Starting phenix.real_space_refine on Tue Feb 13 15:48:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afe_15395/02_2024/8afe_15395.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afe_15395/02_2024/8afe_15395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afe_15395/02_2024/8afe_15395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afe_15395/02_2024/8afe_15395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afe_15395/02_2024/8afe_15395.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afe_15395/02_2024/8afe_15395.pdb" } resolution = 3.3 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= 0.012 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 23 5.16 5 C 4124 2.51 5 N 1282 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 431": "OE1" <-> "OE2" Residue "D ARG 808": "NH1" <-> "NH2" Residue "D ARG 839": "NH1" <-> "NH2" Residue "D ARG 873": "NH1" <-> "NH2" Residue "C ARG 808": "NH1" <-> "NH2" Residue "C ARG 839": "NH1" <-> "NH2" Residue "C ARG 873": "NH1" <-> "NH2" Residue "H GLU 431": "OE1" <-> "OE2" Residue "I ARG 808": "NH1" <-> "NH2" Residue "I ARG 839": "NH1" <-> "NH2" Residue "I ARG 873": "NH1" <-> "NH2" Residue "J ARG 808": "NH1" <-> "NH2" Residue "J ARG 839": "NH1" <-> "NH2" Residue "J ARG 873": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6785 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'TRANS': 95} Chain: "B" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 747 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 333 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "H" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 299 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "I" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 860 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Time building chain proxies: 4.11, per 1000 atoms: 0.61 Number of scatterers: 6785 At special positions: 0 Unit cell: (63.6, 242.475, 88.775, 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 23 16.00 O 1356 8.00 N 1282 7.00 C 4124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 795 " - pdb=" SG CYS D 868 " distance=2.03 Simple disulfide: pdb=" SG CYS C 795 " - pdb=" SG CYS C 868 " distance=2.03 Simple disulfide: pdb=" SG CYS I 795 " - pdb=" SG CYS I 868 " distance=2.03 Simple disulfide: pdb=" SG CYS J 795 " - pdb=" SG CYS J 868 " distance=2.03 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: 2.31 Conformation dependent library (CDL) restraints added in 1.4 seconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1648 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 13 sheets defined 50.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.961A pdb=" N ASP A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 441 removed outlier: 3.647A pdb=" N GLU A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 432 removed outlier: 3.877A pdb=" N ALA B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 442 Processing helix chain 'B' and resid 443 through 446 Processing helix chain 'D' and resid 859 through 863 removed outlier: 3.554A pdb=" N THR D 863 " --> pdb=" O PRO D 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 863 removed outlier: 3.892A pdb=" N THR C 863 " --> pdb=" O PRO C 860 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 163 removed outlier: 3.828A pdb=" N LEU E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 163 removed outlier: 3.591A pdb=" N ALA F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 3.796A pdb=" N ALA G 411 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS G 412 " --> pdb=" O THR G 408 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU G 426 " --> pdb=" O ARG G 422 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA G 427 " --> pdb=" O LEU G 423 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU G 429 " --> pdb=" O SER G 425 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA G 433 " --> pdb=" O LEU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 444 Processing helix chain 'H' and resid 405 through 431 removed outlier: 3.648A pdb=" N HIS H 409 " --> pdb=" O ASP H 405 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU H 410 " --> pdb=" O SER H 406 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE H 420 " --> pdb=" O LEU H 416 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU H 421 " --> pdb=" O GLN H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 441 removed outlier: 3.589A pdb=" N ASP H 440 " --> pdb=" O ALA H 436 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG H 441 " --> pdb=" O ALA H 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 859 through 863 removed outlier: 3.602A pdb=" N THR I 863 " --> pdb=" O PRO I 860 " (cutoff:3.500A) Processing helix chain 'J' and resid 859 through 863 removed outlier: 3.819A pdb=" N THR J 863 " --> pdb=" O PRO J 860 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.711A pdb=" N VAL D 851 " --> pdb=" O CYS D 795 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 850 " --> pdb=" O ASP D 845 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY D 10 " --> pdb=" O THR D 885 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET D 807 " --> pdb=" O VAL D 823 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL D 823 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP D 809 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 870 through 872 Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.550A pdb=" N VAL C 12 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 830 through 832 removed outlier: 7.030A pdb=" N TRP C 809 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL C 823 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET C 807 " --> pdb=" O VAL C 823 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.613A pdb=" N VAL I 851 " --> pdb=" O CYS I 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.809A pdb=" N MET I 807 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL I 823 " --> pdb=" O MET I 807 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP I 809 " --> pdb=" O VAL I 821 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 870 through 872 removed outlier: 3.571A pdb=" N TYR I 872 " --> pdb=" O SER I 875 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N GLY J 10 " --> pdb=" O THR J 885 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N GLY J 10 " --> pdb=" O THR J 885 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 792 through 793 463 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2430 1.34 - 1.46: 1083 1.46 - 1.58: 3290 1.58 - 1.70: 0 1.70 - 1.81: 38 Bond restraints: 6841 Sorted by residual: bond pdb=" CB TRP C 827 " pdb=" CG TRP C 827 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.78e+00 bond pdb=" CG1 ILE D 806 " pdb=" CD1 ILE D 806 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" C TYR J 832 " pdb=" N VAL J 833 " ideal model delta sigma weight residual 1.334 1.317 0.016 1.29e-02 6.01e+03 1.62e+00 bond pdb=" CB ASN I 869 " pdb=" CG ASN I 869 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.59e+00 bond pdb=" C LYS D 859 " pdb=" N PRO D 860 " ideal model delta sigma weight residual 1.337 1.323 0.014 1.11e-02 8.12e+03 1.49e+00 ... (remaining 6836 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.74: 45 105.74 - 112.80: 3715 112.80 - 119.86: 2206 119.86 - 126.92: 3199 126.92 - 133.98: 44 Bond angle restraints: 9209 Sorted by residual: angle pdb=" N ILE J 806 " pdb=" CA ILE J 806 " pdb=" C ILE J 806 " ideal model delta sigma weight residual 108.93 113.36 -4.43 1.35e+00 5.49e-01 1.08e+01 angle pdb=" N ILE D 806 " pdb=" CA ILE D 806 " pdb=" C ILE D 806 " ideal model delta sigma weight residual 109.30 113.38 -4.08 1.31e+00 5.83e-01 9.70e+00 angle pdb=" C ALA E 118 " pdb=" N GLU E 119 " pdb=" CA GLU E 119 " ideal model delta sigma weight residual 120.68 115.81 4.87 1.70e+00 3.46e-01 8.22e+00 angle pdb=" C SER E 112 " pdb=" N ALA E 113 " pdb=" CA ALA E 113 " ideal model delta sigma weight residual 122.42 118.24 4.18 1.55e+00 4.16e-01 7.29e+00 angle pdb=" CA TRP C 827 " pdb=" CB TRP C 827 " pdb=" CG TRP C 827 " ideal model delta sigma weight residual 113.60 108.52 5.08 1.90e+00 2.77e-01 7.16e+00 ... (remaining 9204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 3786 17.25 - 34.51: 381 34.51 - 51.76: 46 51.76 - 69.02: 6 69.02 - 86.27: 14 Dihedral angle restraints: 4233 sinusoidal: 1691 harmonic: 2542 Sorted by residual: dihedral pdb=" CB CYS C 795 " pdb=" SG CYS C 795 " pdb=" SG CYS C 868 " pdb=" CB CYS C 868 " ideal model delta sinusoidal sigma weight residual 93.00 43.73 49.27 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS I 795 " pdb=" SG CYS I 795 " pdb=" SG CYS I 868 " pdb=" CB CYS I 868 " ideal model delta sinusoidal sigma weight residual 93.00 44.90 48.10 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA HIS A 350 " pdb=" C HIS A 350 " pdb=" N ALA A 351 " pdb=" CA ALA A 351 " ideal model delta harmonic sigma weight residual 180.00 -154.67 -25.33 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 4230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 711 0.039 - 0.079: 242 0.079 - 0.118: 79 0.118 - 0.158: 4 0.158 - 0.197: 5 Chirality restraints: 1041 Sorted by residual: chirality pdb=" CB ILE J 842 " pdb=" CA ILE J 842 " pdb=" CG1 ILE J 842 " pdb=" CG2 ILE J 842 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CB ILE I 842 " pdb=" CA ILE I 842 " pdb=" CG1 ILE I 842 " pdb=" CG2 ILE I 842 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CB VAL J 823 " pdb=" CA VAL J 823 " pdb=" CG1 VAL J 823 " pdb=" CG2 VAL J 823 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 1038 not shown) Planarity restraints: 1219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 859 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO C 860 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 860 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 860 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 417 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" CD GLN B 417 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN B 417 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN B 417 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 859 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO J 860 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO J 860 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 860 " 0.021 5.00e-02 4.00e+02 ... (remaining 1216 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 272 2.71 - 3.26: 6877 3.26 - 3.80: 10416 3.80 - 4.35: 13277 4.35 - 4.90: 22214 Nonbonded interactions: 53056 Sorted by model distance: nonbonded pdb=" O THR B 424 " pdb=" ND2 ASN C 831 " model vdw 2.161 2.520 nonbonded pdb=" NH1 ARG D 799 " pdb=" OG SER D 800 " model vdw 2.201 2.520 nonbonded pdb=" OD1 ASP I 802 " pdb=" NH2 ARG I 844 " model vdw 2.245 2.520 nonbonded pdb=" NH1 ARG I 808 " pdb=" OH TYR I 810 " model vdw 2.245 2.520 nonbonded pdb=" O ASP C 862 " pdb=" OH TYR C 866 " model vdw 2.255 2.440 ... (remaining 53051 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' and resid 350 through 445) } ncs_group { reference = (chain 'C' and resid 2 through 887) selection = (chain 'D' and resid 2 through 887) selection = chain 'I' selection = (chain 'J' and resid 2 through 887) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 403 through 441) selection = chain 'H' } 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: 2.030 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: 6.950 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.970 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 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 : 0.006 0.052 6841 Z= 0.377 Angle : 0.699 5.850 9209 Z= 0.430 Chirality : 0.044 0.197 1041 Planarity : 0.004 0.086 1219 Dihedral : 14.166 86.270 2573 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.30 (0.28), residues: 852 helix: -0.24 (0.25), residues: 379 sheet: -2.06 (0.31), residues: 239 loop : 0.03 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 827 HIS 0.005 0.002 HIS A 350 PHE 0.005 0.001 PHE I 840 TYR 0.018 0.002 TYR J 13 ARG 0.013 0.001 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: C 865 VAL cc_start: 0.7852 (m) cc_final: 0.7637 (p) REVERT: I 862 ASP cc_start: 0.7207 (m-30) cc_final: 0.6998 (m-30) REVERT: J 807 MET cc_start: 0.6494 (mmm) cc_final: 0.5574 (mmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2088 time to fit residues: 33.1932 Evaluate side-chains 116 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN E 132 GLN E 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6841 Z= 0.236 Angle : 0.571 7.232 9209 Z= 0.312 Chirality : 0.040 0.162 1041 Planarity : 0.004 0.063 1219 Dihedral : 5.054 21.860 981 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.15 % Allowed : 9.03 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.30), residues: 852 helix: 1.34 (0.26), residues: 381 sheet: -1.76 (0.32), residues: 229 loop : 0.08 (0.44), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 827 HIS 0.004 0.001 HIS B 350 PHE 0.004 0.001 PHE C 840 TYR 0.015 0.002 TYR C 13 ARG 0.007 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: E 128 ARG cc_start: 0.5536 (ttm110) cc_final: 0.5316 (ttm170) REVERT: F 143 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.6742 (mt) REVERT: J 807 MET cc_start: 0.6353 (mmm) cc_final: 0.5794 (mmm) REVERT: J 859 LYS cc_start: 0.6387 (mtmm) cc_final: 0.6141 (mtmm) outliers start: 15 outliers final: 7 residues processed: 113 average time/residue: 0.2080 time to fit residues: 30.8116 Evaluate side-chains 116 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 821 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 0.0020 chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6841 Z= 0.176 Angle : 0.489 5.194 9209 Z= 0.270 Chirality : 0.039 0.138 1041 Planarity : 0.003 0.056 1219 Dihedral : 4.612 21.347 981 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.86 % Allowed : 11.75 % 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: 0.81 (0.30), residues: 852 helix: 2.11 (0.26), residues: 379 sheet: -1.59 (0.32), residues: 243 loop : 0.62 (0.47), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 878 HIS 0.002 0.001 HIS B 350 PHE 0.005 0.001 PHE I 840 TYR 0.010 0.001 TYR C 13 ARG 0.004 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 HIS cc_start: 0.3755 (OUTLIER) cc_final: 0.3374 (m-70) REVERT: E 139 ASN cc_start: 0.6274 (t0) cc_final: 0.5964 (t0) REVERT: F 132 GLN cc_start: 0.8054 (mt0) cc_final: 0.7760 (mt0) REVERT: F 143 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.6758 (mt) outliers start: 13 outliers final: 9 residues processed: 124 average time/residue: 0.2114 time to fit residues: 34.0733 Evaluate side-chains 128 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain F residue 143 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.0170 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6841 Z= 0.265 Angle : 0.532 5.200 9209 Z= 0.293 Chirality : 0.040 0.141 1041 Planarity : 0.004 0.055 1219 Dihedral : 4.856 21.927 981 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.87 % Allowed : 14.18 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.30), residues: 852 helix: 2.14 (0.26), residues: 379 sheet: -1.66 (0.31), residues: 246 loop : 0.63 (0.47), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 878 HIS 0.004 0.001 HIS B 350 PHE 0.005 0.001 PHE I 840 TYR 0.011 0.002 TYR C 13 ARG 0.006 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.796 Fit side-chains REVERT: B 397 GLU cc_start: 0.7453 (tp30) cc_final: 0.7143 (tp30) REVERT: E 139 ASN cc_start: 0.6273 (t0) cc_final: 0.5995 (t0) REVERT: F 143 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.6798 (mt) REVERT: J 807 MET cc_start: 0.6774 (mmm) cc_final: 0.6003 (mmp) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.2004 time to fit residues: 32.1125 Evaluate side-chains 130 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain I residue 886 VAL Chi-restraints excluded: chain J residue 806 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 0 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6841 Z= 0.273 Angle : 0.536 5.355 9209 Z= 0.295 Chirality : 0.040 0.140 1041 Planarity : 0.004 0.052 1219 Dihedral : 4.871 21.550 981 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.72 % Allowed : 14.33 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.30), residues: 852 helix: 2.12 (0.25), residues: 379 sheet: -1.71 (0.31), residues: 246 loop : 0.57 (0.46), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 878 HIS 0.004 0.001 HIS B 350 PHE 0.005 0.001 PHE I 840 TYR 0.011 0.002 TYR C 13 ARG 0.006 0.000 ARG F 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.790 Fit side-chains REVERT: A 350 HIS cc_start: 0.4162 (OUTLIER) cc_final: 0.3633 (m-70) REVERT: B 397 GLU cc_start: 0.7447 (tp30) cc_final: 0.7130 (tp30) REVERT: E 139 ASN cc_start: 0.6276 (t0) cc_final: 0.6039 (t0) REVERT: F 143 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.6773 (mt) REVERT: J 807 MET cc_start: 0.6862 (mmm) cc_final: 0.6178 (mmp) REVERT: J 810 TYR cc_start: 0.5722 (m-80) cc_final: 0.5509 (m-80) outliers start: 26 outliers final: 19 residues processed: 124 average time/residue: 0.1998 time to fit residues: 32.4438 Evaluate side-chains 135 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain I residue 886 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 806 ILE Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 859 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6841 Z= 0.301 Angle : 0.558 6.448 9209 Z= 0.306 Chirality : 0.041 0.141 1041 Planarity : 0.004 0.052 1219 Dihedral : 5.000 22.148 981 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.73 % Allowed : 16.05 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.30), residues: 852 helix: 2.05 (0.25), residues: 379 sheet: -1.84 (0.30), residues: 247 loop : 0.50 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 878 HIS 0.004 0.001 HIS B 350 PHE 0.005 0.001 PHE I 840 TYR 0.012 0.002 TYR C 13 ARG 0.006 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 0.683 Fit side-chains REVERT: A 350 HIS cc_start: 0.4375 (OUTLIER) cc_final: 0.3675 (m-70) REVERT: B 397 GLU cc_start: 0.7424 (tp30) cc_final: 0.7139 (tp30) REVERT: E 139 ASN cc_start: 0.6291 (t0) cc_final: 0.6047 (t0) REVERT: F 143 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7044 (mt) REVERT: I 851 VAL cc_start: 0.7061 (OUTLIER) cc_final: 0.6837 (m) REVERT: J 807 MET cc_start: 0.6832 (mmm) cc_final: 0.6108 (mmp) outliers start: 33 outliers final: 23 residues processed: 129 average time/residue: 0.1929 time to fit residues: 32.7949 Evaluate side-chains 141 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain D residue 868 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain I residue 851 VAL Chi-restraints excluded: chain I residue 886 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 806 ILE Chi-restraints excluded: chain J residue 823 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 67 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6841 Z= 0.218 Angle : 0.499 5.701 9209 Z= 0.275 Chirality : 0.039 0.146 1041 Planarity : 0.003 0.049 1219 Dihedral : 4.684 20.589 981 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.44 % Allowed : 16.19 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.30), residues: 852 helix: 2.32 (0.26), residues: 380 sheet: -1.74 (0.30), residues: 253 loop : 0.59 (0.48), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 878 HIS 0.003 0.001 HIS B 350 PHE 0.005 0.001 PHE I 840 TYR 0.013 0.001 TYR C 13 ARG 0.004 0.000 ARG C 792 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 0.727 Fit side-chains REVERT: A 350 HIS cc_start: 0.4265 (OUTLIER) cc_final: 0.3698 (m-70) REVERT: B 397 GLU cc_start: 0.7371 (tp30) cc_final: 0.7058 (tp30) REVERT: J 807 MET cc_start: 0.6639 (mmm) cc_final: 0.5822 (mmp) outliers start: 31 outliers final: 21 residues processed: 121 average time/residue: 0.1882 time to fit residues: 30.0766 Evaluate side-chains 129 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 806 ILE Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.4980 chunk 24 optimal weight: 0.0870 chunk 15 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 62 optimal weight: 0.0050 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN E 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6841 Z= 0.196 Angle : 0.487 7.006 9209 Z= 0.268 Chirality : 0.038 0.137 1041 Planarity : 0.003 0.048 1219 Dihedral : 4.527 20.326 981 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.73 % Allowed : 16.48 % Favored : 78.80 % 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: 1.06 (0.30), residues: 852 helix: 2.52 (0.25), residues: 380 sheet: -1.65 (0.30), residues: 253 loop : 0.67 (0.48), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 878 HIS 0.002 0.001 HIS B 350 PHE 0.006 0.001 PHE I 840 TYR 0.012 0.001 TYR C 13 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 0.807 Fit side-chains REVERT: A 350 HIS cc_start: 0.4092 (OUTLIER) cc_final: 0.3570 (m-70) REVERT: D 4 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6799 (mp) REVERT: E 128 ARG cc_start: 0.5527 (ttm110) cc_final: 0.5324 (ttm170) REVERT: H 429 LEU cc_start: 0.8334 (mm) cc_final: 0.8063 (mp) REVERT: J 807 MET cc_start: 0.6662 (mmm) cc_final: 0.5838 (mmp) outliers start: 33 outliers final: 22 residues processed: 122 average time/residue: 0.2035 time to fit residues: 32.5553 Evaluate side-chains 130 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain J residue 806 ILE Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 67 optimal weight: 0.0030 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 78 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN E 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6841 Z= 0.191 Angle : 0.484 6.809 9209 Z= 0.266 Chirality : 0.038 0.138 1041 Planarity : 0.003 0.048 1219 Dihedral : 4.453 20.098 981 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.87 % Allowed : 17.05 % Favored : 79.08 % 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: 1.19 (0.30), residues: 852 helix: 2.57 (0.25), residues: 382 sheet: -1.57 (0.31), residues: 253 loop : 0.83 (0.49), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 878 HIS 0.003 0.001 HIS B 350 PHE 0.006 0.001 PHE I 840 TYR 0.011 0.001 TYR J 13 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 0.769 Fit side-chains REVERT: A 350 HIS cc_start: 0.4018 (OUTLIER) cc_final: 0.3575 (m-70) REVERT: B 397 GLU cc_start: 0.7326 (tp30) cc_final: 0.6798 (tp30) REVERT: B 404 ARG cc_start: 0.6637 (ptt-90) cc_final: 0.6225 (ptp-170) REVERT: D 4 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6792 (mp) REVERT: G 415 GLU cc_start: 0.6543 (tp30) cc_final: 0.6342 (tp30) REVERT: H 429 LEU cc_start: 0.8386 (mm) cc_final: 0.8134 (mp) REVERT: J 807 MET cc_start: 0.6649 (mmm) cc_final: 0.5816 (mmp) outliers start: 27 outliers final: 21 residues processed: 119 average time/residue: 0.2044 time to fit residues: 31.8109 Evaluate side-chains 128 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain I residue 886 VAL Chi-restraints excluded: chain J residue 806 ILE Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 0.0170 chunk 60 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN E 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6841 Z= 0.252 Angle : 0.530 7.077 9209 Z= 0.290 Chirality : 0.039 0.136 1041 Planarity : 0.003 0.049 1219 Dihedral : 4.673 20.445 981 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.58 % Allowed : 18.05 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.30), residues: 852 helix: 2.42 (0.25), residues: 381 sheet: -1.65 (0.30), residues: 253 loop : 0.55 (0.47), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 878 HIS 0.004 0.001 HIS B 350 PHE 0.006 0.001 PHE I 840 TYR 0.013 0.002 TYR J 13 ARG 0.004 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.811 Fit side-chains REVERT: A 350 HIS cc_start: 0.4133 (OUTLIER) cc_final: 0.3495 (m-70) REVERT: B 397 GLU cc_start: 0.7358 (tp30) cc_final: 0.7031 (tp30) REVERT: H 429 LEU cc_start: 0.8419 (mm) cc_final: 0.8114 (mp) REVERT: J 807 MET cc_start: 0.6662 (mmm) cc_final: 0.5808 (mmp) outliers start: 25 outliers final: 22 residues processed: 119 average time/residue: 0.2003 time to fit residues: 31.5106 Evaluate side-chains 130 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain I residue 886 VAL Chi-restraints excluded: chain J residue 806 ILE Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN E 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.182932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.172052 restraints weight = 9100.315| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.73 r_work: 0.4106 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6841 Z= 0.319 Angle : 0.572 6.971 9209 Z= 0.312 Chirality : 0.041 0.142 1041 Planarity : 0.004 0.049 1219 Dihedral : 4.944 22.063 981 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.30 % Allowed : 18.91 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.30), residues: 852 helix: 2.16 (0.25), residues: 380 sheet: -1.79 (0.30), residues: 253 loop : 0.52 (0.48), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 878 HIS 0.004 0.001 HIS B 350 PHE 0.006 0.002 PHE I 840 TYR 0.018 0.002 TYR J 13 ARG 0.005 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.48 seconds wall clock time: 34 minutes 45.12 seconds (2085.12 seconds total)