Starting phenix.real_space_refine (version: dev) on Tue Feb 21 08:36:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzv_22581/02_2023/7jzv_22581.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzv_22581/02_2023/7jzv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzv_22581/02_2023/7jzv_22581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzv_22581/02_2023/7jzv_22581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzv_22581/02_2023/7jzv_22581.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzv_22581/02_2023/7jzv_22581.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 105": "OE1" <-> "OE2" Residue "P TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 8.14, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.39 Conformation dependent library (CDL) restraints added in 1.4 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: 5.92 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: 5.80 Time building geometry restraints manager: 6.81 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: 98.50 - 105.63: 1590 105.63 - 112.76: 8122 112.76 - 119.89: 5012 119.89 - 127.02: 6283 127.02 - 134.15: 656 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: 6601 25.39 - 50.77: 1191 50.77 - 76.16: 416 76.16 - 101.54: 7 101.54 - 126.93: 1 Dihedral angle restraints: 8216 sinusoidal: 5047 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 8213 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 2.440 nonbonded pdb=" OP1 DC X 77 " pdb=" OG SER q 47 " model vdw 2.261 2.440 nonbonded pdb=" O ARG A 71 " pdb=" OG SER A 72 " model vdw 2.300 2.440 nonbonded pdb=" OP1 DG Y 67 " pdb=" N VAL p 117 " model vdw 2.306 2.520 nonbonded pdb=" OG SER O 32 " pdb=" OP1 DC X 100 " model vdw 2.334 2.440 ... (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 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 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. 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: 0.790 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: 4.930 Check model and map are aligned: 0.220 Process input model: 46.320 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 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 15158 Z= 0.768 Angle : 1.325 12.099 21663 Z= 0.881 Chirality : 0.069 0.354 2459 Planarity : 0.004 0.049 1791 Dihedral : 24.069 126.927 6166 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 % 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 327 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 329 average time/residue: 0.3183 time to fit residues: 141.3625 Evaluate side-chains 250 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5567 ------------------------------------------------------------------------------- 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: 0.7980 chunk 99 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 103 ASN N 110 ASN N 112 GLN ** O 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 15158 Z= 0.246 Angle : 0.650 11.187 21663 Z= 0.377 Chirality : 0.039 0.243 2459 Planarity : 0.005 0.044 1791 Dihedral : 28.017 145.178 3998 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.68 % Favored : 98.23 % Rotamer Outliers : 2.47 % 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: 1.89 (0.24), residues: 1073 helix: 1.99 (0.19), residues: 682 sheet: 0.17 (1.29), residues: 18 loop : -0.00 (0.29), residues: 373 *********************** 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 309 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 286 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 294 average time/residue: 0.2928 time to fit residues: 119.7663 Evaluate side-chains 277 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 261 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1255 time to fit residues: 5.3234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 81 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN B 98 ASN N 24 GLN N 94 ASN O 84 ASN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 82 HIS ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 93 GLN q 25 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 15158 Z= 0.204 Angle : 0.597 10.368 21663 Z= 0.345 Chirality : 0.037 0.197 2459 Planarity : 0.004 0.049 1791 Dihedral : 28.329 147.191 3998 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.04 % Rotamer Outliers : 1.83 % 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: 2.03 (0.25), residues: 1073 helix: 2.17 (0.19), residues: 685 sheet: 0.43 (1.27), residues: 18 loop : -0.14 (0.29), residues: 370 *********************** 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 295 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 278 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 289 average time/residue: 0.2886 time to fit residues: 117.9998 Evaluate side-chains 267 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 262 time to evaluate : 1.484 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1315 time to fit residues: 2.7841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 126 optimal weight: 0.1980 chunk 62 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN N 24 GLN ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 93 GLN q 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 15158 Z= 0.193 Angle : 0.567 7.817 21663 Z= 0.331 Chirality : 0.036 0.191 2459 Planarity : 0.004 0.055 1791 Dihedral : 28.227 149.690 3998 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.58 % Favored : 98.32 % Rotamer Outliers : 1.83 % 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: 1.97 (0.25), residues: 1073 helix: 2.16 (0.19), residues: 684 sheet: 0.82 (1.30), residues: 18 loop : -0.28 (0.29), residues: 371 *********************** 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 291 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 274 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 280 average time/residue: 0.3128 time to fit residues: 123.2218 Evaluate side-chains 272 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 262 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1747 time to fit residues: 4.3908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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** N 24 GLN ** p 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 15158 Z= 0.289 Angle : 0.631 11.613 21663 Z= 0.357 Chirality : 0.037 0.202 2459 Planarity : 0.005 0.055 1791 Dihedral : 28.394 151.802 3998 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer Outliers : 2.69 % 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: 1.54 (0.25), residues: 1073 helix: 1.78 (0.19), residues: 684 sheet: 1.49 (1.35), residues: 18 loop : -0.39 (0.30), residues: 371 *********************** 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 316 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 291 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 301 average time/residue: 0.2948 time to fit residues: 123.8227 Evaluate side-chains 298 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 283 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1596 time to fit residues: 5.5887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 105 optimal weight: 0.0370 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 103 ASN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 HIS ** p 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 15158 Z= 0.189 Angle : 0.595 12.902 21663 Z= 0.336 Chirality : 0.035 0.155 2459 Planarity : 0.004 0.044 1791 Dihedral : 28.311 153.211 3998 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.86 % Rotamer Outliers : 1.61 % 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: 1.84 (0.25), residues: 1073 helix: 2.11 (0.20), residues: 681 sheet: 1.65 (1.38), residues: 18 loop : -0.47 (0.30), residues: 374 *********************** 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 291 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 276 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 281 average time/residue: 0.3031 time to fit residues: 118.3261 Evaluate side-chains 273 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 265 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1276 time to fit residues: 3.5123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 106 optimal weight: 0.1980 chunk 70 optimal weight: 20.0000 chunk 126 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN Q 25 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 47 GLN p 93 GLN ** q 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 15158 Z= 0.246 Angle : 0.624 13.857 21663 Z= 0.347 Chirality : 0.036 0.194 2459 Planarity : 0.004 0.054 1791 Dihedral : 28.288 154.458 3998 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.52 % Favored : 97.39 % Rotamer Outliers : 1.51 % 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: 1.76 (0.25), residues: 1073 helix: 2.05 (0.19), residues: 681 sheet: 1.77 (1.36), residues: 18 loop : -0.52 (0.30), residues: 374 *********************** 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 294 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 280 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 285 average time/residue: 0.3077 time to fit residues: 121.5428 Evaluate side-chains 281 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 270 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1651 time to fit residues: 4.3487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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** P 93 GLN Q 25 ASN n 38 ASN ** n 84 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 15158 Z= 0.266 Angle : 0.653 14.506 21663 Z= 0.360 Chirality : 0.037 0.181 2459 Planarity : 0.005 0.055 1791 Dihedral : 28.316 156.808 3998 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.58 % Rotamer Outliers : 1.83 % 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: 1.57 (0.25), residues: 1073 helix: 1.89 (0.19), residues: 682 sheet: 1.69 (1.37), residues: 18 loop : -0.58 (0.31), residues: 373 *********************** 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 311 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 294 time to evaluate : 1.278 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 298 average time/residue: 0.3229 time to fit residues: 132.4992 Evaluate side-chains 290 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 282 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1511 time to fit residues: 3.7252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 70 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 0.0270 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN Q 25 ASN ** n 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 47 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 15158 Z= 0.197 Angle : 0.647 15.353 21663 Z= 0.355 Chirality : 0.036 0.195 2459 Planarity : 0.004 0.055 1791 Dihedral : 28.266 157.740 3998 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.92 % Rotamer Outliers : 0.54 % 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: 1.75 (0.25), residues: 1073 helix: 2.03 (0.19), residues: 682 sheet: 1.88 (1.41), residues: 18 loop : -0.52 (0.31), residues: 373 *********************** 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 284 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 279 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 281 average time/residue: 0.3144 time to fit residues: 121.0997 Evaluate side-chains 272 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1296 time to fit residues: 2.1085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 93 GLN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 38 ASN ** n 84 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 15158 Z= 0.211 Angle : 0.654 15.131 21663 Z= 0.358 Chirality : 0.036 0.229 2459 Planarity : 0.005 0.054 1791 Dihedral : 28.195 158.651 3998 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.20 % Rotamer Outliers : 0.86 % 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: 1.75 (0.25), residues: 1073 helix: 2.00 (0.19), residues: 680 sheet: 2.05 (1.44), residues: 18 loop : -0.45 (0.32), residues: 375 ********************** 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 282 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 274 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 275 average time/residue: 0.3145 time to fit residues: 119.5616 Evaluate side-chains 273 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 268 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1409 time to fit residues: 2.9310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 13 optimal weight: 0.0870 chunk 19 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 18 HIS Q 25 ASN n 38 ASN ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 47 GLN ** p 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 76 GLN ** q 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.206905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128733 restraints weight = 21292.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.133362 restraints weight = 11380.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.136142 restraints weight = 8042.086| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 15158 Z= 0.377 Angle : 0.727 14.175 21663 Z= 0.398 Chirality : 0.040 0.253 2459 Planarity : 0.005 0.062 1791 Dihedral : 28.363 161.517 3998 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer Outliers : 0.32 % 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: 1.29 (0.25), residues: 1073 helix: 1.61 (0.19), residues: 683 sheet: 2.15 (1.46), residues: 18 loop : -0.59 (0.32), residues: 372 =============================================================================== Job complete usr+sys time: 2799.82 seconds wall clock time: 51 minutes 12.86 seconds (3072.86 seconds total)