Starting phenix.real_space_refine on Thu Sep 26 07:09:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkd_33248/09_2024/7xkd_33248.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkd_33248/09_2024/7xkd_33248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkd_33248/09_2024/7xkd_33248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkd_33248/09_2024/7xkd_33248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkd_33248/09_2024/7xkd_33248.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkd_33248/09_2024/7xkd_33248.cif" } resolution = 2.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5427 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5087 2.51 5 N 1372 2.21 5 O 1455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7962 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2086 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'AND': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.36, per 1000 atoms: 0.67 Number of scatterers: 7962 At special positions: 0 Unit cell: (103.887, 109.242, 95.319, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1455 8.00 N 1372 7.00 C 5087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 686 " - pdb=" SG CYS R 770 " distance=2.03 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: 2.30 Conformation dependent library (CDL) restraints added in 997.4 milliseconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 41.3% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.550A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.547A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 58' Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.576A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.893A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.520A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 25 removed outlier: 4.026A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 617 through 645 Processing helix chain 'R' and resid 646 through 649 Processing helix chain 'R' and resid 651 through 677 Processing helix chain 'R' and resid 682 through 716 Processing helix chain 'R' and resid 725 through 749 Proline residue: R 738 - end of helix Processing helix chain 'R' and resid 750 through 753 removed outlier: 3.781A pdb=" N TYR R 753 " --> pdb=" O PRO R 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 750 through 753' Processing helix chain 'R' and resid 776 through 783 Processing helix chain 'R' and resid 783 through 809 Processing helix chain 'R' and resid 820 through 834 removed outlier: 3.989A pdb=" N LEU R 824 " --> pdb=" O SER R 820 " (cutoff:3.500A) Processing helix chain 'R' and resid 835 through 838 Processing helix chain 'R' and resid 839 through 845 removed outlier: 4.145A pdb=" N PHE R 843 " --> pdb=" O GLY R 839 " (cutoff:3.500A) Processing helix chain 'R' and resid 849 through 862 removed outlier: 3.718A pdb=" N LEU R 862 " --> pdb=" O ILE R 858 " (cutoff:3.500A) Processing helix chain 'R' and resid 862 through 872 Processing helix chain 'R' and resid 875 through 883 removed outlier: 3.505A pdb=" N ARG R 879 " --> pdb=" O LYS R 875 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.476A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.631A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.934A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.791A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.718A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.745A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.587A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.853A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1283 1.31 - 1.44: 2278 1.44 - 1.56: 4493 1.56 - 1.69: 8 1.69 - 1.81: 66 Bond restraints: 8128 Sorted by residual: bond pdb=" C5 AND R1001 " pdb=" C6 AND R1001 " ideal model delta sigma weight residual 1.332 1.683 -0.351 2.00e-02 2.50e+03 3.09e+02 bond pdb=" C15 AND R1001 " pdb=" C16 AND R1001 " ideal model delta sigma weight residual 1.535 1.741 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C14 AND R1001 " pdb=" C15 AND R1001 " ideal model delta sigma weight residual 1.529 1.682 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C13 AND R1001 " pdb=" C17 AND R1001 " ideal model delta sigma weight residual 1.514 1.660 -0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C11 AND R1001 " pdb=" C12 AND R1001 " ideal model delta sigma weight residual 1.531 1.642 -0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 8123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10705 1.68 - 3.37: 222 3.37 - 5.05: 61 5.05 - 6.74: 19 6.74 - 8.42: 6 Bond angle restraints: 11013 Sorted by residual: angle pdb=" C ALA N 101 " pdb=" N PRO N 102 " pdb=" CA PRO N 102 " ideal model delta sigma weight residual 120.03 124.44 -4.41 9.90e-01 1.02e+00 1.99e+01 angle pdb=" CA PRO G 53 " pdb=" N PRO G 53 " pdb=" CD PRO G 53 " ideal model delta sigma weight residual 112.00 106.26 5.74 1.40e+00 5.10e-01 1.68e+01 angle pdb=" N ALA B 140 " pdb=" CA ALA B 140 " pdb=" C ALA B 140 " ideal model delta sigma weight residual 108.49 115.17 -6.68 1.65e+00 3.67e-01 1.64e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.53 119.12 -5.59 1.39e+00 5.18e-01 1.62e+01 angle pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta sigma weight residual 119.05 123.35 -4.30 1.11e+00 8.12e-01 1.50e+01 ... (remaining 11008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4245 17.29 - 34.57: 464 34.57 - 51.86: 103 51.86 - 69.14: 22 69.14 - 86.43: 6 Dihedral angle restraints: 4840 sinusoidal: 1920 harmonic: 2920 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 6.57 86.43 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CB CYS R 686 " pdb=" SG CYS R 686 " pdb=" SG CYS R 770 " pdb=" CB CYS R 770 " ideal model delta sinusoidal sigma weight residual -86.00 -125.04 39.04 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 4837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1127 0.078 - 0.156: 112 0.156 - 0.235: 2 0.235 - 0.313: 1 0.313 - 0.391: 1 Chirality restraints: 1243 Sorted by residual: chirality pdb=" C13 AND R1001 " pdb=" C12 AND R1001 " pdb=" C14 AND R1001 " pdb=" C17 AND R1001 " both_signs ideal model delta sigma weight residual False -2.72 -2.32 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C9 AND R1001 " pdb=" C10 AND R1001 " pdb=" C11 AND R1001 " pdb=" C8 AND R1001 " both_signs ideal model delta sigma weight residual False -2.46 -2.74 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1240 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG N 98 " 0.024 2.00e-02 2.50e+03 4.84e-02 2.34e+01 pdb=" C ARG N 98 " -0.084 2.00e-02 2.50e+03 pdb=" O ARG N 98 " 0.032 2.00e-02 2.50e+03 pdb=" N CYS N 99 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.076 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO G 53 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO N 14 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.026 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 37 2.45 - 3.06: 5344 3.06 - 3.67: 11902 3.67 - 4.29: 18288 4.29 - 4.90: 30575 Nonbonded interactions: 66146 Sorted by model distance: nonbonded pdb=" O CYS B 204 " pdb=" OD1 ASP B 228 " model vdw 1.832 3.040 nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.055 3.040 nonbonded pdb=" OD1 ASN A 278 " pdb=" OG SER A 352 " model vdw 2.210 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.215 3.120 nonbonded pdb=" CA ASN A 279 " pdb=" OD2 ASP N 106 " model vdw 2.217 3.470 ... (remaining 66141 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.150 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.007 0.351 8128 Z= 0.485 Angle : 0.682 8.425 11013 Z= 0.378 Chirality : 0.046 0.391 1243 Planarity : 0.006 0.112 1394 Dihedral : 15.111 85.281 2945 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.94 % Allowed : 17.22 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 988 helix: 2.40 (0.26), residues: 375 sheet: -0.04 (0.33), residues: 229 loop : -1.07 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.011 0.001 HIS A 357 PHE 0.012 0.001 PHE R 634 TYR 0.012 0.001 TYR N 60 ARG 0.014 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8813 (mm110) cc_final: 0.8095 (pt0) REVERT: A 381 ASP cc_start: 0.8517 (t70) cc_final: 0.8103 (t70) REVERT: G 13 ARG cc_start: 0.8406 (mtm110) cc_final: 0.7964 (mtm110) outliers start: 8 outliers final: 7 residues processed: 166 average time/residue: 1.3922 time to fit residues: 242.9895 Evaluate side-chains 133 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8128 Z= 0.215 Angle : 0.559 5.449 11013 Z= 0.304 Chirality : 0.042 0.149 1243 Planarity : 0.004 0.067 1394 Dihedral : 4.991 47.171 1163 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.42 % Allowed : 20.17 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.27), residues: 988 helix: 2.54 (0.26), residues: 373 sheet: 0.01 (0.34), residues: 222 loop : -1.04 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.008 0.001 HIS A 357 PHE 0.012 0.001 PHE R 634 TYR 0.016 0.001 TYR A 339 ARG 0.009 0.001 ARG R 650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 0.701 Fit side-chains REVERT: A 12 GLN cc_start: 0.8255 (mm110) cc_final: 0.7893 (pt0) REVERT: A 38 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8142 (mmt90) REVERT: A 220 HIS cc_start: 0.8291 (m170) cc_final: 0.8000 (m170) REVERT: A 296 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8500 (mp) REVERT: B 23 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8680 (tppt) REVERT: B 61 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8469 (ppp) REVERT: N 65 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8780 (ttpt) REVERT: R 646 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7150 (tm-30) outliers start: 29 outliers final: 8 residues processed: 152 average time/residue: 1.2695 time to fit residues: 203.7296 Evaluate side-chains 139 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 0.0670 chunk 71 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8128 Z= 0.184 Angle : 0.543 8.358 11013 Z= 0.290 Chirality : 0.042 0.144 1243 Planarity : 0.004 0.057 1394 Dihedral : 4.264 36.096 1153 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.77 % Allowed : 20.64 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 988 helix: 2.58 (0.26), residues: 373 sheet: -0.02 (0.33), residues: 223 loop : -0.97 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.012 0.001 TYR A 339 ARG 0.009 0.001 ARG R 650 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 0.959 Fit side-chains REVERT: A 12 GLN cc_start: 0.8288 (mm110) cc_final: 0.7889 (pt0) REVERT: A 13 ARG cc_start: 0.8172 (mpt180) cc_final: 0.7834 (mtm-85) REVERT: A 38 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8108 (mmt90) REVERT: A 209 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: A 220 HIS cc_start: 0.8291 (m170) cc_final: 0.8073 (m-70) REVERT: B 10 GLU cc_start: 0.8524 (tp30) cc_final: 0.8274 (tp30) REVERT: B 23 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8671 (tppt) REVERT: B 61 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8497 (ppp) REVERT: B 325 MET cc_start: 0.8671 (mmt) cc_final: 0.8465 (mmm) REVERT: G 47 GLU cc_start: 0.8476 (pm20) cc_final: 0.8182 (pm20) REVERT: N 3 GLN cc_start: 0.8179 (tt0) cc_final: 0.7913 (tt0) REVERT: R 646 GLU cc_start: 0.7272 (tm-30) cc_final: 0.7053 (tm-30) outliers start: 32 outliers final: 14 residues processed: 166 average time/residue: 1.2838 time to fit residues: 224.9800 Evaluate side-chains 149 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 680 TYR Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.0000 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 25 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 overall best weight: 0.8264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 668 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8128 Z= 0.208 Angle : 0.557 6.853 11013 Z= 0.296 Chirality : 0.042 0.142 1243 Planarity : 0.004 0.053 1394 Dihedral : 4.273 35.656 1153 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.01 % Allowed : 20.64 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.87 (0.27), residues: 988 helix: 2.53 (0.26), residues: 374 sheet: -0.01 (0.34), residues: 223 loop : -1.02 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.014 0.001 TYR A 339 ARG 0.011 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 0.916 Fit side-chains REVERT: A 12 GLN cc_start: 0.8310 (mm110) cc_final: 0.7897 (pt0) REVERT: A 13 ARG cc_start: 0.8153 (mpt180) cc_final: 0.7929 (mpp-170) REVERT: A 38 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8136 (mmt90) REVERT: B 10 GLU cc_start: 0.8622 (tp30) cc_final: 0.8241 (tp30) REVERT: B 23 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8691 (tppt) REVERT: B 61 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8474 (ppp) REVERT: B 234 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.7279 (t80) REVERT: B 256 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7570 (ptt-90) REVERT: G 47 GLU cc_start: 0.8505 (pm20) cc_final: 0.8196 (pm20) REVERT: N 3 GLN cc_start: 0.8175 (tt0) cc_final: 0.7928 (tt0) REVERT: R 646 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6981 (tm-30) REVERT: R 650 ARG cc_start: 0.8296 (mmt90) cc_final: 0.8017 (mmt90) outliers start: 34 outliers final: 16 residues processed: 162 average time/residue: 1.2772 time to fit residues: 218.5190 Evaluate side-chains 142 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 680 TYR Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN R 849 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8128 Z= 0.182 Angle : 0.552 5.987 11013 Z= 0.295 Chirality : 0.042 0.146 1243 Planarity : 0.004 0.050 1394 Dihedral : 4.194 34.077 1153 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.36 % Allowed : 22.05 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.27), residues: 988 helix: 2.50 (0.26), residues: 375 sheet: 0.06 (0.34), residues: 221 loop : -1.02 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 865 TYR 0.009 0.001 TYR N 95 ARG 0.014 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.044 Fit side-chains REVERT: A 12 GLN cc_start: 0.8284 (mm110) cc_final: 0.7913 (pt0) REVERT: A 13 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7876 (mpp-170) REVERT: A 38 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8102 (mmt90) REVERT: B 10 GLU cc_start: 0.8649 (tp30) cc_final: 0.8225 (tp30) REVERT: B 23 LYS cc_start: 0.8954 (mmmm) cc_final: 0.8705 (tppt) REVERT: B 61 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8536 (ppp) REVERT: B 127 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8653 (ptpt) REVERT: B 234 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.7250 (t80) REVERT: B 256 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7413 (ptt-90) REVERT: R 623 ILE cc_start: 0.9096 (mm) cc_final: 0.8895 (mp) REVERT: R 646 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6989 (tm-30) REVERT: R 862 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7960 (pp) outliers start: 37 outliers final: 14 residues processed: 154 average time/residue: 1.2525 time to fit residues: 203.6296 Evaluate side-chains 148 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 0.0070 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 7 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 91 optimal weight: 0.0370 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8128 Z= 0.152 Angle : 0.552 9.085 11013 Z= 0.291 Chirality : 0.041 0.138 1243 Planarity : 0.004 0.052 1394 Dihedral : 4.015 31.574 1153 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.01 % Allowed : 22.17 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 988 helix: 2.67 (0.26), residues: 369 sheet: 0.23 (0.34), residues: 214 loop : -0.97 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 676 HIS 0.003 0.000 HIS A 357 PHE 0.012 0.001 PHE R 865 TYR 0.013 0.001 TYR N 60 ARG 0.016 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8281 (mm110) cc_final: 0.7965 (pt0) REVERT: A 13 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7879 (mpp-170) REVERT: B 10 GLU cc_start: 0.8614 (tp30) cc_final: 0.8176 (tp30) REVERT: B 23 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8718 (tppt) REVERT: B 215 GLU cc_start: 0.8758 (pm20) cc_final: 0.8286 (pm20) REVERT: B 217 MET cc_start: 0.7278 (pmt) cc_final: 0.6646 (pmt) REVERT: B 234 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7477 (t80) REVERT: G 29 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7757 (tppp) REVERT: R 623 ILE cc_start: 0.9072 (mm) cc_final: 0.8868 (mp) REVERT: R 862 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7986 (pp) outliers start: 34 outliers final: 12 residues processed: 165 average time/residue: 1.1968 time to fit residues: 209.3214 Evaluate side-chains 150 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 680 TYR Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN N 123 GLN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8128 Z= 0.291 Angle : 0.612 7.873 11013 Z= 0.324 Chirality : 0.044 0.146 1243 Planarity : 0.004 0.049 1394 Dihedral : 4.319 35.039 1153 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.01 % Allowed : 23.11 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.85 (0.27), residues: 988 helix: 2.47 (0.26), residues: 375 sheet: 0.02 (0.34), residues: 223 loop : -1.03 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 676 HIS 0.007 0.001 HIS A 357 PHE 0.012 0.001 PHE R 769 TYR 0.029 0.002 TYR R 680 ARG 0.012 0.001 ARG R 650 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 0.929 Fit side-chains REVERT: A 12 GLN cc_start: 0.8288 (mm110) cc_final: 0.7891 (pt0) REVERT: A 38 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8146 (mmt90) REVERT: A 46 LEU cc_start: 0.8459 (tp) cc_final: 0.8192 (tt) REVERT: B 10 GLU cc_start: 0.8650 (tp30) cc_final: 0.8188 (tp30) REVERT: B 127 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8636 (ptpt) REVERT: B 234 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.7251 (t80) REVERT: B 256 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7475 (ptt-90) REVERT: G 13 ARG cc_start: 0.8257 (mtm110) cc_final: 0.7982 (mtm110) REVERT: R 646 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6913 (tm-30) REVERT: R 768 ASP cc_start: 0.5576 (p0) cc_final: 0.5070 (m-30) REVERT: R 862 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7924 (pp) outliers start: 34 outliers final: 16 residues processed: 150 average time/residue: 1.3567 time to fit residues: 214.6140 Evaluate side-chains 148 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 728 LEU Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8128 Z= 0.221 Angle : 0.607 7.936 11013 Z= 0.321 Chirality : 0.043 0.145 1243 Planarity : 0.004 0.053 1394 Dihedral : 4.304 34.623 1153 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.54 % Allowed : 23.58 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.80 (0.27), residues: 988 helix: 2.44 (0.26), residues: 375 sheet: 0.06 (0.34), residues: 217 loop : -1.10 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 676 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.012 0.001 TYR N 60 ARG 0.012 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 0.979 Fit side-chains REVERT: A 12 GLN cc_start: 0.8265 (mm110) cc_final: 0.7893 (pt0) REVERT: A 13 ARG cc_start: 0.8286 (mpt180) cc_final: 0.8059 (mpt180) REVERT: A 38 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8124 (mmt90) REVERT: A 46 LEU cc_start: 0.8381 (tp) cc_final: 0.8133 (tt) REVERT: B 10 GLU cc_start: 0.8684 (tp30) cc_final: 0.8222 (tp30) REVERT: B 61 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8614 (pp-130) REVERT: B 127 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8604 (ptpt) REVERT: B 155 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.8021 (t0) REVERT: B 215 GLU cc_start: 0.8791 (pm20) cc_final: 0.8102 (pm20) REVERT: B 217 MET cc_start: 0.7152 (pmt) cc_final: 0.6478 (pmt) REVERT: B 234 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.7360 (t80) REVERT: B 325 MET cc_start: 0.8694 (mmt) cc_final: 0.8484 (mmm) REVERT: G 13 ARG cc_start: 0.8324 (mtm110) cc_final: 0.8116 (mtm110) REVERT: R 623 ILE cc_start: 0.9127 (mm) cc_final: 0.8926 (mp) REVERT: R 822 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8168 (tm-30) REVERT: R 862 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7952 (pp) outliers start: 30 outliers final: 17 residues processed: 153 average time/residue: 1.2506 time to fit residues: 202.5990 Evaluate side-chains 156 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 744 ILE Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0020 chunk 88 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8128 Z= 0.214 Angle : 0.613 8.520 11013 Z= 0.324 Chirality : 0.043 0.157 1243 Planarity : 0.004 0.056 1394 Dihedral : 4.284 34.386 1153 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.54 % Allowed : 23.47 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.27), residues: 988 helix: 2.42 (0.26), residues: 375 sheet: 0.07 (0.34), residues: 216 loop : -1.10 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 676 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.013 0.001 TYR N 60 ARG 0.013 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 0.807 Fit side-chains REVERT: A 12 GLN cc_start: 0.8196 (mm110) cc_final: 0.7953 (pt0) REVERT: A 13 ARG cc_start: 0.8259 (mpt180) cc_final: 0.8032 (mpt180) REVERT: A 38 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8105 (mmt90) REVERT: A 46 LEU cc_start: 0.8284 (tp) cc_final: 0.8046 (tt) REVERT: B 10 GLU cc_start: 0.8662 (tp30) cc_final: 0.8222 (tp30) REVERT: B 61 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8604 (pp-130) REVERT: B 127 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8543 (ptpt) REVERT: B 215 GLU cc_start: 0.8862 (pm20) cc_final: 0.8154 (pm20) REVERT: B 217 MET cc_start: 0.7211 (pmt) cc_final: 0.6505 (pmt) REVERT: B 234 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.7335 (t80) REVERT: G 13 ARG cc_start: 0.8338 (mtm110) cc_final: 0.8130 (mtm110) REVERT: R 623 ILE cc_start: 0.9124 (mm) cc_final: 0.8917 (mp) REVERT: R 822 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8231 (tm-30) REVERT: R 862 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7953 (pp) outliers start: 30 outliers final: 20 residues processed: 156 average time/residue: 1.2250 time to fit residues: 202.1197 Evaluate side-chains 157 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN N 123 GLN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8128 Z= 0.235 Angle : 0.641 8.251 11013 Z= 0.338 Chirality : 0.043 0.176 1243 Planarity : 0.004 0.060 1394 Dihedral : 4.317 34.593 1153 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.07 % Allowed : 24.53 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 988 helix: 2.46 (0.27), residues: 375 sheet: 0.04 (0.34), residues: 217 loop : -1.08 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 676 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.013 0.001 TYR N 60 ARG 0.014 0.001 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 0.925 Fit side-chains REVERT: A 12 GLN cc_start: 0.8243 (mm110) cc_final: 0.7946 (pt0) REVERT: A 13 ARG cc_start: 0.8245 (mpt180) cc_final: 0.7987 (mpt180) REVERT: A 38 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8101 (mmt90) REVERT: A 46 LEU cc_start: 0.8352 (tp) cc_final: 0.8115 (tt) REVERT: B 10 GLU cc_start: 0.8701 (tp30) cc_final: 0.8264 (tp30) REVERT: B 61 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8602 (pp-130) REVERT: B 127 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8536 (ptpt) REVERT: B 215 GLU cc_start: 0.8894 (pm20) cc_final: 0.8652 (pm20) REVERT: B 234 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.7346 (t80) REVERT: R 623 ILE cc_start: 0.9109 (mm) cc_final: 0.8906 (mp) REVERT: R 711 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8387 (mtp) REVERT: R 822 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8219 (tm-30) REVERT: R 862 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7951 (pp) outliers start: 26 outliers final: 19 residues processed: 153 average time/residue: 1.2088 time to fit residues: 195.8113 Evaluate side-chains 155 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN N 31 ASN ** R 860 ASN ** 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 = 0.3436 r_free = 0.3436 target = 0.094210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.070711 restraints weight = 14314.431| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.83 r_work: 0.2904 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8128 Z= 0.218 Angle : 0.623 9.126 11013 Z= 0.330 Chirality : 0.043 0.175 1243 Planarity : 0.004 0.060 1394 Dihedral : 4.301 34.318 1153 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.42 % Allowed : 23.94 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 988 helix: 2.44 (0.27), residues: 375 sheet: 0.05 (0.34), residues: 217 loop : -1.08 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 676 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.012 0.001 TYR N 60 ARG 0.014 0.001 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3831.74 seconds wall clock time: 70 minutes 37.63 seconds (4237.63 seconds total)