Starting phenix.real_space_refine on Wed May 8 23:20:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpu_34944/05_2024/8hpu_34944.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpu_34944/05_2024/8hpu_34944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpu_34944/05_2024/8hpu_34944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpu_34944/05_2024/8hpu_34944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpu_34944/05_2024/8hpu_34944.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpu_34944/05_2024/8hpu_34944.pdb" } resolution = 2.56 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= 0.075 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 3142 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 34 5.16 5 C 5224 2.51 5 N 1390 2.21 5 O 1633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "L ASP 83": "OD1" <-> "OD2" Residue "N TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 172": "OD1" <-> "OD2" Residue "N TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 8281 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1555 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1547 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Conformer: "B" Number of residues, atoms: 194, 1547 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} bond proxies already assigned to first conformer: 1584 Chain: "H" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "M" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1656 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "N" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.71, per 1000 atoms: 0.69 Number of scatterers: 8281 At special positions: 0 Unit cell: (117.6, 124.32, 120.12, 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 34 16.00 O 1633 8.00 N 1390 7.00 C 5224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 375 " distance=2.03 Simple disulfide: pdb=" SG CYS A 393 " - pdb=" SG CYS A 446 " distance=2.04 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 539 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.04 Simple disulfide: pdb=" SG CYS H 231 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS M 149 " - pdb=" SG CYS M 205 " distance=2.04 Simple disulfide: pdb=" SG CYS M 225 " - pdb=" SG CYS N 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 136 " - pdb=" SG CYS N 196 " distance=2.04 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 Links applied NAG-ASN " NAG A1201 " - " ASN A 357 " Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.9 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1996 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 23 sheets defined 8.4% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.583A pdb=" N VAL A 355 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.564A pdb=" N TRP A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 385 Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.869A pdb=" N LEU A 401 " --> pdb=" O PRO A 398 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN A 402 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 404 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.644A pdb=" N THR H 92 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.796A pdb=" N LEU H 204 " --> pdb=" O SER H 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'M' and resid 165 through 167 No H-bonds generated for 'chain 'M' and resid 165 through 167' Processing helix chain 'M' and resid 196 through 201 removed outlier: 4.488A pdb=" N THR M 200 " --> pdb=" O SER M 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 185 through 190 removed outlier: 3.867A pdb=" N LYS N 190 " --> pdb=" O ALA N 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 372 Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 468 Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.194A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.350A pdb=" N PHE H 101 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE H 115 " --> pdb=" O PHE H 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.212A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.212A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.180A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.954A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 145 through 151 Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.825A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.389A pdb=" N TYR M 33 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.732A pdb=" N CYS M 95 " --> pdb=" O TRP M 112 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP M 112 " --> pdb=" O CYS M 95 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG M 97 " --> pdb=" O ASP M 110 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA M 108 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.953A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.953A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 160 through 163 removed outlier: 3.586A pdb=" N TYR M 203 " --> pdb=" O VAL M 220 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.630A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.618A pdb=" N GLU N 107 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 116 through 120 removed outlier: 5.744A pdb=" N TYR N 175 " --> pdb=" O ASN N 140 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER N 176 " --> pdb=" O THR N 166 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 155 through 157 removed outlier: 4.155A pdb=" N TRP N 150 " --> pdb=" O GLN N 157 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 879 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: 2.83 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2642 1.34 - 1.46: 2053 1.46 - 1.58: 3752 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 8487 Sorted by residual: bond pdb=" CA CYS A 393 " pdb=" CB CYS A 393 " ideal model delta sigma weight residual 1.530 1.496 0.034 1.53e-02 4.27e+03 5.06e+00 bond pdb=" C PHE M 102 " pdb=" N PRO M 103 " ideal model delta sigma weight residual 1.334 1.345 -0.012 8.40e-03 1.42e+04 1.99e+00 bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C ALA A 386 " pdb=" N PRO A 387 " ideal model delta sigma weight residual 1.337 1.350 -0.014 1.06e-02 8.90e+03 1.66e+00 bond pdb=" C ASP N 187 " pdb=" N TYR N 188 " ideal model delta sigma weight residual 1.332 1.315 0.017 1.40e-02 5.10e+03 1.49e+00 ... (remaining 8482 not shown) Histogram of bond angle deviations from ideal: 100.17 - 107.44: 358 107.44 - 114.71: 4844 114.71 - 121.98: 4333 121.98 - 129.24: 1967 129.24 - 136.51: 51 Bond angle restraints: 11553 Sorted by residual: angle pdb=" C LEU H 139 " pdb=" N ALA H 140 " pdb=" CA ALA H 140 " ideal model delta sigma weight residual 120.94 136.51 -15.57 1.90e+00 2.77e-01 6.72e+01 angle pdb=" CA CYS A 446 " pdb=" CB CYS A 446 " pdb=" SG CYS A 446 " ideal model delta sigma weight residual 114.40 128.26 -13.86 2.30e+00 1.89e-01 3.63e+01 angle pdb=" N CYS A 393 " pdb=" CA CYS A 393 " pdb=" C CYS A 393 " ideal model delta sigma weight residual 107.88 116.19 -8.31 1.41e+00 5.03e-01 3.47e+01 angle pdb=" N CYS A 446 " pdb=" CA CYS A 446 " pdb=" C CYS A 446 " ideal model delta sigma weight residual 107.88 113.55 -5.67 1.41e+00 5.03e-01 1.61e+01 angle pdb=" CA GLY A 445 " pdb=" C GLY A 445 " pdb=" O GLY A 445 " ideal model delta sigma weight residual 122.24 117.97 4.27 1.08e+00 8.57e-01 1.56e+01 ... (remaining 11548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4625 17.65 - 35.31: 366 35.31 - 52.96: 68 52.96 - 70.61: 15 70.61 - 88.26: 13 Dihedral angle restraints: 5087 sinusoidal: 1963 harmonic: 3124 Sorted by residual: dihedral pdb=" CA ASP H 116 " pdb=" C ASP H 116 " pdb=" N PRO H 117 " pdb=" CA PRO H 117 " ideal model delta harmonic sigma weight residual -180.00 -131.45 -48.55 0 5.00e+00 4.00e-02 9.43e+01 dihedral pdb=" CB CYS A 393 " pdb=" SG CYS A 393 " pdb=" SG CYS A 446 " pdb=" CB CYS A 446 " ideal model delta sinusoidal sigma weight residual -86.00 -11.06 -74.94 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS H 155 " pdb=" SG CYS H 155 " pdb=" SG CYS H 211 " pdb=" CB CYS H 211 " ideal model delta sinusoidal sigma weight residual 93.00 154.84 -61.84 1 1.00e+01 1.00e-02 5.07e+01 ... (remaining 5084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1001 0.051 - 0.101: 231 0.101 - 0.152: 54 0.152 - 0.203: 3 0.203 - 0.253: 1 Chirality restraints: 1290 Sorted by residual: chirality pdb=" CA CYS A 393 " pdb=" N CYS A 393 " pdb=" C CYS A 393 " pdb=" CB CYS A 393 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA LYS M 215 " pdb=" N LYS M 215 " pdb=" C LYS M 215 " pdb=" CB LYS M 215 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA CYS A 446 " pdb=" N CYS A 446 " pdb=" C CYS A 446 " pdb=" CB CYS A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 1287 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 163 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO H 164 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 164 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 164 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 116 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO H 117 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO H 117 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 117 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 131 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO M 132 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO M 132 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO M 132 " -0.026 5.00e-02 4.00e+02 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 832 2.75 - 3.29: 7851 3.29 - 3.83: 13703 3.83 - 4.36: 16707 4.36 - 4.90: 28781 Nonbonded interactions: 67874 Sorted by model distance: nonbonded pdb=" NH2 ARG N 61 " pdb=" OE2 GLU N 81 " model vdw 2.215 2.520 nonbonded pdb=" OD1 ASP A 456 " pdb=" OH TYR A 465 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR A 514 " pdb=" OH TYR L 33 " model vdw 2.258 2.440 nonbonded pdb=" CB CYS A 393 " pdb=" CB CYS A 446 " model vdw 2.276 3.072 nonbonded pdb=" NE2 GLN L 148 " pdb=" O GLN L 156 " model vdw 2.286 2.520 ... (remaining 67869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 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: 9.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 28.090 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.350 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.003 0.044 8487 Z= 0.206 Angle : 0.692 15.572 11553 Z= 0.365 Chirality : 0.046 0.253 1290 Planarity : 0.005 0.057 1488 Dihedral : 13.597 88.265 3049 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.11 % Allowed : 0.21 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.10 % 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: -0.21 (0.26), residues: 1071 helix: -2.94 (0.64), residues: 41 sheet: 0.91 (0.25), residues: 427 loop : -0.72 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 150 HIS 0.010 0.001 HIS A 519 PHE 0.017 0.001 PHE A 391 TYR 0.018 0.002 TYR L 174 ARG 0.003 0.000 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.6168 (p90) cc_final: 0.5852 (p90) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 1.4154 time to fit residues: 198.6729 Evaluate side-chains 86 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.2980 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 219 ASN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8487 Z= 0.210 Angle : 0.641 15.188 11553 Z= 0.330 Chirality : 0.045 0.199 1290 Planarity : 0.005 0.065 1488 Dihedral : 5.436 46.666 1189 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.50 % Allowed : 9.86 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.09 (0.26), residues: 1071 helix: -2.74 (0.66), residues: 40 sheet: 0.97 (0.24), residues: 430 loop : -0.64 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 150 HIS 0.009 0.001 HIS A 519 PHE 0.013 0.001 PHE N 141 TYR 0.015 0.002 TYR L 174 ARG 0.008 0.001 ARG N 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.6170 (p90) cc_final: 0.5860 (p90) outliers start: 13 outliers final: 3 residues processed: 101 average time/residue: 1.2582 time to fit residues: 135.4051 Evaluate side-chains 86 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 199 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 85 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8487 Z= 0.199 Angle : 0.622 16.164 11553 Z= 0.319 Chirality : 0.045 0.204 1290 Planarity : 0.005 0.069 1488 Dihedral : 5.236 45.013 1189 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.25 % Allowed : 11.90 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.02 (0.26), residues: 1071 helix: -2.76 (0.66), residues: 40 sheet: 1.06 (0.25), residues: 430 loop : -0.62 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 450 HIS 0.007 0.001 HIS A 519 PHE 0.020 0.001 PHE A 391 TYR 0.014 0.001 TYR L 141 ARG 0.010 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.6195 (p90) cc_final: 0.5848 (p90) REVERT: M 64 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7296 (mmtm) outliers start: 20 outliers final: 7 residues processed: 110 average time/residue: 1.2455 time to fit residues: 146.3273 Evaluate side-chains 95 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 126 GLN Chi-restraints excluded: chain N residue 138 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8487 Z= 0.227 Angle : 0.634 16.340 11553 Z= 0.327 Chirality : 0.045 0.211 1290 Planarity : 0.005 0.071 1488 Dihedral : 5.274 44.552 1189 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.68 % Allowed : 13.83 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.06 (0.26), residues: 1071 helix: -2.70 (0.67), residues: 40 sheet: 1.02 (0.25), residues: 432 loop : -0.65 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 450 HIS 0.007 0.001 HIS A 519 PHE 0.020 0.002 PHE N 141 TYR 0.015 0.002 TYR L 141 ARG 0.009 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 PHE cc_start: 0.5445 (OUTLIER) cc_final: 0.5083 (m-80) REVERT: H 116 ASP cc_start: 0.5596 (OUTLIER) cc_final: 0.5356 (m-30) REVERT: H 160 TYR cc_start: 0.6218 (p90) cc_final: 0.5856 (p90) REVERT: M 64 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7248 (mmtm) outliers start: 24 outliers final: 11 residues processed: 110 average time/residue: 1.2762 time to fit residues: 149.4425 Evaluate side-chains 99 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 126 GLN Chi-restraints excluded: chain N residue 138 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 214 ASN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8487 Z= 0.212 Angle : 0.634 14.760 11553 Z= 0.325 Chirality : 0.045 0.169 1290 Planarity : 0.005 0.070 1488 Dihedral : 5.187 42.933 1189 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.54 % Allowed : 14.26 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1071 helix: -2.68 (0.69), residues: 40 sheet: 1.03 (0.25), residues: 432 loop : -0.64 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 450 HIS 0.006 0.001 HIS A 519 PHE 0.025 0.001 PHE A 391 TYR 0.017 0.002 TYR L 141 ARG 0.010 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 PHE cc_start: 0.5388 (OUTLIER) cc_final: 0.5052 (m-80) REVERT: H 160 TYR cc_start: 0.6180 (p90) cc_final: 0.5864 (p90) REVERT: M 64 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7286 (mmtm) outliers start: 32 outliers final: 16 residues processed: 114 average time/residue: 1.1048 time to fit residues: 134.4986 Evaluate side-chains 103 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 188 TYR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 210 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8487 Z= 0.260 Angle : 0.672 17.346 11553 Z= 0.345 Chirality : 0.046 0.197 1290 Planarity : 0.005 0.070 1488 Dihedral : 5.370 41.738 1189 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.64 % Allowed : 15.43 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.14 (0.26), residues: 1071 helix: -2.78 (0.67), residues: 40 sheet: 0.96 (0.24), residues: 427 loop : -0.69 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 114 HIS 0.006 0.001 HIS A 519 PHE 0.019 0.002 PHE A 391 TYR 0.020 0.002 TYR L 141 ARG 0.010 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 90 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.6181 (p90) cc_final: 0.5821 (p90) REVERT: M 64 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7299 (mmtm) outliers start: 33 outliers final: 21 residues processed: 115 average time/residue: 1.0446 time to fit residues: 128.3374 Evaluate side-chains 107 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain H residue 68 ARG Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 211 CYS Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 188 TYR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 210 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 47 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -build -allalt -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: