Starting phenix.real_space_refine on Thu Feb 15 21:53:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isj_35692/02_2024/8isj_35692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isj_35692/02_2024/8isj_35692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isj_35692/02_2024/8isj_35692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isj_35692/02_2024/8isj_35692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isj_35692/02_2024/8isj_35692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isj_35692/02_2024/8isj_35692_updated.pdb" } resolution = 3.0 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= 0.030 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 106 5.16 5 C 8611 2.51 5 N 2319 2.21 5 O 2497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 91": "OE1" <-> "OE2" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13533 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6730 Classifications: {'peptide': 859} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 824} Chain breaks: 5 Chain: "B" Number of atoms: 6717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 857, 6717 Classifications: {'peptide': 857} Link IDs: {'PTRANS': 34, 'TRANS': 822} Chain breaks: 5 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.29, per 1000 atoms: 0.54 Number of scatterers: 13533 At special positions: 0 Unit cell: (109.65, 125.8, 142.8, 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 106 16.00 O 2497 8.00 N 2319 7.00 C 8611 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.30 Conformation dependent library (CDL) restraints added in 2.5 seconds 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 13 sheets defined 36.5% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 101 through 107 removed outlier: 4.398A pdb=" N GLU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 132 Processing helix chain 'A' and resid 135 through 146 removed outlier: 4.189A pdb=" N ALA A 140 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 200 through 212 removed outlier: 5.130A pdb=" N LYS A 206 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 Processing helix chain 'A' and resid 276 through 283 removed outlier: 4.088A pdb=" N MET A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 383 through 399 removed outlier: 4.445A pdb=" N GLU A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 424 removed outlier: 3.881A pdb=" N MET A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 490 through 493 No H-bonds generated for 'chain 'A' and resid 490 through 493' Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.612A pdb=" N ASP A 574 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 786 Processing helix chain 'A' and resid 790 through 792 No H-bonds generated for 'chain 'A' and resid 790 through 792' Processing helix chain 'A' and resid 815 through 831 removed outlier: 4.219A pdb=" N VAL A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 923 removed outlier: 3.575A pdb=" N ARG A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 892 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN A 906 " --> pdb=" O TYR A 902 " (cutoff:3.500A) Proline residue: A 910 - end of helix Processing helix chain 'A' and resid 928 through 949 Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 970 through 979 Processing helix chain 'A' and resid 982 through 987 Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1009 through 1025 Processing helix chain 'A' and resid 1066 through 1073 Processing helix chain 'A' and resid 1080 through 1095 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 197 through 213 removed outlier: 3.926A pdb=" N LEU B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 234 Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 381 through 424 removed outlier: 4.004A pdb=" N GLN B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B 403 " --> pdb=" O ASN B 399 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 465 through 478 Processing helix chain 'B' and resid 570 through 587 Processing helix chain 'B' and resid 780 through 786 Processing helix chain 'B' and resid 815 through 830 Processing helix chain 'B' and resid 877 through 892 removed outlier: 3.715A pdb=" N ARG B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR B 892 " --> pdb=" O LEU B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 923 Proline residue: B 910 - end of helix Processing helix chain 'B' and resid 928 through 948 Processing helix chain 'B' and resid 954 through 957 No H-bonds generated for 'chain 'B' and resid 954 through 957' Processing helix chain 'B' and resid 970 through 987 removed outlier: 3.797A pdb=" N VAL B 981 " --> pdb=" O SER B 977 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET B 983 " --> pdb=" O SER B 979 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS B 984 " --> pdb=" O GLN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1001 No H-bonds generated for 'chain 'B' and resid 998 through 1001' Processing helix chain 'B' and resid 1009 through 1025 Processing helix chain 'B' and resid 1066 through 1072 Processing helix chain 'B' and resid 1081 through 1095 Processing sheet with id= A, first strand: chain 'A' and resid 156 through 159 removed outlier: 3.814A pdb=" N ALA A 98 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP A 90 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 96 " --> pdb=" O ASP A 90 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 255 through 257 removed outlier: 3.516A pdb=" N VAL A 239 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A 341 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU A 368 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET A 339 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL A 370 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 337 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N HIS A 372 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA A 335 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 455 through 458 removed outlier: 6.789A pdb=" N THR A 746 " --> pdb=" O SER A 486 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 835 through 842 removed outlier: 3.804A pdb=" N GLU A 835 " --> pdb=" O VAL A 855 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 855 " --> pdb=" O GLU A 835 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 966 through 969 Processing sheet with id= F, first strand: chain 'A' and resid 991 through 994 removed outlier: 5.974A pdb=" N GLN A1032 " --> pdb=" O THR A1060 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 167 through 174 Processing sheet with id= H, first strand: chain 'B' and resid 250 through 256 removed outlier: 6.618A pdb=" N ALA B 241 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU B 255 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 239 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP B 366 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 341 " --> pdb=" O TRP B 366 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU B 368 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET B 339 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL B 370 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU B 337 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS B 372 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 335 " --> pdb=" O HIS B 372 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 455 through 460 removed outlier: 3.806A pdb=" N GLY B 507 " --> pdb=" O ARG B 523 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.049A pdb=" N PHE B 745 " --> pdb=" O GLN B 757 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 757 " --> pdb=" O PHE B 745 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE B 755 " --> pdb=" O ARG B 747 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 835 through 842 removed outlier: 3.745A pdb=" N GLU B 835 " --> pdb=" O VAL B 855 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 855 " --> pdb=" O GLU B 835 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 966 through 969 Processing sheet with id= M, first strand: chain 'B' and resid 991 through 994 removed outlier: 5.720A pdb=" N GLN B1032 " --> pdb=" O THR B1060 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1674 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: 4.52 Time building geometry restraints manager: 5.61 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: 4193 1.34 - 1.46: 2014 1.46 - 1.58: 7405 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 13784 Sorted by residual: bond pdb=" N VAL A1079 " pdb=" CA VAL A1079 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N VAL A 398 " pdb=" CA VAL A 398 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" CAP O6E B1201 " pdb=" CBL O6E B1201 " ideal model delta sigma weight residual 1.448 1.388 0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" CAB O6E B1201 " pdb=" CBI O6E B1201 " ideal model delta sigma weight residual 1.449 1.389 0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" CAP O6E A1201 " pdb=" CBL O6E A1201 " ideal model delta sigma weight residual 1.448 1.389 0.059 2.00e-02 2.50e+03 8.75e+00 ... (remaining 13779 not shown) Histogram of bond angle deviations from ideal: 97.44 - 105.33: 279 105.33 - 113.23: 7682 113.23 - 121.12: 6852 121.12 - 129.01: 3708 129.01 - 136.91: 92 Bond angle restraints: 18613 Sorted by residual: angle pdb=" N TYR A 385 " pdb=" CA TYR A 385 " pdb=" C TYR A 385 " ideal model delta sigma weight residual 114.56 104.47 10.09 1.27e+00 6.20e-01 6.31e+01 angle pdb=" N GLU A 401 " pdb=" CA GLU A 401 " pdb=" C GLU A 401 " ideal model delta sigma weight residual 112.88 105.13 7.75 1.29e+00 6.01e-01 3.61e+01 angle pdb=" C MET A 192 " pdb=" CA MET A 192 " pdb=" CB MET A 192 " ideal model delta sigma weight residual 117.23 109.58 7.65 1.36e+00 5.41e-01 3.16e+01 angle pdb=" N ALA A 386 " pdb=" CA ALA A 386 " pdb=" C ALA A 386 " ideal model delta sigma weight residual 113.28 107.01 6.27 1.22e+00 6.72e-01 2.64e+01 angle pdb=" N LYS A 400 " pdb=" CA LYS A 400 " pdb=" C LYS A 400 " ideal model delta sigma weight residual 113.30 106.67 6.63 1.34e+00 5.57e-01 2.45e+01 ... (remaining 18608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7341 17.90 - 35.81: 843 35.81 - 53.71: 212 53.71 - 71.61: 31 71.61 - 89.52: 12 Dihedral angle restraints: 8439 sinusoidal: 3471 harmonic: 4968 Sorted by residual: dihedral pdb=" CD ARG B 384 " pdb=" NE ARG B 384 " pdb=" CZ ARG B 384 " pdb=" NH1 ARG B 384 " ideal model delta sinusoidal sigma weight residual 0.00 33.18 -33.18 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" CA ALA A 428 " pdb=" C ALA A 428 " pdb=" N PRO A 429 " pdb=" CA PRO A 429 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA TYR A 902 " pdb=" C TYR A 902 " pdb=" N ILE A 903 " pdb=" CA ILE A 903 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 8436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1753 0.055 - 0.110: 288 0.110 - 0.164: 71 0.164 - 0.219: 7 0.219 - 0.274: 5 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CB VAL A 398 " pdb=" CA VAL A 398 " pdb=" CG1 VAL A 398 " pdb=" CG2 VAL A 398 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ILE B 74 " pdb=" N ILE B 74 " pdb=" C ILE B 74 " pdb=" CB ILE B 74 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA VAL A 338 " pdb=" N VAL A 338 " pdb=" C VAL A 338 " pdb=" CB VAL A 338 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2121 not shown) Planarity restraints: 2368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " -0.133 2.00e-02 2.50e+03 1.45e-01 5.22e+02 pdb=" CAP O6E B1201 " 0.138 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " 0.120 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " -0.067 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " 0.012 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " -0.041 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " -0.027 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " 0.012 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " -0.281 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " 0.267 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " 0.023 2.00e-02 2.50e+03 1.33e-01 4.41e+02 pdb=" CAP O6E A1201 " -0.205 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " -0.009 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " 0.058 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " 0.008 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " 0.010 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.013 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " 0.010 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " 0.298 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " -0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E A1201 " 0.138 2.00e-02 2.50e+03 9.21e-02 2.12e+02 pdb=" CAO O6E A1201 " -0.023 2.00e-02 2.50e+03 pdb=" CAP O6E A1201 " 0.062 2.00e-02 2.50e+03 pdb=" CAR O6E A1201 " -0.156 2.00e-02 2.50e+03 pdb=" CAV O6E A1201 " 0.054 2.00e-02 2.50e+03 pdb=" CBB O6E A1201 " 0.027 2.00e-02 2.50e+03 pdb=" CBH O6E A1201 " -0.069 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " -0.011 2.00e-02 2.50e+03 pdb=" CBO O6E A1201 " -0.130 2.00e-02 2.50e+03 pdb=" NAE O6E A1201 " 0.108 2.00e-02 2.50e+03 ... (remaining 2365 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 485 2.72 - 3.26: 13059 3.26 - 3.81: 20871 3.81 - 4.35: 25051 4.35 - 4.90: 43655 Nonbonded interactions: 103121 Sorted by model distance: nonbonded pdb=" O VAL A1079 " pdb=" OG SER A1080 " model vdw 2.173 2.440 nonbonded pdb=" OG SER B 100 " pdb=" OD1 ASN B 102 " model vdw 2.200 2.440 nonbonded pdb=" OG SER A 985 " pdb=" O VAL A 990 " model vdw 2.221 2.440 nonbonded pdb=" OD2 ASP A1018 " pdb=" OG SER A1085 " model vdw 2.239 2.440 nonbonded pdb=" O SER A 104 " pdb=" OG1 THR A 108 " model vdw 2.270 2.440 ... (remaining 103116 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' and (resid 73 through 588 or resid 742 through 1040 or resid 1050 thr \ ough 1119 or resid 1201)) selection = (chain 'B' and (resid 73 through 110 or resid 121 through 1119 or resid 1201)) } 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.640 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 37.810 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.004 0.060 13784 Z= 0.253 Angle : 0.722 11.074 18613 Z= 0.403 Chirality : 0.046 0.274 2124 Planarity : 0.009 0.265 2368 Dihedral : 16.090 89.518 5211 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.96 % Favored : 94.98 % Rotamer: Outliers : 0.20 % Allowed : 21.08 % Favored : 78.72 % 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: 0.13 (0.21), residues: 1692 helix: 1.60 (0.21), residues: 665 sheet: 0.34 (0.28), residues: 337 loop : -1.61 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 366 HIS 0.008 0.001 HIS A 324 PHE 0.043 0.001 PHE B 916 TYR 0.026 0.001 TYR B 478 ARG 0.003 0.000 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: A 251 GLU cc_start: 0.7727 (tt0) cc_final: 0.7454 (tt0) REVERT: A 782 MET cc_start: 0.8731 (tpt) cc_final: 0.8510 (tpt) REVERT: B 210 ARG cc_start: 0.7421 (ttm170) cc_final: 0.7153 (ptm160) REVERT: B 474 TRP cc_start: 0.6413 (t60) cc_final: 0.6059 (t60) REVERT: B 548 MET cc_start: 0.3824 (tmm) cc_final: 0.3609 (ttt) REVERT: B 797 MET cc_start: 0.9162 (tpp) cc_final: 0.8923 (tpt) REVERT: B 881 GLN cc_start: 0.8019 (mm110) cc_final: 0.7589 (mt0) REVERT: B 919 LYS cc_start: 0.7056 (tmmt) cc_final: 0.6854 (mttt) outliers start: 3 outliers final: 0 residues processed: 169 average time/residue: 1.2281 time to fit residues: 228.8282 Evaluate side-chains 129 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 0.0670 chunk 81 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 399 ASN A 469 GLN A 873 GLN A 941 GLN ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN B 372 HIS B 757 GLN B 827 ASN B 880 GLN ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13784 Z= 0.253 Angle : 0.599 7.842 18613 Z= 0.297 Chirality : 0.042 0.161 2124 Planarity : 0.004 0.062 2368 Dihedral : 5.728 88.260 1911 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.32 % Favored : 93.62 % Rotamer: Outliers : 4.65 % Allowed : 18.79 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1692 helix: 1.55 (0.21), residues: 670 sheet: 0.26 (0.28), residues: 343 loop : -1.65 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 366 HIS 0.004 0.001 HIS A 324 PHE 0.027 0.002 PHE B 916 TYR 0.019 0.002 TYR A 242 ARG 0.004 0.000 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 147 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7282 (mmt) REVERT: A 564 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6838 (ttm110) REVERT: A 824 VAL cc_start: 0.8687 (t) cc_final: 0.8479 (p) REVERT: A 896 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7280 (ttm170) REVERT: B 531 ARG cc_start: 0.6587 (mtm-85) cc_final: 0.6255 (mtm-85) REVERT: B 548 MET cc_start: 0.3866 (OUTLIER) cc_final: 0.3596 (ttp) REVERT: B 576 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7866 (mp) REVERT: B 881 GLN cc_start: 0.8043 (mm110) cc_final: 0.7652 (mt0) outliers start: 69 outliers final: 28 residues processed: 192 average time/residue: 1.0543 time to fit residues: 224.9090 Evaluate side-chains 167 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 936 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13784 Z= 0.277 Angle : 0.605 8.232 18613 Z= 0.300 Chirality : 0.042 0.159 2124 Planarity : 0.004 0.062 2368 Dihedral : 5.585 88.699 1911 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.09 % Rotamer: Outliers : 4.65 % Allowed : 20.47 % Favored : 74.88 % 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: 0.04 (0.21), residues: 1692 helix: 1.50 (0.20), residues: 672 sheet: 0.26 (0.28), residues: 340 loop : -1.66 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 366 HIS 0.005 0.001 HIS A 172 PHE 0.019 0.002 PHE B 745 TYR 0.021 0.002 TYR B 327 ARG 0.004 0.000 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 137 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.8008 (p) REVERT: A 564 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6892 (ttm110) REVERT: A 896 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7265 (ttm170) REVERT: B 210 ARG cc_start: 0.7767 (ttm170) cc_final: 0.7546 (ttp-170) REVERT: B 531 ARG cc_start: 0.6574 (mtm-85) cc_final: 0.6272 (mtm-85) REVERT: B 548 MET cc_start: 0.3774 (OUTLIER) cc_final: 0.3414 (ttp) REVERT: B 576 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7861 (mp) REVERT: B 742 MET cc_start: 0.5961 (ttm) cc_final: 0.5601 (ttm) REVERT: B 762 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8394 (mp) REVERT: B 920 MET cc_start: 0.5135 (mmt) cc_final: 0.4718 (mmt) outliers start: 69 outliers final: 40 residues processed: 182 average time/residue: 1.0317 time to fit residues: 209.8204 Evaluate side-chains 174 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 128 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 936 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 155 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 30.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 HIS B 881 GLN B 935 GLN ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13784 Z= 0.399 Angle : 0.679 8.761 18613 Z= 0.339 Chirality : 0.046 0.227 2124 Planarity : 0.005 0.059 2368 Dihedral : 5.825 89.352 1911 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.27 % Favored : 92.67 % Rotamer: Outliers : 5.32 % Allowed : 20.94 % Favored : 73.74 % 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: -0.26 (0.21), residues: 1692 helix: 1.19 (0.20), residues: 675 sheet: 0.11 (0.28), residues: 341 loop : -1.76 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 366 HIS 0.006 0.001 HIS A 172 PHE 0.026 0.002 PHE B 745 TYR 0.022 0.002 TYR B 327 ARG 0.005 0.000 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 135 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6881 (ttm110) REVERT: A 896 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7254 (ttm170) REVERT: B 531 ARG cc_start: 0.6622 (mtm-85) cc_final: 0.6310 (mtm-85) REVERT: B 548 MET cc_start: 0.3981 (OUTLIER) cc_final: 0.3534 (ttp) REVERT: B 576 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7860 (mp) REVERT: B 742 MET cc_start: 0.6094 (ttm) cc_final: 0.5705 (ttm) REVERT: B 762 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8373 (mp) REVERT: B 1022 MET cc_start: 0.5251 (ppp) cc_final: 0.4287 (ppp) outliers start: 79 outliers final: 46 residues processed: 191 average time/residue: 1.0521 time to fit residues: 224.4600 Evaluate side-chains 179 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 128 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 936 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 HIS B 881 GLN B 935 GLN ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13784 Z= 0.348 Angle : 0.659 9.000 18613 Z= 0.326 Chirality : 0.044 0.174 2124 Planarity : 0.005 0.060 2368 Dihedral : 5.732 87.798 1911 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.86 % Favored : 93.09 % Rotamer: Outliers : 4.98 % Allowed : 21.89 % Favored : 73.13 % 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: -0.27 (0.21), residues: 1692 helix: 1.17 (0.20), residues: 672 sheet: 0.11 (0.28), residues: 341 loop : -1.74 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 366 HIS 0.005 0.001 HIS B 249 PHE 0.023 0.002 PHE B 745 TYR 0.022 0.002 TYR B 327 ARG 0.004 0.000 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 136 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6893 (ttm110) REVERT: A 896 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7214 (ttm170) REVERT: B 531 ARG cc_start: 0.6579 (mtm-85) cc_final: 0.6228 (mtm-85) REVERT: B 548 MET cc_start: 0.3824 (OUTLIER) cc_final: 0.3397 (ttp) REVERT: B 576 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7883 (mp) REVERT: B 762 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8431 (mp) REVERT: B 915 MET cc_start: 0.7153 (tpp) cc_final: 0.6781 (tpp) outliers start: 74 outliers final: 49 residues processed: 192 average time/residue: 1.0099 time to fit residues: 216.4274 Evaluate side-chains 182 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 128 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 936 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 164 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN B 877 HIS ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13784 Z= 0.162 Angle : 0.570 9.304 18613 Z= 0.281 Chirality : 0.040 0.157 2124 Planarity : 0.004 0.063 2368 Dihedral : 5.230 86.839 1911 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.62 % Rotamer: Outliers : 4.24 % Allowed : 22.29 % Favored : 73.47 % 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: 0.17 (0.21), residues: 1692 helix: 1.60 (0.21), residues: 672 sheet: 0.30 (0.28), residues: 341 loop : -1.56 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 366 HIS 0.005 0.001 HIS A 324 PHE 0.015 0.001 PHE A 869 TYR 0.023 0.001 TYR B 327 ARG 0.003 0.000 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 144 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 896 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7276 (ttm170) REVERT: B 210 ARG cc_start: 0.7724 (ttm170) cc_final: 0.7501 (ttt-90) REVERT: B 469 GLN cc_start: 0.7266 (mm-40) cc_final: 0.6941 (mm-40) REVERT: B 548 MET cc_start: 0.3912 (OUTLIER) cc_final: 0.3482 (ttp) REVERT: B 576 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8015 (mp) REVERT: B 742 MET cc_start: 0.5949 (ttm) cc_final: 0.5626 (ttm) REVERT: B 919 LYS cc_start: 0.7054 (tmmt) cc_final: 0.6841 (mtmt) REVERT: B 965 MET cc_start: 0.2347 (OUTLIER) cc_final: 0.2142 (tpt) outliers start: 63 outliers final: 40 residues processed: 189 average time/residue: 1.0466 time to fit residues: 220.8030 Evaluate side-chains 175 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 131 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 965 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 163 optimal weight: 20.0000 chunk 102 optimal weight: 0.0670 chunk 99 optimal weight: 0.6980 chunk 75 optimal weight: 30.0000 chunk 101 optimal weight: 0.9990 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 GLN ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13784 Z= 0.329 Angle : 0.646 9.306 18613 Z= 0.320 Chirality : 0.043 0.161 2124 Planarity : 0.005 0.060 2368 Dihedral : 5.547 87.840 1911 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.68 % Favored : 93.26 % Rotamer: Outliers : 4.92 % Allowed : 22.56 % Favored : 72.53 % 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: -0.08 (0.21), residues: 1692 helix: 1.34 (0.21), residues: 671 sheet: 0.21 (0.28), residues: 341 loop : -1.65 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 366 HIS 0.005 0.001 HIS B 249 PHE 0.021 0.002 PHE B 745 TYR 0.024 0.002 TYR B 478 ARG 0.009 0.000 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 131 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8327 (ttt) REVERT: A 896 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7243 (ttm170) REVERT: B 210 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7611 (ttt-90) REVERT: B 531 ARG cc_start: 0.6388 (mtm-85) cc_final: 0.6067 (mtm-85) REVERT: B 548 MET cc_start: 0.4075 (OUTLIER) cc_final: 0.3568 (ttp) REVERT: B 576 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7973 (mp) REVERT: B 742 MET cc_start: 0.5968 (ttm) cc_final: 0.5667 (ttm) REVERT: B 762 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8427 (mp) outliers start: 73 outliers final: 51 residues processed: 189 average time/residue: 0.9999 time to fit residues: 211.3473 Evaluate side-chains 184 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 128 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain B residue 1024 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13784 Z= 0.214 Angle : 0.609 9.518 18613 Z= 0.298 Chirality : 0.041 0.156 2124 Planarity : 0.004 0.063 2368 Dihedral : 5.359 88.103 1911 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.50 % Favored : 94.44 % Rotamer: Outliers : 4.38 % Allowed : 23.16 % Favored : 72.46 % 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: 0.07 (0.21), residues: 1692 helix: 1.46 (0.21), residues: 675 sheet: 0.25 (0.28), residues: 343 loop : -1.56 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 366 HIS 0.006 0.001 HIS A 324 PHE 0.016 0.002 PHE B 745 TYR 0.025 0.001 TYR B 478 ARG 0.007 0.000 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 135 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8278 (ttt) REVERT: A 564 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6825 (ttm110) REVERT: A 896 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7263 (ttm170) REVERT: B 210 ARG cc_start: 0.7790 (ttm170) cc_final: 0.7511 (ttt-90) REVERT: B 214 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7538 (mp) REVERT: B 469 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7098 (mm110) REVERT: B 576 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7994 (mp) REVERT: B 742 MET cc_start: 0.6018 (ttm) cc_final: 0.5709 (ttm) REVERT: B 762 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8416 (mp) REVERT: B 881 GLN cc_start: 0.8019 (mt0) cc_final: 0.7674 (mt0) outliers start: 65 outliers final: 50 residues processed: 185 average time/residue: 1.0443 time to fit residues: 215.3893 Evaluate side-chains 188 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 132 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1024 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 0.0470 chunk 46 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13784 Z= 0.210 Angle : 0.611 11.960 18613 Z= 0.298 Chirality : 0.041 0.156 2124 Planarity : 0.004 0.062 2368 Dihedral : 5.325 88.462 1911 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.09 % Rotamer: Outliers : 4.31 % Allowed : 23.03 % Favored : 72.66 % 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: 0.10 (0.21), residues: 1692 helix: 1.44 (0.21), residues: 676 sheet: 0.32 (0.28), residues: 341 loop : -1.52 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 366 HIS 0.006 0.001 HIS A 324 PHE 0.015 0.001 PHE B 745 TYR 0.024 0.001 TYR A 902 ARG 0.007 0.000 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 135 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8282 (ttt) REVERT: A 564 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6822 (ttm110) REVERT: A 896 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7268 (ttm170) REVERT: B 210 ARG cc_start: 0.7797 (ttm170) cc_final: 0.7492 (ttt-90) REVERT: B 214 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7519 (mp) REVERT: B 576 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8004 (mp) REVERT: B 742 MET cc_start: 0.5969 (ttm) cc_final: 0.5665 (ttm) REVERT: B 762 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8400 (mp) outliers start: 64 outliers final: 52 residues processed: 185 average time/residue: 1.0676 time to fit residues: 219.6305 Evaluate side-chains 189 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 131 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1024 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 155 optimal weight: 0.0370 chunk 134 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 143 optimal weight: 0.1980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13784 Z= 0.193 Angle : 0.614 12.606 18613 Z= 0.299 Chirality : 0.041 0.156 2124 Planarity : 0.004 0.063 2368 Dihedral : 5.276 89.091 1911 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 3.77 % Allowed : 23.91 % Favored : 72.32 % 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: 0.13 (0.21), residues: 1692 helix: 1.46 (0.21), residues: 677 sheet: 0.26 (0.28), residues: 352 loop : -1.48 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 366 HIS 0.007 0.001 HIS A 324 PHE 0.017 0.001 PHE B 916 TYR 0.027 0.001 TYR B 478 ARG 0.008 0.000 ARG A 891 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 137 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8303 (ttt) REVERT: A 896 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7255 (ttm170) REVERT: B 210 ARG cc_start: 0.7793 (ttm170) cc_final: 0.7532 (ttt-90) REVERT: B 214 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7418 (mp) REVERT: B 326 GLN cc_start: 0.7935 (tt0) cc_final: 0.7680 (tt0) REVERT: B 469 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7132 (mm-40) REVERT: B 576 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8004 (mp) REVERT: B 742 MET cc_start: 0.5946 (ttm) cc_final: 0.5648 (ttm) REVERT: B 762 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8384 (mp) REVERT: B 1087 MET cc_start: 0.8026 (ppp) cc_final: 0.6864 (ptp) outliers start: 56 outliers final: 47 residues processed: 181 average time/residue: 1.0698 time to fit residues: 215.5665 Evaluate side-chains 180 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 128 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 1024 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 135 optimal weight: 0.0970 chunk 56 optimal weight: 0.5980 chunk 138 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.232704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.152296 restraints weight = 15717.769| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.60 r_work: 0.3630 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13784 Z= 0.160 Angle : 0.600 9.511 18613 Z= 0.294 Chirality : 0.041 0.164 2124 Planarity : 0.004 0.063 2368 Dihedral : 5.134 89.982 1911 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 3.03 % Allowed : 24.71 % Favored : 72.26 % 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: 0.26 (0.21), residues: 1692 helix: 1.53 (0.21), residues: 680 sheet: 0.38 (0.28), residues: 351 loop : -1.41 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 366 HIS 0.007 0.001 HIS B 877 PHE 0.016 0.001 PHE B 916 TYR 0.022 0.001 TYR B 327 ARG 0.012 0.000 ARG A 891 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4471.81 seconds wall clock time: 80 minutes 33.56 seconds (4833.56 seconds total)