 HIS B 223 PHE 0.023 0.002 PHE A 415 TYR 0.019 0.002 TYR B 577 ARG 0.002 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.964 Fit side-chains REVERT: B 426 MET cc_start: 0.7931 (mmt) cc_final: 0.7689 (mmt) REVERT: B 594 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7926 (t) outliers start: 22 outliers final: 11 residues processed: 102 average time/residue: 0.9220 time to fit residues: 102.5417 Evaluate side-chains 72 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 594 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.0470 chunk 31 optimal weight: 0.0770 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 0.5836 ------------------------------------------------------------------------------- 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: 0.7904 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8692 Z= 0.185 Angle : 0.538 8.232 11780 Z= 0.278 Chirality : 0.042 0.137 1362 Planarity : 0.005 0.042 1398 Dihedral : 9.048 58.858 1566 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.77 % Allowed : 9.51 % Favored : 87.72 % 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: 2.30 (0.27), residues: 984 helix: 1.97 (0.19), residues: 686 sheet: 1.59 (1.15), residues: 24 loop : 0.51 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 504 HIS 0.002 0.001 HIS B 223 PHE 0.018 0.001 PHE A 99 TYR 0.018 0.002 TYR B 170 ARG 0.002 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 0.903 Fit side-chains REVERT: A 585 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6628 (mt) REVERT: B 585 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6280 (mt) outliers start: 25 outliers final: 10 residues processed: 95 average time/residue: 0.7972 time to fit residues: 84.2671 Evaluate side-chains 78 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 688 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7917 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8692 Z= 0.193 Angle : 0.526 9.091 11780 Z= 0.269 Chirality : 0.042 0.134 1362 Planarity : 0.005 0.045 1398 Dihedral : 8.937 59.941 1562 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.99 % Allowed : 10.07 % Favored : 86.95 % 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: 2.40 (0.27), residues: 984 helix: 2.02 (0.19), residues: 686 sheet: 1.33 (1.14), residues: 24 loop : 0.65 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 504 HIS 0.002 0.001 HIS B 168 PHE 0.024 0.001 PHE A 415 TYR 0.014 0.002 TYR B 170 ARG 0.001 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 0.990 Fit side-chains REVERT: A 585 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6485 (mt) REVERT: B 585 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6370 (mt) outliers start: 27 outliers final: 16 residues processed: 88 average time/residue: 0.8791 time to fit residues: 85.0113 Evaluate side-chains 82 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 418 PHE Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7918 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8692 Z= 0.193 Angle : 0.533 9.618 11780 Z= 0.268 Chirality : 0.042 0.131 1362 Planarity : 0.005 0.048 1398 Dihedral : 8.702 59.954 1562 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.54 % Allowed : 10.62 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.49 (0.27), residues: 984 helix: 2.10 (0.19), residues: 686 sheet: 0.05 (1.01), residues: 30 loop : 0.83 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 504 HIS 0.002 0.001 HIS B 223 PHE 0.017 0.001 PHE A 99 TYR 0.012 0.001 TYR B 170 ARG 0.002 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 1.012 Fit side-chains REVERT: A 426 MET cc_start: 0.8098 (mmt) cc_final: 0.7687 (mmt) REVERT: A 585 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6373 (mt) REVERT: B 426 MET cc_start: 0.8055 (mmt) cc_final: 0.7638 (mmt) REVERT: B 585 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6312 (mt) outliers start: 23 outliers final: 10 residues processed: 95 average time/residue: 0.7614 time to fit residues: 80.1873 Evaluate side-chains 81 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 50 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.7895 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8692 Z= 0.162 Angle : 0.509 9.691 11780 Z= 0.255 Chirality : 0.041 0.139 1362 Planarity : 0.005 0.051 1398 Dihedral : 8.475 58.216 1562 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.65 % Allowed : 10.95 % Favored : 86.39 % 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: 2.64 (0.27), residues: 984 helix: 2.22 (0.20), residues: 688 sheet: 0.05 (1.01), residues: 30 loop : 0.87 (0.42), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 504 HIS 0.001 0.001 HIS B 168 PHE 0.024 0.001 PHE B 415 TYR 0.011 0.001 TYR A 572 ARG 0.001 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 0.952 Fit side-chains REVERT: A 426 MET cc_start: 0.8069 (mmt) cc_final: 0.7760 (mmt) REVERT: A 474 PHE cc_start: 0.7551 (m-80) cc_final: 0.7282 (m-10) REVERT: B 426 MET cc_start: 0.8009 (mmt) cc_final: 0.7574 (mmt) outliers start: 24 outliers final: 16 residues processed: 95 average time/residue: 0.7891 time to fit residues: 82.7893 Evaluate side-chains 88 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN B 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8692 Z= 0.188 Angle : 0.525 8.927 11780 Z= 0.264 Chirality : 0.042 0.188 1362 Planarity : 0.005 0.054 1398 Dihedral : 8.525 59.895 1562 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.88 % Allowed : 10.95 % Favored : 86.17 % 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: 2.57 (0.27), residues: 984 helix: 2.16 (0.20), residues: 688 sheet: -0.15 (1.02), residues: 30 loop : 0.85 (0.42), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 504 HIS 0.002 0.001 HIS B 223 PHE 0.018 0.001 PHE B 99 TYR 0.015 0.001 TYR A 469 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 74 time to evaluate : 0.957 Fit side-chains REVERT: A 426 MET cc_start: 0.8056 (mmt) cc_final: 0.7623 (mmt) REVERT: A 474 PHE cc_start: 0.7500 (m-80) cc_final: 0.7256 (m-10) REVERT: B 426 MET cc_start: 0.8032 (mmt) cc_final: 0.7701 (mmt) outliers start: 26 outliers final: 20 residues processed: 93 average time/residue: 0.7747 time to fit residues: 79.8361 Evaluate side-chains 91 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 TRP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 688 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7925 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8692 Z= 0.194 Angle : 0.536 10.581 11780 Z= 0.267 Chirality : 0.043 0.195 1362 Planarity : 0.005 0.055 1398 Dihedral : 8.546 58.908 1562 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.54 % Allowed : 11.50 % Favored : 85.95 % 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: 2.49 (0.27), residues: 984 helix: 2.11 (0.19), residues: 688 sheet: -0.36 (1.01), residues: 30 loop : 0.84 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 504 HIS 0.002 0.001 HIS B 223 PHE 0.023 0.001 PHE A 415 TYR 0.015 0.001 TYR B 469 ARG 0.001 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.980 Fit side-chains REVERT: A 413 LEU cc_start: 0.8742 (tp) cc_final: 0.8458 (mt) REVERT: A 426 MET cc_start: 0.8051 (mmt) cc_final: 0.7637 (mmt) REVERT: A 474 PHE cc_start: 0.7464 (m-80) cc_final: 0.7248 (m-10) REVERT: B 426 MET cc_start: 0.8028 (mmt) cc_final: 0.7543 (mmt) outliers start: 23 outliers final: 17 residues processed: 91 average time/residue: 0.8634 time to fit residues: 86.5910 Evaluate side-chains 88 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 TRP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 688 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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: 0.7913 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8692 Z= 0.179 Angle : 0.544 10.384 11780 Z= 0.270 Chirality : 0.043 0.245 1362 Planarity : 0.005 0.056 1398 Dihedral : 8.444 58.354 1562 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.10 % Allowed : 12.17 % Favored : 85.73 % 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: 2.54 (0.27), residues: 984 helix: 2.15 (0.20), residues: 688 sheet: -0.36 (1.01), residues: 30 loop : 0.83 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 504 HIS 0.002 0.001 HIS A 223 PHE 0.017 0.001 PHE A 99 TYR 0.016 0.001 TYR A 469 ARG 0.001 0.000 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.888 Fit side-chains REVERT: A 426 MET cc_start: 0.8095 (mmt) cc_final: 0.7639 (mmt) REVERT: A 474 PHE cc_start: 0.7422 (m-80) cc_final: 0.7214 (m-10) REVERT: B 426 MET cc_start: 0.8065 (mmt) cc_final: 0.7663 (mmt) outliers start: 19 outliers final: 14 residues processed: 88 average time/residue: 0.8027 time to fit residues: 77.9091 Evaluate side-chains 87 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 TRP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 688 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.7985 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8692 Z= 0.323 Angle : 0.606 10.267 11780 Z= 0.303 Chirality : 0.046 0.275 1362 Planarity : 0.005 0.058 1398 Dihedral : 8.983 59.521 1562 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.66 % Allowed : 12.94 % Favored : 85.40 % 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: 2.13 (0.27), residues: 984 helix: 1.88 (0.19), residues: 686 sheet: -0.81 (1.03), residues: 30 loop : 0.62 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 504 HIS 0.003 0.001 HIS B 223 PHE 0.024 0.002 PHE A 99 TYR 0.015 0.002 TYR A 577 ARG 0.002 0.000 ARG A 311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 1.049 Fit side-chains REVERT: A 426 MET cc_start: 0.8112 (mmt) cc_final: 0.7739 (mmt) REVERT: A 474 PHE cc_start: 0.7447 (m-80) cc_final: 0.7240 (m-10) REVERT: B 426 MET cc_start: 0.8096 (mmt) cc_final: 0.7695 (mmt) outliers start: 15 outliers final: 13 residues processed: 84 average time/residue: 0.8605 time to fit residues: 79.7370 Evaluate side-chains 82 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 504 TRP Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 504 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.126442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102957 restraints weight = 12792.256| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.89 r_work: 0.3331 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8692 Z= 0.215 Angle : 0.559 10.153 11780 Z= 0.280 Chirality : 0.044 0.260 1362 Planarity : 0.005 0.061 1398 Dihedral : 8.774 58.266 1562 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.44 % Allowed : 13.27 % Favored : 85.29 % 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: 2.27 (0.27), residues: 984 helix: 2.00 (0.19), residues: 686 sheet: -0.73 (1.04), residues: 30 loop : 0.62 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 504 HIS 0.003 0.001 HIS B 223 PHE 0.019 0.001 PHE B 99 TYR 0.017 0.001 TYR A 469 ARG 0.001 0.000 ARG A 311 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2528.43 seconds wall clock time: 45 minutes 18.88 seconds (2718.88 seconds total)