Starting phenix.real_space_refine on Sat Aug 3 06:30:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umx_42387/08_2024/8umx_42387.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umx_42387/08_2024/8umx_42387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umx_42387/08_2024/8umx_42387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umx_42387/08_2024/8umx_42387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umx_42387/08_2024/8umx_42387.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umx_42387/08_2024/8umx_42387.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4505 2.51 5 N 1282 2.21 5 O 1352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 538": "OE1" <-> "OE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "E ASP 59": "OD1" <-> "OD2" Residue "E GLU 67": "OE1" <-> "OE2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "E ASP 124": "OD1" <-> "OD2" Residue "F ASP 55": "OD1" <-> "OD2" Residue "F ASP 59": "OD1" <-> "OD2" Residue "F ASP 116": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7166 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "B" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2566 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain: "C" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2325 Classifications: {'peptide': 287} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 265} Chain: "D" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "E" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 609 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "F" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Time building chain proxies: 7.15, per 1000 atoms: 1.00 Number of scatterers: 7166 At special positions: 0 Unit cell: (94.848, 94.848, 173.056, 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 27 16.00 O 1352 8.00 N 1282 7.00 C 4505 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 52.2% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 517 through 543 Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.982A pdb=" N VAL A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 18 removed outlier: 3.613A pdb=" N THR B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.684A pdb=" N HIS B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.765A pdb=" N ALA B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 66 removed outlier: 3.706A pdb=" N GLN B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 85 removed outlier: 3.926A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 111 Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.968A pdb=" N ALA B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.627A pdb=" N LEU B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 150 through 163 Processing helix chain 'B' and resid 168 through 187 removed outlier: 3.506A pdb=" N LEU B 175 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 207 through 222 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.669A pdb=" N LYS B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 297 through 318 Processing helix chain 'C' and resid 51 through 74 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 119 through 132 Processing helix chain 'C' and resid 147 through 173 removed outlier: 3.611A pdb=" N LEU C 160 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C 171 " --> pdb=" O ASP C 167 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.547A pdb=" N PHE C 188 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 removed outlier: 3.571A pdb=" N GLU C 225 " --> pdb=" O SER C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 240 through 254 removed outlier: 3.816A pdb=" N GLN C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C 247 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL C 251 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'E' and resid 75 through 80 Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'F' and resid 75 through 80 removed outlier: 3.937A pdb=" N ARG F 80 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 136 removed outlier: 3.628A pdb=" N MET F 132 " --> pdb=" O PRO F 128 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 78 through 81 Processing sheet with id=AA2, first strand: chain 'C' and resid 78 through 81 removed outlier: 3.759A pdb=" N CYS C 218 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU C 102 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER C 182 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU C 104 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 258 through 259 removed outlier: 3.784A pdb=" N LEU C 259 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N MET D 73 " --> pdb=" O LEU C 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 262 through 264 removed outlier: 3.801A pdb=" N ILE C 293 " --> pdb=" O ASN C 264 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL C 296 " --> pdb=" O PRO C 300 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR C 303 " --> pdb=" O GLU C 318 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TYR C 313 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.744A pdb=" N ILE C 268 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU D 97 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLN D 108 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE D 99 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR D 118 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 86 through 88 removed outlier: 6.752A pdb=" N GLN F 108 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE F 125 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE F 106 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE F 99 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN F 108 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU F 97 " --> pdb=" O GLN F 108 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR E 74 " --> pdb=" O PRO F 61 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS F 63 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG E 72 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR F 65 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ARG E 70 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU F 67 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU E 68 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY F 69 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL E 66 " --> pdb=" O GLY F 69 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU E 64 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET F 73 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP E 98 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 99 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ILE E 106 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ILE E 125 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN E 108 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR E 118 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 87 " --> pdb=" O VAL E 120 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1134 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: 2.07 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2489 1.34 - 1.46: 1318 1.46 - 1.58: 3393 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 7253 Sorted by residual: bond pdb=" CB ASP E 59 " pdb=" CG ASP E 59 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.51e+00 bond pdb=" CG LEU E 97 " pdb=" CD1 LEU E 97 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CB ASP E 116 " pdb=" CG ASP E 116 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.38e+00 bond pdb=" CB ASP F 90 " pdb=" CG ASP F 90 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" CB LYS C 108 " pdb=" CG LYS C 108 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 ... (remaining 7248 not shown) Histogram of bond angle deviations from ideal: 97.67 - 104.99: 126 104.99 - 112.30: 3742 112.30 - 119.61: 2529 119.61 - 126.92: 3360 126.92 - 134.23: 56 Bond angle restraints: 9813 Sorted by residual: angle pdb=" N ASP D 116 " pdb=" CA ASP D 116 " pdb=" CB ASP D 116 " ideal model delta sigma weight residual 114.17 109.01 5.16 1.14e+00 7.69e-01 2.05e+01 angle pdb=" CA LYS C 170 " pdb=" CB LYS C 170 " pdb=" CG LYS C 170 " ideal model delta sigma weight residual 114.10 122.71 -8.61 2.00e+00 2.50e-01 1.85e+01 angle pdb=" CA LYS C 108 " pdb=" CB LYS C 108 " pdb=" CG LYS C 108 " ideal model delta sigma weight residual 114.10 122.16 -8.06 2.00e+00 2.50e-01 1.63e+01 angle pdb=" CA GLU A 538 " pdb=" CB GLU A 538 " pdb=" CG GLU A 538 " ideal model delta sigma weight residual 114.10 121.68 -7.58 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA MET D 73 " pdb=" CB MET D 73 " pdb=" CG MET D 73 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 ... (remaining 9808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 3849 17.76 - 35.52: 504 35.52 - 53.29: 124 53.29 - 71.05: 27 71.05 - 88.81: 8 Dihedral angle restraints: 4512 sinusoidal: 1892 harmonic: 2620 Sorted by residual: dihedral pdb=" CA ARG C 44 " pdb=" C ARG C 44 " pdb=" N ARG C 45 " pdb=" CA ARG C 45 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP E 59 " pdb=" C ASP E 59 " pdb=" N ILE E 60 " pdb=" CA ILE E 60 " ideal model delta harmonic sigma weight residual 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA THR E 127 " pdb=" C THR E 127 " pdb=" N PRO E 128 " pdb=" CA PRO E 128 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 4509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 892 0.047 - 0.095: 221 0.095 - 0.142: 51 0.142 - 0.189: 6 0.189 - 0.237: 1 Chirality restraints: 1171 Sorted by residual: chirality pdb=" CB ILE F 60 " pdb=" CA ILE F 60 " pdb=" CG1 ILE F 60 " pdb=" CG2 ILE F 60 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE D 125 " pdb=" N ILE D 125 " pdb=" C ILE D 125 " pdb=" CB ILE D 125 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA ILE F 57 " pdb=" N ILE F 57 " pdb=" C ILE F 57 " pdb=" CB ILE F 57 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 1168 not shown) Planarity restraints: 1282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 59 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C ASP E 59 " -0.043 2.00e-02 2.50e+03 pdb=" O ASP E 59 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE E 60 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 116 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C ASP E 116 " 0.033 2.00e-02 2.50e+03 pdb=" O ASP E 116 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS E 117 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 127 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO F 128 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 128 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 128 " 0.026 5.00e-02 4.00e+02 ... (remaining 1279 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 363 2.72 - 3.26: 7841 3.26 - 3.81: 12254 3.81 - 4.35: 13715 4.35 - 4.90: 22407 Nonbonded interactions: 56580 Sorted by model distance: nonbonded pdb=" O GLY B 194 " pdb=" OG1 THR B 198 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR D 74 " pdb=" OE1 GLU D 77 " model vdw 2.185 3.040 nonbonded pdb=" N GLU E 77 " pdb=" OE1 GLU E 77 " model vdw 2.200 3.120 nonbonded pdb=" ND2 ASN D 102 " pdb=" O PRO E 61 " model vdw 2.200 3.120 nonbonded pdb=" OG1 THR F 127 " pdb=" OE1 GLU F 130 " model vdw 2.201 3.040 ... (remaining 56575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 56 through 134) selection = chain 'E' selection = (chain 'F' and resid 56 through 134) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.720 Find NCS groups from input model: 0.150 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 0.039 7253 Z= 0.204 Angle : 0.771 9.869 9813 Z= 0.391 Chirality : 0.045 0.237 1171 Planarity : 0.004 0.049 1282 Dihedral : 17.117 88.811 2806 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 0.50 % Allowed : 28.81 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.01 (0.30), residues: 894 helix: 1.15 (0.26), residues: 426 sheet: -1.56 (0.53), residues: 95 loop : -0.88 (0.35), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 246 HIS 0.002 0.001 HIS C 295 PHE 0.027 0.002 PHE B 234 TYR 0.006 0.001 TYR C 165 ARG 0.005 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5575 (tpt) cc_final: 0.4092 (tpt) REVERT: B 321 MET cc_start: 0.7563 (mmt) cc_final: 0.7178 (mmt) REVERT: C 223 MET cc_start: 0.9229 (mmm) cc_final: 0.8968 (mmm) REVERT: C 288 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8044 (mmtt) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.2159 time to fit residues: 14.9792 Evaluate side-chains 44 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain F residue 60 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7253 Z= 0.197 Angle : 0.662 8.085 9813 Z= 0.340 Chirality : 0.043 0.200 1171 Planarity : 0.005 0.047 1282 Dihedral : 4.758 46.698 1003 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.70 % Favored : 95.19 % Rotamer: Outliers : 4.78 % Allowed : 23.40 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.05 (0.29), residues: 894 helix: 1.16 (0.25), residues: 434 sheet: -1.16 (0.56), residues: 81 loop : -0.98 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 554 HIS 0.007 0.001 HIS C 241 PHE 0.016 0.001 PHE B 26 TYR 0.011 0.001 TYR E 104 ARG 0.009 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 47 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6038 (tpt) cc_final: 0.4716 (tpt) REVERT: B 113 MET cc_start: 0.7558 (pmm) cc_final: 0.6874 (pmm) REVERT: C 223 MET cc_start: 0.9259 (mmm) cc_final: 0.9054 (mmm) REVERT: C 264 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8612 (t0) outliers start: 38 outliers final: 17 residues processed: 83 average time/residue: 0.1755 time to fit residues: 20.3424 Evaluate side-chains 59 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN C 103 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7253 Z= 0.171 Angle : 0.623 7.799 9813 Z= 0.316 Chirality : 0.043 0.173 1171 Planarity : 0.004 0.061 1282 Dihedral : 4.679 49.155 999 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 4.15 % Allowed : 23.52 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.01 (0.29), residues: 894 helix: 1.24 (0.25), residues: 433 sheet: -1.19 (0.51), residues: 90 loop : -1.18 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 246 HIS 0.008 0.001 HIS C 241 PHE 0.012 0.001 PHE B 234 TYR 0.011 0.001 TYR E 104 ARG 0.005 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 44 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6148 (tpt) cc_final: 0.4901 (tpt) REVERT: B 93 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9370 (mm) REVERT: B 113 MET cc_start: 0.7429 (pmm) cc_final: 0.7072 (pmm) REVERT: C 223 MET cc_start: 0.9238 (mmm) cc_final: 0.9026 (mmm) REVERT: C 264 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8567 (t0) outliers start: 33 outliers final: 16 residues processed: 74 average time/residue: 0.1746 time to fit residues: 18.3666 Evaluate side-chains 57 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 39 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7253 Z= 0.162 Angle : 0.634 10.306 9813 Z= 0.314 Chirality : 0.043 0.232 1171 Planarity : 0.004 0.056 1282 Dihedral : 4.622 48.914 999 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.91 % Favored : 95.97 % Rotamer: Outliers : 4.65 % Allowed : 23.14 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.03 (0.29), residues: 894 helix: 1.20 (0.25), residues: 437 sheet: -0.96 (0.53), residues: 89 loop : -1.14 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 169 HIS 0.007 0.001 HIS C 241 PHE 0.011 0.001 PHE B 234 TYR 0.009 0.001 TYR E 104 ARG 0.004 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 40 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6118 (tpt) cc_final: 0.4861 (tpt) REVERT: B 93 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9347 (mm) REVERT: B 113 MET cc_start: 0.7515 (pmm) cc_final: 0.7306 (pmm) REVERT: C 223 MET cc_start: 0.9244 (mmm) cc_final: 0.9022 (mmm) outliers start: 37 outliers final: 20 residues processed: 74 average time/residue: 0.2001 time to fit residues: 20.4042 Evaluate side-chains 59 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 38 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 71 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7253 Z= 0.261 Angle : 0.677 12.945 9813 Z= 0.341 Chirality : 0.042 0.159 1171 Planarity : 0.004 0.052 1282 Dihedral : 4.702 51.448 999 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.59 % Favored : 94.30 % Rotamer: Outliers : 4.53 % Allowed : 23.52 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.00 (0.29), residues: 894 helix: 1.23 (0.25), residues: 437 sheet: -1.24 (0.50), residues: 91 loop : -1.15 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.011 0.002 PHE B 59 TYR 0.011 0.001 TYR C 313 ARG 0.007 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 40 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 MET cc_start: 0.8315 (ppp) cc_final: 0.7824 (tmm) REVERT: A 539 MET cc_start: 0.8513 (ptm) cc_final: 0.8033 (ptm) REVERT: B 1 MET cc_start: 0.6755 (tpt) cc_final: 0.5705 (tpt) REVERT: C 223 MET cc_start: 0.9290 (mmm) cc_final: 0.9083 (mmm) outliers start: 36 outliers final: 25 residues processed: 73 average time/residue: 0.2113 time to fit residues: 20.7095 Evaluate side-chains 64 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 39 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 0.4980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7253 Z= 0.195 Angle : 0.649 10.388 9813 Z= 0.322 Chirality : 0.043 0.288 1171 Planarity : 0.004 0.042 1282 Dihedral : 4.643 54.673 999 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 4.28 % Allowed : 24.40 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.11 (0.29), residues: 894 helix: 1.29 (0.25), residues: 438 sheet: -1.13 (0.50), residues: 90 loop : -1.07 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.011 0.001 PHE B 234 TYR 0.007 0.001 TYR E 104 ARG 0.005 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 42 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 MET cc_start: 0.8527 (ptm) cc_final: 0.7981 (ptm) REVERT: B 1 MET cc_start: 0.6509 (tpt) cc_final: 0.5388 (tpt) REVERT: B 330 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7598 (t80) REVERT: C 223 MET cc_start: 0.9289 (mmm) cc_final: 0.9066 (mmm) outliers start: 34 outliers final: 26 residues processed: 74 average time/residue: 0.1945 time to fit residues: 19.6312 Evaluate side-chains 67 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 40 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7253 Z= 0.261 Angle : 0.696 10.469 9813 Z= 0.349 Chirality : 0.043 0.279 1171 Planarity : 0.004 0.044 1282 Dihedral : 4.759 54.050 999 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 4.15 % Allowed : 25.53 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.02 (0.29), residues: 894 helix: 1.16 (0.25), residues: 439 sheet: -1.12 (0.51), residues: 91 loop : -1.05 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.010 0.002 PHE B 59 TYR 0.010 0.001 TYR C 313 ARG 0.007 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 41 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 MET cc_start: 0.8715 (ppp) cc_final: 0.8029 (tmm) REVERT: A 539 MET cc_start: 0.8501 (ptm) cc_final: 0.8196 (ptm) REVERT: B 1 MET cc_start: 0.6927 (tpt) cc_final: 0.5507 (tpt) REVERT: B 93 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9378 (mm) REVERT: B 330 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7709 (t80) REVERT: C 157 MET cc_start: 0.9105 (ptp) cc_final: 0.8827 (ptp) REVERT: C 223 MET cc_start: 0.9367 (mmm) cc_final: 0.9157 (mmm) outliers start: 33 outliers final: 27 residues processed: 72 average time/residue: 0.2259 time to fit residues: 22.5928 Evaluate side-chains 68 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 39 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7253 Z= 0.190 Angle : 0.682 11.095 9813 Z= 0.337 Chirality : 0.043 0.328 1171 Planarity : 0.004 0.038 1282 Dihedral : 4.715 53.265 999 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 4.03 % Allowed : 25.66 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.23 (0.29), residues: 894 helix: 1.23 (0.25), residues: 438 sheet: -0.76 (0.57), residues: 76 loop : -0.89 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.027 0.001 PHE B 112 TYR 0.008 0.001 TYR C 313 ARG 0.005 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 40 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 MET cc_start: 0.8671 (ppp) cc_final: 0.8050 (tmm) REVERT: A 539 MET cc_start: 0.8469 (ptm) cc_final: 0.8158 (ptm) REVERT: B 1 MET cc_start: 0.6740 (tpt) cc_final: 0.5282 (tpt) REVERT: B 93 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9369 (mm) REVERT: B 330 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7767 (t80) REVERT: C 108 LYS cc_start: 0.9489 (mmtt) cc_final: 0.9178 (mmtm) outliers start: 32 outliers final: 28 residues processed: 70 average time/residue: 0.2224 time to fit residues: 21.2134 Evaluate side-chains 70 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 40 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7253 Z= 0.183 Angle : 0.685 11.689 9813 Z= 0.336 Chirality : 0.044 0.329 1171 Planarity : 0.004 0.033 1282 Dihedral : 4.656 53.219 999 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 3.77 % Allowed : 25.66 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.29 (0.29), residues: 894 helix: 1.21 (0.25), residues: 442 sheet: -0.69 (0.57), residues: 76 loop : -0.81 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.026 0.001 PHE B 112 TYR 0.007 0.001 TYR C 313 ARG 0.005 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 41 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 MET cc_start: 0.8436 (ppp) cc_final: 0.7508 (tmm) REVERT: B 1 MET cc_start: 0.6463 (tpt) cc_final: 0.5169 (tpt) REVERT: B 93 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9368 (mm) REVERT: C 223 MET cc_start: 0.9166 (mmm) cc_final: 0.8707 (mmm) outliers start: 30 outliers final: 26 residues processed: 70 average time/residue: 0.2100 time to fit residues: 19.9343 Evaluate side-chains 65 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 38 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.0030 chunk 73 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7253 Z= 0.206 Angle : 0.726 11.841 9813 Z= 0.358 Chirality : 0.045 0.349 1171 Planarity : 0.004 0.041 1282 Dihedral : 4.313 17.273 995 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 3.77 % Allowed : 26.16 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.24 (0.29), residues: 894 helix: 1.20 (0.25), residues: 441 sheet: -0.89 (0.56), residues: 79 loop : -0.82 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.021 0.001 PHE B 112 TYR 0.008 0.001 TYR C 313 ARG 0.008 0.000 ARG A 535 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 39 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6677 (tpt) cc_final: 0.5460 (tpt) REVERT: B 93 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9371 (mm) REVERT: C 223 MET cc_start: 0.9179 (mmm) cc_final: 0.8751 (mmm) outliers start: 30 outliers final: 28 residues processed: 68 average time/residue: 0.2128 time to fit residues: 19.7205 Evaluate side-chains 68 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 39 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.034173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.025571 restraints weight = 103455.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.026052 restraints weight = 67958.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.026389 restraints weight = 51076.238| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7253 Z= 0.223 Angle : 0.756 11.654 9813 Z= 0.378 Chirality : 0.045 0.335 1171 Planarity : 0.004 0.033 1282 Dihedral : 4.362 17.309 995 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 3.65 % Allowed : 26.42 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.23 (0.29), residues: 894 helix: 1.18 (0.25), residues: 441 sheet: -0.90 (0.56), residues: 79 loop : -0.80 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.021 0.001 PHE B 112 TYR 0.008 0.001 TYR C 313 ARG 0.010 0.000 ARG A 535 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1746.66 seconds wall clock time: 32 minutes 35.88 seconds (1955.88 seconds total)