Starting phenix.real_space_refine on Thu Jul 31 22:26:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzv_22581/07_2025/7jzv_22581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzv_22581/07_2025/7jzv_22581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jzv_22581/07_2025/7jzv_22581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzv_22581/07_2025/7jzv_22581.map" model { file = "/net/cci-nas-00/data/ceres_data/7jzv_22581/07_2025/7jzv_22581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzv_22581/07_2025/7jzv_22581.cif" } resolution = 3.9 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= 0.341 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 278 5.49 5 S 40 5.16 5 C 8141 2.51 5 N 2655 2.21 5 O 3221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 14339 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1995 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 233} Chain: "B" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 753 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "N" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 801 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "O" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "P" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 737 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "Q" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "X" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2867 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "Y" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2832 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "n" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 801 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "o" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "p" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 738 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "q" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 158 SG CYS A 24 39.145 94.485 61.272 1.00 0.00 S ATOM 179 SG CYS A 27 39.227 98.258 60.501 1.00 0.00 S ATOM 315 SG CYS A 44 40.524 95.739 57.903 1.00 0.00 S ATOM 341 SG CYS A 47 42.509 96.352 61.146 1.00 0.00 S ATOM 272 SG CYS A 39 39.960 81.280 58.237 1.00 0.00 S ATOM 449 SG CYS A 61 40.030 83.271 61.518 1.00 0.00 S ATOM 470 SG CYS A 64 38.101 79.951 61.319 1.00 0.00 S ATOM 2193 SG CYS B 50 32.099 79.651 33.041 1.00 0.00 S ATOM 2216 SG CYS B 53 31.426 80.808 36.612 1.00 0.00 S ATOM 2353 SG CYS B 71 29.123 78.212 35.069 1.00 0.00 S ATOM 2373 SG CYS B 74 32.738 77.193 35.933 1.00 0.00 S ATOM 2309 SG CYS B 66 43.282 80.267 39.532 1.00 0.00 S ATOM 2429 SG CYS B 83 41.408 78.130 36.901 1.00 0.00 S ATOM 2449 SG CYS B 86 44.672 79.930 35.954 1.00 0.00 S Time building chain proxies: 12.77, per 1000 atoms: 0.89 Number of scatterers: 14339 At special positions: 0 Unit cell: (121.8, 124.95, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 40 16.00 P 278 15.00 O 3221 8.00 N 2655 7.00 C 8141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.93 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 44 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 27 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 47 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 24 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" NE2 HIS A 41 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 64 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 61 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 39 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 53 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 50 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 74 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" ND1 HIS B 68 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 86 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 66 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 83 " Number of angles added : 18 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 64.9% alpha, 4.8% beta 137 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 6.90 Creating SS restraints... Processing helix chain 'A' and resid 7 through 22 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 77 through 97 removed outlier: 3.930A pdb=" N LEU A 95 " --> pdb=" O CYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.528A pdb=" N CYS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 4.993A pdb=" N ILE A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 removed outlier: 4.045A pdb=" N LYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 46 removed outlier: 3.746A pdb=" N GLY B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 81 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 98 through 122 Processing helix chain 'N' and resid 16 through 21 Processing helix chain 'N' and resid 26 through 37 Processing helix chain 'N' and resid 46 through 73 Processing helix chain 'N' and resid 79 through 90 Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'N' and resid 112 through 116 Processing helix chain 'O' and resid 37 through 47 Processing helix chain 'O' and resid 55 through 84 Processing helix chain 'O' and resid 90 through 102 Processing helix chain 'O' and resid 105 through 124 Processing helix chain 'P' and resid 47 through 57 Processing helix chain 'P' and resid 63 through 76 Processing helix chain 'P' and resid 85 through 114 Processing helix chain 'P' and resid 120 through 132 Processing helix chain 'Q' and resid 24 through 29 Processing helix chain 'Q' and resid 30 through 41 Processing helix chain 'Q' and resid 49 through 76 Processing helix chain 'Q' and resid 82 through 93 Processing helix chain 'n' and resid 16 through 22 Processing helix chain 'n' and resid 26 through 37 Processing helix chain 'n' and resid 46 through 73 Processing helix chain 'n' and resid 79 through 89 Processing helix chain 'n' and resid 90 through 98 Processing helix chain 'n' and resid 112 through 116 Processing helix chain 'o' and resid 37 through 49 Processing helix chain 'o' and resid 55 through 84 Processing helix chain 'o' and resid 90 through 102 Processing helix chain 'o' and resid 103 through 124 removed outlier: 3.585A pdb=" N LYS o 108 " --> pdb=" O GLY o 104 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 56 Processing helix chain 'p' and resid 63 through 76 Processing helix chain 'p' and resid 85 through 114 Processing helix chain 'p' and resid 120 through 133 Processing helix chain 'q' and resid 25 through 29 Processing helix chain 'q' and resid 30 through 41 Processing helix chain 'q' and resid 49 through 76 removed outlier: 3.707A pdb=" N GLU q 53 " --> pdb=" O LEU q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 82 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 4.279A pdb=" N SER A 59 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 225 Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 70 removed outlier: 5.266A pdb=" N HIS B 68 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU B 63 " --> pdb=" O HIS B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 42 through 43 removed outlier: 7.042A pdb=" N ARG N 42 " --> pdb=" O ILE O 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'N' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'N' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'P' and resid 83 through 84 removed outlier: 7.096A pdb=" N ARG P 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'P' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'Q' and resid 96 through 98 removed outlier: 6.713A pdb=" N THR Q 96 " --> pdb=" O THR n 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'n' and resid 42 through 43 removed outlier: 6.992A pdb=" N ARG n 42 " --> pdb=" O ILE o 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'n' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'p' and resid 83 through 84 removed outlier: 6.743A pdb=" N ARG p 83 " --> pdb=" O VAL q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'p' and resid 118 through 119 541 hydrogen bonds defined for protein. 1578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 702 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3799 1.34 - 1.49: 5485 1.49 - 1.63: 5793 1.63 - 1.77: 28 1.77 - 1.92: 53 Bond restraints: 15158 Sorted by residual: bond pdb=" NE ARG p 134 " pdb=" CZ ARG p 134 " ideal model delta sigma weight residual 1.326 1.376 -0.050 1.10e-02 8.26e+03 2.06e+01 bond pdb=" CB HIS p 113 " pdb=" CG HIS p 113 " ideal model delta sigma weight residual 1.497 1.434 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" CA CYS B 53 " pdb=" CB CYS B 53 " ideal model delta sigma weight residual 1.524 1.593 -0.068 1.53e-02 4.27e+03 1.99e+01 bond pdb=" CB HIS P 113 " pdb=" CG HIS P 113 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" CB HIS Q 75 " pdb=" CG HIS Q 75 " ideal model delta sigma weight residual 1.497 1.438 0.059 1.40e-02 5.10e+03 1.76e+01 ... (remaining 15153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 20300 2.42 - 4.84: 1136 4.84 - 7.26: 209 7.26 - 9.68: 17 9.68 - 12.10: 1 Bond angle restraints: 21663 Sorted by residual: angle pdb=" C LYS A 263 " pdb=" N PRO A 264 " pdb=" CA PRO A 264 " ideal model delta sigma weight residual 119.66 126.00 -6.34 7.30e-01 1.88e+00 7.54e+01 angle pdb=" C HIS O 49 " pdb=" N PRO O 50 " pdb=" CA PRO O 50 " ideal model delta sigma weight residual 119.56 128.20 -8.64 1.01e+00 9.80e-01 7.32e+01 angle pdb=" C PRO A 264 " pdb=" N PRO A 265 " pdb=" CA PRO A 265 " ideal model delta sigma weight residual 120.31 128.06 -7.75 9.80e-01 1.04e+00 6.25e+01 angle pdb=" C ASP A 312 " pdb=" N PRO A 313 " pdb=" CA PRO A 313 " ideal model delta sigma weight residual 119.92 128.19 -8.27 1.07e+00 8.73e-01 5.97e+01 angle pdb=" C GLY A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.92 127.81 -7.89 1.07e+00 8.73e-01 5.44e+01 ... (remaining 21658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.39: 6719 25.39 - 50.77: 1311 50.77 - 76.16: 422 76.16 - 101.54: 7 101.54 - 126.93: 1 Dihedral angle restraints: 8460 sinusoidal: 5291 harmonic: 3169 Sorted by residual: dihedral pdb=" CA HIS O 49 " pdb=" C HIS O 49 " pdb=" N PRO O 50 " pdb=" CA PRO O 50 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" C4' DT Y 53 " pdb=" C3' DT Y 53 " pdb=" O3' DT Y 53 " pdb=" P DT Y 54 " ideal model delta sinusoidal sigma weight residual 220.00 93.07 126.93 1 3.50e+01 8.16e-04 1.25e+01 dihedral pdb=" CA PRO o 103 " pdb=" C PRO o 103 " pdb=" N GLY o 104 " pdb=" CA GLY o 104 " ideal model delta harmonic sigma weight residual 180.00 163.90 16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 8457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1723 0.071 - 0.142: 628 0.142 - 0.212: 102 0.212 - 0.283: 4 0.283 - 0.354: 2 Chirality restraints: 2459 Sorted by residual: chirality pdb=" CA CYS B 71 " pdb=" N CYS B 71 " pdb=" C CYS B 71 " pdb=" CB CYS B 71 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA CYS B 53 " pdb=" N CYS B 53 " pdb=" C CYS B 53 " pdb=" CB CYS B 53 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ARG N 88 " pdb=" N ARG N 88 " pdb=" C ARG N 88 " pdb=" CB ARG N 88 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2456 not shown) Planarity restraints: 1791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 347 " 0.024 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C MET A 347 " -0.084 2.00e-02 2.50e+03 pdb=" O MET A 347 " 0.030 2.00e-02 2.50e+03 pdb=" OXT MET A 347 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 102 " -0.024 2.00e-02 2.50e+03 4.85e-02 2.36e+01 pdb=" C GLY Q 102 " 0.084 2.00e-02 2.50e+03 pdb=" O GLY Q 102 " -0.030 2.00e-02 2.50e+03 pdb=" OXT GLY Q 102 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 293 " -0.037 2.00e-02 2.50e+03 1.79e-02 8.05e+00 pdb=" CG TRP A 293 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 293 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 293 " 0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP A 293 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 293 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 293 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 293 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 293 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 293 " -0.020 2.00e-02 2.50e+03 ... (remaining 1788 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 422 2.67 - 3.23: 12480 3.23 - 3.79: 24765 3.79 - 4.34: 34308 4.34 - 4.90: 47805 Nonbonded interactions: 119780 Sorted by model distance: nonbonded pdb=" OG1 THR Q 30 " pdb=" OP2 DA X 58 " model vdw 2.117 3.040 nonbonded pdb=" OP1 DC X 77 " pdb=" OG SER q 47 " model vdw 2.261 3.040 nonbonded pdb=" O ARG A 71 " pdb=" OG SER A 72 " model vdw 2.300 3.040 nonbonded pdb=" OP1 DG Y 67 " pdb=" N VAL p 117 " model vdw 2.306 3.120 nonbonded pdb=" OG SER O 32 " pdb=" OP1 DC X 100 " model vdw 2.334 3.040 ... (remaining 119775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = (chain 'o' and resid 31 through 124) } ncs_group { reference = (chain 'P' and resid 46 through 134) selection = (chain 'p' and resid 46 through 134) } ncs_group { reference = (chain 'Q' and resid 25 through 102) selection = chain 'q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 48.950 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 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 : 0.013 0.109 15174 Z= 0.676 Angle : 1.325 12.099 21681 Z= 0.881 Chirality : 0.069 0.354 2459 Planarity : 0.004 0.049 1791 Dihedral : 24.149 126.927 6410 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.49 % Favored : 98.32 % Rotamer: Outliers : 0.22 % Allowed : 0.32 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.60 (0.23), residues: 1073 helix: 0.62 (0.17), residues: 676 sheet: -0.17 (1.32), residues: 18 loop : 0.29 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.006 TRP A 293 HIS 0.004 0.001 HIS O 109 PHE 0.015 0.003 PHE p 67 TYR 0.026 0.003 TYR o 40 ARG 0.004 0.000 ARG n 20 Details of bonding type rmsd hydrogen bonds : bond 0.19128 ( 892) hydrogen bonds : angle 5.82510 ( 2280) metal coordination : bond 0.03260 ( 16) metal coordination : angle 1.84034 ( 18) covalent geometry : bond 0.01260 (15158) covalent geometry : angle 1.32456 (21663) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 327 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.5569 (tt0) cc_final: 0.5320 (tt0) REVERT: A 25 PRO cc_start: 0.7787 (Cg_exo) cc_final: 0.7279 (Cg_endo) REVERT: A 52 LEU cc_start: 0.7041 (mt) cc_final: 0.5730 (mt) REVERT: N 39 TYR cc_start: 0.8373 (m-80) cc_final: 0.8000 (m-80) REVERT: O 36 SER cc_start: 0.8125 (p) cc_final: 0.7808 (m) REVERT: O 108 LYS cc_start: 0.7870 (mttt) cc_final: 0.7266 (mtpt) REVERT: P 60 LEU cc_start: 0.7035 (mt) cc_final: 0.6811 (mt) REVERT: Q 52 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6911 (mm-30) REVERT: Q 53 GLU cc_start: 0.7836 (tp30) cc_final: 0.7453 (tp30) REVERT: p 60 LEU cc_start: 0.8272 (mt) cc_final: 0.7723 (mt) outliers start: 2 outliers final: 0 residues processed: 329 average time/residue: 0.3659 time to fit residues: 163.0818 Evaluate side-chains 251 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.8980 chunk 99 optimal weight: 0.0970 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN O 84 ASN P 113 HIS Q 25 ASN ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 76 GLN q 25 ASN q 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.220874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.149155 restraints weight = 21901.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154342 restraints weight = 11196.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.157499 restraints weight = 7642.385| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 15174 Z= 0.185 Angle : 0.846 38.549 21681 Z= 0.393 Chirality : 0.039 0.193 2459 Planarity : 0.005 0.044 1791 Dihedral : 27.641 145.005 4242 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.58 % Favored : 98.32 % Rotamer: Outliers : 2.47 % Allowed : 8.28 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.24), residues: 1073 helix: 2.01 (0.19), residues: 686 sheet: 0.35 (1.28), residues: 18 loop : -0.05 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 34 HIS 0.010 0.001 HIS B 36 PHE 0.025 0.002 PHE A 46 TYR 0.028 0.002 TYR B 87 ARG 0.006 0.000 ARG p 131 Details of bonding type rmsd hydrogen bonds : bond 0.06406 ( 892) hydrogen bonds : angle 3.71260 ( 2280) metal coordination : bond 0.02668 ( 16) metal coordination : angle 18.54068 ( 18) covalent geometry : bond 0.00394 (15158) covalent geometry : angle 0.65635 (21663) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 283 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8710 (mt) cc_final: 0.8171 (mt) REVERT: A 71 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7950 (mtm110) REVERT: A 81 GLN cc_start: 0.9189 (mt0) cc_final: 0.8794 (pt0) REVERT: N 39 TYR cc_start: 0.9026 (m-80) cc_final: 0.8720 (m-80) REVERT: N 74 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8476 (mmmm) REVERT: N 95 LYS cc_start: 0.8902 (tppt) cc_final: 0.7946 (tptt) REVERT: O 108 LYS cc_start: 0.8692 (mttt) cc_final: 0.8109 (mtpt) REVERT: O 113 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7329 (mm-30) REVERT: O 116 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8063 (ptmm) REVERT: P 73 GLU cc_start: 0.7625 (tp30) cc_final: 0.7306 (tp30) REVERT: P 93 GLN cc_start: 0.8813 (tt0) cc_final: 0.8529 (tt0) REVERT: Q 27 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8238 (mm110) REVERT: Q 35 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.7558 (mtp85) REVERT: Q 44 LYS cc_start: 0.8872 (tttm) cc_final: 0.8620 (tttm) REVERT: Q 52 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7869 (mm-30) REVERT: Q 74 GLU cc_start: 0.8241 (tt0) cc_final: 0.7784 (tt0) REVERT: n 84 GLN cc_start: 0.8084 (tt0) cc_final: 0.7818 (tt0) REVERT: n 88 ARG cc_start: 0.7620 (mmt180) cc_final: 0.7274 (tpp80) REVERT: n 95 LYS cc_start: 0.8760 (mttt) cc_final: 0.8064 (ttmt) REVERT: o 109 HIS cc_start: 0.8255 (m-70) cc_final: 0.8040 (m-70) REVERT: p 120 MET cc_start: 0.7807 (mmm) cc_final: 0.7561 (mmm) REVERT: q 40 ARG cc_start: 0.8812 (ttm170) cc_final: 0.8609 (ttm170) outliers start: 23 outliers final: 15 residues processed: 290 average time/residue: 0.3526 time to fit residues: 143.2671 Evaluate side-chains 278 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 262 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 86 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 124 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 11 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN N 94 ASN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 HIS n 82 HIS ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 93 GLN q 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.213838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141373 restraints weight = 21205.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.146117 restraints weight = 10819.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149145 restraints weight = 7420.463| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15174 Z= 0.193 Angle : 0.713 24.529 21681 Z= 0.363 Chirality : 0.038 0.227 2459 Planarity : 0.005 0.052 1791 Dihedral : 28.005 146.820 4242 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.04 % Rotamer: Outliers : 2.90 % Allowed : 10.75 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1073 helix: 1.99 (0.19), residues: 688 sheet: 0.87 (1.28), residues: 18 loop : -0.26 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 34 HIS 0.008 0.001 HIS p 113 PHE 0.020 0.002 PHE o 70 TYR 0.019 0.002 TYR B 87 ARG 0.004 0.000 ARG Q 36 Details of bonding type rmsd hydrogen bonds : bond 0.05300 ( 892) hydrogen bonds : angle 3.59548 ( 2280) metal coordination : bond 0.02444 ( 16) metal coordination : angle 12.07870 ( 18) covalent geometry : bond 0.00427 (15158) covalent geometry : angle 0.62218 (21663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 286 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8864 (mt) cc_final: 0.8622 (mt) REVERT: A 71 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8145 (mtm-85) REVERT: N 74 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8549 (mmmm) REVERT: N 77 ARG cc_start: 0.7834 (mtm180) cc_final: 0.7584 (mtm180) REVERT: N 95 LYS cc_start: 0.9048 (tppt) cc_final: 0.8740 (tppp) REVERT: O 59 MET cc_start: 0.8772 (tpp) cc_final: 0.8039 (tpp) REVERT: O 63 ASN cc_start: 0.8223 (m-40) cc_final: 0.7928 (m-40) REVERT: O 84 ASN cc_start: 0.8488 (t0) cc_final: 0.7920 (t0) REVERT: O 86 ARG cc_start: 0.7615 (tpp80) cc_final: 0.7262 (tpp80) REVERT: O 99 ARG cc_start: 0.8252 (mtm180) cc_final: 0.7866 (mtm180) REVERT: O 108 LYS cc_start: 0.8959 (mttt) cc_final: 0.8322 (mtpt) REVERT: O 113 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7676 (mm-30) REVERT: O 116 LYS cc_start: 0.8650 (ttpp) cc_final: 0.7883 (tttp) REVERT: P 54 TYR cc_start: 0.7831 (m-80) cc_final: 0.7526 (m-80) REVERT: P 73 GLU cc_start: 0.7909 (tp30) cc_final: 0.7673 (tp30) REVERT: P 90 MET cc_start: 0.8043 (mmt) cc_final: 0.7818 (mmt) REVERT: Q 30 THR cc_start: 0.9351 (p) cc_final: 0.8790 (t) REVERT: Q 44 LYS cc_start: 0.8819 (tttm) cc_final: 0.8227 (ttmm) REVERT: Q 74 GLU cc_start: 0.8254 (tt0) cc_final: 0.7819 (tt0) REVERT: n 74 LYS cc_start: 0.8890 (mttt) cc_final: 0.8304 (tttt) REVERT: n 84 GLN cc_start: 0.8145 (tt0) cc_final: 0.7748 (tt0) REVERT: q 88 TYR cc_start: 0.8810 (m-10) cc_final: 0.8258 (m-80) outliers start: 27 outliers final: 16 residues processed: 296 average time/residue: 0.2928 time to fit residues: 121.9335 Evaluate side-chains 281 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 264 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain N residue 94 ASN Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 91 GLU Chi-restraints excluded: chain p residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 70 optimal weight: 20.0000 chunk 119 optimal weight: 0.9990 chunk 5 optimal weight: 30.0000 chunk 65 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 81 GLN N 24 GLN P 113 HIS ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 93 GLN q 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.215554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.139705 restraints weight = 21664.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144581 restraints weight = 11331.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.147661 restraints weight = 7891.506| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15174 Z= 0.165 Angle : 0.674 24.137 21681 Z= 0.341 Chirality : 0.036 0.192 2459 Planarity : 0.004 0.059 1791 Dihedral : 27.792 149.454 4242 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.58 % Favored : 98.32 % Rotamer: Outliers : 2.58 % Allowed : 13.66 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1073 helix: 2.15 (0.19), residues: 682 sheet: 1.26 (1.30), residues: 18 loop : -0.33 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 293 HIS 0.008 0.001 HIS p 113 PHE 0.015 0.002 PHE p 67 TYR 0.021 0.002 TYR o 40 ARG 0.006 0.000 ARG O 79 Details of bonding type rmsd hydrogen bonds : bond 0.04701 ( 892) hydrogen bonds : angle 3.43824 ( 2280) metal coordination : bond 0.01134 ( 16) metal coordination : angle 12.02906 ( 18) covalent geometry : bond 0.00368 (15158) covalent geometry : angle 0.57800 (21663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 277 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8099 (mtm-85) REVERT: N 36 LYS cc_start: 0.8388 (tttt) cc_final: 0.8043 (tttt) REVERT: N 39 TYR cc_start: 0.8865 (m-80) cc_final: 0.8630 (m-10) REVERT: N 74 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8546 (mmmm) REVERT: N 95 LYS cc_start: 0.9123 (tppt) cc_final: 0.8172 (tptt) REVERT: O 59 MET cc_start: 0.8694 (tpp) cc_final: 0.7932 (mmm) REVERT: O 63 ASN cc_start: 0.8240 (m-40) cc_final: 0.7899 (m-40) REVERT: O 84 ASN cc_start: 0.8599 (t0) cc_final: 0.6823 (t0) REVERT: O 86 ARG cc_start: 0.7775 (tpp80) cc_final: 0.6870 (mpp80) REVERT: O 108 LYS cc_start: 0.8943 (mttt) cc_final: 0.8320 (mtpt) REVERT: O 116 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8015 (tttp) REVERT: P 90 MET cc_start: 0.8116 (mmt) cc_final: 0.7894 (mmt) REVERT: Q 30 THR cc_start: 0.9367 (p) cc_final: 0.8844 (t) REVERT: Q 44 LYS cc_start: 0.8730 (tttm) cc_final: 0.8143 (ttmm) REVERT: Q 62 LEU cc_start: 0.9318 (mm) cc_final: 0.9084 (mm) REVERT: Q 74 GLU cc_start: 0.8249 (tt0) cc_final: 0.7795 (tt0) REVERT: n 39 TYR cc_start: 0.8353 (m-80) cc_final: 0.7964 (m-80) REVERT: n 51 MET cc_start: 0.7831 (ttt) cc_final: 0.7606 (ttt) REVERT: n 74 LYS cc_start: 0.9006 (mttt) cc_final: 0.8470 (tttt) REVERT: n 84 GLN cc_start: 0.8106 (tt0) cc_final: 0.7786 (tt0) REVERT: o 93 GLU cc_start: 0.8578 (mp0) cc_final: 0.8096 (mp0) REVERT: q 92 ARG cc_start: 0.8223 (mtp-110) cc_final: 0.7888 (mtp-110) outliers start: 24 outliers final: 14 residues processed: 287 average time/residue: 0.3716 time to fit residues: 147.9098 Evaluate side-chains 275 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 260 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain p residue 97 GLU Chi-restraints excluded: chain q residue 62 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 ASN N 112 GLN P 113 HIS ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.210615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133525 restraints weight = 21695.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.138290 restraints weight = 11337.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141215 restraints weight = 7894.580| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15174 Z= 0.220 Angle : 0.709 23.612 21681 Z= 0.359 Chirality : 0.037 0.207 2459 Planarity : 0.005 0.059 1791 Dihedral : 27.863 151.576 4242 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.86 % Rotamer: Outliers : 3.76 % Allowed : 14.52 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.25), residues: 1073 helix: 2.06 (0.19), residues: 684 sheet: 1.51 (1.35), residues: 18 loop : -0.41 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 34 HIS 0.007 0.001 HIS p 113 PHE 0.017 0.002 PHE P 67 TYR 0.030 0.002 TYR o 40 ARG 0.005 0.001 ARG O 79 Details of bonding type rmsd hydrogen bonds : bond 0.04894 ( 892) hydrogen bonds : angle 3.62440 ( 2280) metal coordination : bond 0.01091 ( 16) metal coordination : angle 11.66734 ( 18) covalent geometry : bond 0.00496 (15158) covalent geometry : angle 0.62479 (21663) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8123 (mtm-85) REVERT: N 36 LYS cc_start: 0.8402 (tttt) cc_final: 0.8040 (tttt) REVERT: N 39 TYR cc_start: 0.8829 (m-80) cc_final: 0.8561 (m-10) REVERT: N 74 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8588 (mmmm) REVERT: N 94 ASN cc_start: 0.8916 (t0) cc_final: 0.8703 (t0) REVERT: O 63 ASN cc_start: 0.8358 (m-40) cc_final: 0.8107 (m-40) REVERT: O 84 ASN cc_start: 0.8704 (t0) cc_final: 0.8353 (t0) REVERT: O 85 LYS cc_start: 0.8479 (tppt) cc_final: 0.8213 (ttmt) REVERT: O 108 LYS cc_start: 0.9064 (mttt) cc_final: 0.8468 (mtpt) REVERT: O 113 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7515 (mm-30) REVERT: O 116 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8032 (tttp) REVERT: P 100 LEU cc_start: 0.9394 (mt) cc_final: 0.9040 (mt) REVERT: Q 27 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8292 (mm110) REVERT: Q 30 THR cc_start: 0.9430 (p) cc_final: 0.8893 (t) REVERT: Q 44 LYS cc_start: 0.8849 (tttm) cc_final: 0.8284 (ttmm) REVERT: Q 74 GLU cc_start: 0.8205 (tt0) cc_final: 0.7924 (tt0) REVERT: Q 84 MET cc_start: 0.7991 (mmt) cc_final: 0.7587 (mmt) REVERT: n 39 TYR cc_start: 0.8543 (m-80) cc_final: 0.8288 (m-80) REVERT: n 73 ASN cc_start: 0.8695 (t0) cc_final: 0.8451 (t0) REVERT: n 74 LYS cc_start: 0.9100 (mttt) cc_final: 0.8576 (tttt) REVERT: n 84 GLN cc_start: 0.8090 (tt0) cc_final: 0.7766 (tt0) REVERT: o 71 GLU cc_start: 0.7466 (tp30) cc_final: 0.7081 (tp30) REVERT: q 88 TYR cc_start: 0.8712 (m-10) cc_final: 0.8176 (m-80) outliers start: 35 outliers final: 25 residues processed: 301 average time/residue: 0.2957 time to fit residues: 124.4248 Evaluate side-chains 302 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 26 ILE Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 80 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 96 optimal weight: 0.0570 chunk 55 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN N 24 GLN p 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.213654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136894 restraints weight = 21852.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141747 restraints weight = 11371.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144766 restraints weight = 7884.695| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15174 Z= 0.155 Angle : 0.681 24.332 21681 Z= 0.338 Chirality : 0.035 0.209 2459 Planarity : 0.004 0.057 1791 Dihedral : 27.785 153.303 4242 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 2.69 % Allowed : 17.85 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.25), residues: 1073 helix: 2.26 (0.19), residues: 681 sheet: 1.53 (1.37), residues: 18 loop : -0.41 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 34 HIS 0.015 0.001 HIS n 31 PHE 0.013 0.002 PHE P 67 TYR 0.029 0.002 TYR o 40 ARG 0.006 0.000 ARG O 79 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 892) hydrogen bonds : angle 3.42233 ( 2280) metal coordination : bond 0.01117 ( 16) metal coordination : angle 11.63420 ( 18) covalent geometry : bond 0.00339 (15158) covalent geometry : angle 0.59254 (21663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 275 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8142 (mtm-85) REVERT: A 78 ARG cc_start: 0.9040 (mmp80) cc_final: 0.8660 (mmp80) REVERT: N 36 LYS cc_start: 0.8395 (tttt) cc_final: 0.8018 (tttt) REVERT: N 39 TYR cc_start: 0.8717 (m-80) cc_final: 0.8313 (m-10) REVERT: N 74 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8604 (mmmm) REVERT: O 62 MET cc_start: 0.9068 (mmt) cc_final: 0.8868 (mmm) REVERT: O 63 ASN cc_start: 0.8341 (m-40) cc_final: 0.8048 (m-40) REVERT: O 71 GLU cc_start: 0.8347 (tp30) cc_final: 0.7861 (tp30) REVERT: O 84 ASN cc_start: 0.8721 (t0) cc_final: 0.8323 (t0) REVERT: O 108 LYS cc_start: 0.9004 (mttt) cc_final: 0.8392 (mtpt) REVERT: O 113 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7435 (mm-30) REVERT: O 116 LYS cc_start: 0.8728 (ttpp) cc_final: 0.8161 (tttp) REVERT: P 100 LEU cc_start: 0.9356 (mt) cc_final: 0.9084 (mt) REVERT: Q 27 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8270 (mm-40) REVERT: Q 59 LYS cc_start: 0.8342 (tttm) cc_final: 0.8111 (tptm) REVERT: Q 74 GLU cc_start: 0.8137 (tt0) cc_final: 0.7813 (tt0) REVERT: Q 84 MET cc_start: 0.7949 (mmt) cc_final: 0.7597 (mmt) REVERT: n 39 TYR cc_start: 0.8540 (m-80) cc_final: 0.8303 (m-80) REVERT: n 73 ASN cc_start: 0.8644 (t0) cc_final: 0.8214 (t0) REVERT: n 74 LYS cc_start: 0.9141 (mttt) cc_final: 0.8551 (tptm) REVERT: n 84 GLN cc_start: 0.8028 (tt0) cc_final: 0.7687 (tt0) REVERT: o 47 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7515 (tt0) REVERT: o 71 GLU cc_start: 0.7392 (tp30) cc_final: 0.6994 (tp30) REVERT: o 99 ARG cc_start: 0.8703 (mtp180) cc_final: 0.8291 (ttm170) REVERT: p 90 MET cc_start: 0.8580 (tpt) cc_final: 0.8349 (mmt) outliers start: 25 outliers final: 19 residues processed: 284 average time/residue: 0.2957 time to fit residues: 117.4376 Evaluate side-chains 285 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 265 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 92 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 93 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** q 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.210372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133577 restraints weight = 21680.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.138361 restraints weight = 11289.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141251 restraints weight = 7834.839| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15174 Z= 0.198 Angle : 0.704 23.667 21681 Z= 0.351 Chirality : 0.036 0.215 2459 Planarity : 0.004 0.059 1791 Dihedral : 27.807 154.945 4242 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 3.55 % Allowed : 17.42 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1073 helix: 2.09 (0.19), residues: 683 sheet: 1.80 (1.39), residues: 18 loop : -0.48 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 34 HIS 0.016 0.001 HIS n 31 PHE 0.014 0.002 PHE P 67 TYR 0.035 0.002 TYR o 40 ARG 0.006 0.000 ARG Q 92 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 892) hydrogen bonds : angle 3.59001 ( 2280) metal coordination : bond 0.00971 ( 16) metal coordination : angle 11.73319 ( 18) covalent geometry : bond 0.00447 (15158) covalent geometry : angle 0.61800 (21663) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 285 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.8481 (Cg_exo) cc_final: 0.8277 (Cg_endo) REVERT: A 78 ARG cc_start: 0.9105 (mmp80) cc_final: 0.8468 (mmm-85) REVERT: N 36 LYS cc_start: 0.8399 (tttt) cc_final: 0.8044 (tttt) REVERT: N 39 TYR cc_start: 0.8752 (m-80) cc_final: 0.8279 (m-10) REVERT: N 74 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8607 (mmmm) REVERT: O 37 TYR cc_start: 0.8856 (m-80) cc_final: 0.8553 (m-80) REVERT: O 63 ASN cc_start: 0.8399 (m-40) cc_final: 0.8148 (m-40) REVERT: O 71 GLU cc_start: 0.8365 (tp30) cc_final: 0.7862 (tp30) REVERT: O 84 ASN cc_start: 0.8755 (t0) cc_final: 0.8325 (t0) REVERT: O 108 LYS cc_start: 0.9055 (mttt) cc_final: 0.8434 (mtpt) REVERT: O 113 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7340 (mm-30) REVERT: O 116 LYS cc_start: 0.8744 (ttpp) cc_final: 0.8180 (tttp) REVERT: P 100 LEU cc_start: 0.9393 (mt) cc_final: 0.9138 (mt) REVERT: Q 27 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8380 (mm-40) REVERT: Q 30 THR cc_start: 0.9379 (p) cc_final: 0.8858 (t) REVERT: Q 59 LYS cc_start: 0.8478 (tttm) cc_final: 0.8184 (tptm) REVERT: Q 74 GLU cc_start: 0.8103 (tt0) cc_final: 0.7877 (tt0) REVERT: Q 84 MET cc_start: 0.8085 (mmt) cc_final: 0.7749 (mmt) REVERT: n 35 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7660 (mtm-85) REVERT: n 73 ASN cc_start: 0.8696 (t0) cc_final: 0.8248 (t0) REVERT: n 74 LYS cc_start: 0.9165 (mttt) cc_final: 0.8519 (tptm) REVERT: o 71 GLU cc_start: 0.7396 (tp30) cc_final: 0.6888 (tp30) REVERT: q 36 ARG cc_start: 0.9044 (mtm-85) cc_final: 0.7665 (mtm180) outliers start: 33 outliers final: 28 residues processed: 298 average time/residue: 0.2992 time to fit residues: 123.3526 Evaluate side-chains 309 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 281 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 26 ILE Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 71 THR Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 102 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 25 ASN ** q 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.212446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.136149 restraints weight = 21547.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.141001 restraints weight = 11193.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143967 restraints weight = 7752.168| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15174 Z= 0.161 Angle : 0.692 24.272 21681 Z= 0.341 Chirality : 0.035 0.179 2459 Planarity : 0.004 0.058 1791 Dihedral : 27.781 156.180 4242 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 2.69 % Allowed : 18.17 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.25), residues: 1073 helix: 2.20 (0.19), residues: 683 sheet: 1.84 (1.37), residues: 18 loop : -0.38 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 34 HIS 0.013 0.001 HIS n 31 PHE 0.017 0.002 PHE o 70 TYR 0.032 0.002 TYR o 40 ARG 0.007 0.000 ARG O 79 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 892) hydrogen bonds : angle 3.45369 ( 2280) metal coordination : bond 0.00894 ( 16) metal coordination : angle 11.48765 ( 18) covalent geometry : bond 0.00358 (15158) covalent geometry : angle 0.60779 (21663) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 292 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.8481 (Cg_exo) cc_final: 0.8255 (Cg_endo) REVERT: A 208 LYS cc_start: 0.7536 (mmmt) cc_final: 0.7327 (mmmt) REVERT: N 36 LYS cc_start: 0.8397 (tttt) cc_final: 0.7915 (tttt) REVERT: N 39 TYR cc_start: 0.8662 (m-80) cc_final: 0.8256 (m-10) REVERT: N 74 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8613 (mmmm) REVERT: O 37 TYR cc_start: 0.8841 (m-80) cc_final: 0.8554 (m-80) REVERT: O 63 ASN cc_start: 0.8403 (m-40) cc_final: 0.8090 (m-40) REVERT: O 71 GLU cc_start: 0.8324 (tp30) cc_final: 0.7828 (tp30) REVERT: O 84 ASN cc_start: 0.8699 (t0) cc_final: 0.8332 (t0) REVERT: O 108 LYS cc_start: 0.8968 (mttt) cc_final: 0.8381 (mtpt) REVERT: O 116 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8093 (tttp) REVERT: Q 27 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8355 (mm-40) REVERT: Q 59 LYS cc_start: 0.8421 (tttm) cc_final: 0.8140 (tptm) REVERT: Q 84 MET cc_start: 0.7953 (mmt) cc_final: 0.7583 (mmt) REVERT: n 35 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7681 (mtm-85) REVERT: n 73 ASN cc_start: 0.8634 (t0) cc_final: 0.8238 (t0) REVERT: n 74 LYS cc_start: 0.9164 (mttt) cc_final: 0.8563 (tptm) REVERT: n 84 GLN cc_start: 0.8005 (tt0) cc_final: 0.7711 (tt0) REVERT: o 47 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7533 (tt0) REVERT: o 71 GLU cc_start: 0.7375 (tp30) cc_final: 0.7170 (tp30) REVERT: o 99 ARG cc_start: 0.8606 (mtp180) cc_final: 0.8262 (ttm170) outliers start: 25 outliers final: 21 residues processed: 304 average time/residue: 0.3478 time to fit residues: 147.1672 Evaluate side-chains 302 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 281 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 90 THR Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 51 optimal weight: 0.2980 chunk 18 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 0.0070 chunk 21 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 9 optimal weight: 8.9990 chunk 62 optimal weight: 0.0270 chunk 64 optimal weight: 3.9990 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 HIS ** q 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.215289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.140155 restraints weight = 21580.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.145078 restraints weight = 11184.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.148101 restraints weight = 7736.051| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15174 Z= 0.144 Angle : 0.700 24.263 21681 Z= 0.344 Chirality : 0.036 0.249 2459 Planarity : 0.004 0.059 1791 Dihedral : 27.708 156.920 4242 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.86 % Rotamer: Outliers : 2.04 % Allowed : 19.14 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.25), residues: 1073 helix: 2.29 (0.19), residues: 684 sheet: 1.84 (1.36), residues: 18 loop : -0.31 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 34 HIS 0.009 0.001 HIS n 31 PHE 0.012 0.001 PHE p 67 TYR 0.032 0.001 TYR o 40 ARG 0.007 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 892) hydrogen bonds : angle 3.46061 ( 2280) metal coordination : bond 0.00863 ( 16) metal coordination : angle 11.31519 ( 18) covalent geometry : bond 0.00306 (15158) covalent geometry : angle 0.61950 (21663) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 276 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.8468 (Cg_exo) cc_final: 0.8246 (Cg_endo) REVERT: N 20 ARG cc_start: 0.8609 (mtt90) cc_final: 0.8288 (mtm-85) REVERT: N 36 LYS cc_start: 0.8358 (tttt) cc_final: 0.7924 (tttt) REVERT: N 39 TYR cc_start: 0.8581 (m-80) cc_final: 0.8197 (m-10) REVERT: N 74 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8640 (mmmm) REVERT: O 37 TYR cc_start: 0.8831 (m-80) cc_final: 0.8516 (m-80) REVERT: O 59 MET cc_start: 0.8766 (tpp) cc_final: 0.7918 (mmm) REVERT: O 63 ASN cc_start: 0.8329 (m-40) cc_final: 0.7925 (m-40) REVERT: O 71 GLU cc_start: 0.8438 (tp30) cc_final: 0.7859 (tp30) REVERT: O 84 ASN cc_start: 0.8683 (t0) cc_final: 0.8294 (t0) REVERT: O 99 ARG cc_start: 0.8045 (mtm180) cc_final: 0.7801 (mtm180) REVERT: O 108 LYS cc_start: 0.8888 (mttt) cc_final: 0.8289 (mtpt) REVERT: Q 27 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8359 (mm-40) REVERT: Q 35 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.7829 (mtp85) REVERT: Q 44 LYS cc_start: 0.8732 (tttm) cc_final: 0.8161 (ttmm) REVERT: Q 59 LYS cc_start: 0.8346 (tttm) cc_final: 0.8131 (tptm) REVERT: Q 74 GLU cc_start: 0.8236 (tt0) cc_final: 0.7910 (tt0) REVERT: Q 84 MET cc_start: 0.7890 (mmt) cc_final: 0.7487 (mmt) REVERT: Q 92 ARG cc_start: 0.7212 (tpm170) cc_final: 0.6812 (tpm170) REVERT: n 73 ASN cc_start: 0.8607 (t0) cc_final: 0.8288 (t0) REVERT: n 74 LYS cc_start: 0.9185 (mttt) cc_final: 0.8620 (tptm) REVERT: o 47 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7567 (tt0) REVERT: o 71 GLU cc_start: 0.7354 (tp30) cc_final: 0.6902 (tp30) REVERT: o 99 ARG cc_start: 0.8444 (mtp180) cc_final: 0.8112 (ttm170) REVERT: p 129 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7157 (tpp80) outliers start: 19 outliers final: 17 residues processed: 284 average time/residue: 0.3208 time to fit residues: 124.8641 Evaluate side-chains 287 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 270 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 98 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 75 HIS ** 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 = 0.4335 r_free = 0.4335 target = 0.212021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.135578 restraints weight = 21312.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.140327 restraints weight = 11092.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.143316 restraints weight = 7713.972| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15174 Z= 0.178 Angle : 0.709 22.843 21681 Z= 0.352 Chirality : 0.036 0.180 2459 Planarity : 0.004 0.072 1791 Dihedral : 27.732 158.141 4242 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.52 % Favored : 97.39 % Rotamer: Outliers : 2.37 % Allowed : 20.22 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.25), residues: 1073 helix: 2.26 (0.19), residues: 682 sheet: 1.89 (1.36), residues: 18 loop : -0.37 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 34 HIS 0.031 0.002 HIS n 31 PHE 0.018 0.002 PHE o 70 TYR 0.029 0.002 TYR o 40 ARG 0.010 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 892) hydrogen bonds : angle 3.57977 ( 2280) metal coordination : bond 0.00860 ( 16) metal coordination : angle 11.03938 ( 18) covalent geometry : bond 0.00400 (15158) covalent geometry : angle 0.63424 (21663) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 274 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8963 (mttt) cc_final: 0.8607 (mttt) REVERT: A 208 LYS cc_start: 0.7492 (mmmt) cc_final: 0.7218 (mmmt) REVERT: B 43 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7597 (mtm-85) REVERT: N 36 LYS cc_start: 0.8374 (tttt) cc_final: 0.7917 (tttt) REVERT: N 39 TYR cc_start: 0.8660 (m-80) cc_final: 0.8181 (m-10) REVERT: N 61 GLU cc_start: 0.8215 (tp30) cc_final: 0.7970 (tt0) REVERT: N 74 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8634 (mmmm) REVERT: O 37 TYR cc_start: 0.8827 (m-80) cc_final: 0.8499 (m-80) REVERT: O 59 MET cc_start: 0.8821 (tpp) cc_final: 0.8066 (tpp) REVERT: O 63 ASN cc_start: 0.8337 (m-40) cc_final: 0.8077 (m-40) REVERT: O 71 GLU cc_start: 0.8326 (tp30) cc_final: 0.7795 (tp30) REVERT: O 84 ASN cc_start: 0.8689 (t0) cc_final: 0.8305 (t0) REVERT: O 99 ARG cc_start: 0.8103 (mtm180) cc_final: 0.7831 (mtm180) REVERT: O 108 LYS cc_start: 0.8976 (mttt) cc_final: 0.8345 (mtpt) REVERT: Q 27 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8488 (mm-40) REVERT: Q 30 THR cc_start: 0.9403 (p) cc_final: 0.8872 (t) REVERT: Q 59 LYS cc_start: 0.8488 (tttm) cc_final: 0.8192 (tptm) REVERT: Q 74 GLU cc_start: 0.8203 (tt0) cc_final: 0.7985 (tt0) REVERT: Q 84 MET cc_start: 0.8063 (mmt) cc_final: 0.7690 (mmt) REVERT: Q 92 ARG cc_start: 0.7168 (tpm170) cc_final: 0.6793 (tpm170) REVERT: n 38 ASN cc_start: 0.8163 (t0) cc_final: 0.7955 (t0) REVERT: n 73 ASN cc_start: 0.8634 (t0) cc_final: 0.8308 (t0) REVERT: n 74 LYS cc_start: 0.9192 (mttt) cc_final: 0.8670 (tptm) REVERT: o 47 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7533 (tt0) REVERT: o 71 GLU cc_start: 0.7462 (tp30) cc_final: 0.7090 (tp30) outliers start: 22 outliers final: 19 residues processed: 283 average time/residue: 0.3133 time to fit residues: 121.9711 Evaluate side-chains 291 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 272 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 77 LYS Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 8 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 70 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.212646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136526 restraints weight = 21589.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141420 restraints weight = 11133.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.144370 restraints weight = 7705.534| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15174 Z= 0.163 Angle : 0.708 23.217 21681 Z= 0.348 Chirality : 0.036 0.209 2459 Planarity : 0.004 0.055 1791 Dihedral : 27.748 159.851 4242 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.42 % Favored : 97.48 % Rotamer: Outliers : 2.47 % Allowed : 20.43 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.26), residues: 1073 helix: 2.29 (0.20), residues: 682 sheet: 1.78 (1.37), residues: 18 loop : -0.41 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 34 HIS 0.024 0.001 HIS n 31 PHE 0.017 0.002 PHE o 70 TYR 0.028 0.002 TYR o 40 ARG 0.013 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 892) hydrogen bonds : angle 3.52826 ( 2280) metal coordination : bond 0.00917 ( 16) metal coordination : angle 11.24074 ( 18) covalent geometry : bond 0.00361 (15158) covalent geometry : angle 0.63006 (21663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5329.54 seconds wall clock time: 96 minutes 3.77 seconds (5763.77 seconds total)