Starting phenix.real_space_refine on Mon Mar 11 05:37:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umx_42387/03_2024/8umx_42387.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umx_42387/03_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_42387/03_2024/8umx_42387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umx_42387/03_2024/8umx_42387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umx_42387/03_2024/8umx_42387.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umx_42387/03_2024/8umx_42387.pdb" } 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-5265/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: 4.37, per 1000 atoms: 0.61 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: 2.94 Conformation dependent library (CDL) restraints added in 1.4 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: 0.92 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: 2.15 Time building geometry restraints manager: 3.19 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 2.440 nonbonded pdb=" OG1 THR D 74 " pdb=" OE1 GLU D 77 " model vdw 2.185 2.440 nonbonded pdb=" N GLU E 77 " pdb=" OE1 GLU E 77 " model vdw 2.200 2.520 nonbonded pdb=" ND2 ASN D 102 " pdb=" O PRO E 61 " model vdw 2.200 2.520 nonbonded pdb=" OG1 THR F 127 " pdb=" OE1 GLU F 130 " model vdw 2.201 2.440 ... (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 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: 8.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 27.500 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.400 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: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.640 ------------------------------------------------------------------------------- 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 : 0.889 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: 0.2380 time to fit residues: 16.3644 Evaluate side-chains 44 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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: 1.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1082 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= 0.195 Angle : 0.632 8.160 9813 Z= 0.324 Chirality : 0.042 0.192 1171 Planarity : 0.004 0.045 1282 Dihedral : 4.540 39.674 1003 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.41 % Rotamer: Outliers : 4.40 % Allowed : 24.78 % Favored : 70.82 % 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: 0.17 (0.29), residues: 894 helix: 1.24 (0.25), residues: 433 sheet: -1.14 (0.56), residues: 82 loop : -0.88 (0.35), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 554 HIS 0.007 0.001 HIS C 241 PHE 0.015 0.001 PHE B 26 TYR 0.010 0.001 TYR E 104 ARG 0.003 0.000 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 80 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 45 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5855 (tpt) cc_final: 0.4390 (tpt) REVERT: B 113 MET cc_start: 0.7798 (pmm) cc_final: 0.7231 (pmm) REVERT: B 321 MET cc_start: 0.7412 (mmt) cc_final: 0.7049 (mmt) REVERT: C 223 MET cc_start: 0.9255 (mmm) cc_final: 0.9054 (mmm) REVERT: C 245 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.9003 (m-40) REVERT: C 264 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.7966 (t0) outliers start: 35 outliers final: 13 residues processed: 77 average time/residue: 0.1750 time to fit residues: 19.1538 Evaluate side-chains 55 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 162 LEU Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain F residue 111 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: 3.9990 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 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** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1593 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= 0.179 Angle : 0.601 7.778 9813 Z= 0.306 Chirality : 0.041 0.181 1171 Planarity : 0.004 0.046 1282 Dihedral : 4.170 18.243 995 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 4.78 % Allowed : 24.15 % Favored : 71.07 % 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: 0.17 (0.29), residues: 894 helix: 1.31 (0.25), residues: 430 sheet: -0.97 (0.55), residues: 82 loop : -1.00 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 246 HIS 0.006 0.001 HIS C 241 PHE 0.012 0.001 PHE B 26 TYR 0.011 0.001 TYR E 104 ARG 0.004 0.000 ARG E 80 *********************** 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 82 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 44 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6067 (tpt) cc_final: 0.4613 (tpt) REVERT: B 113 MET cc_start: 0.7822 (pmm) cc_final: 0.7483 (pmm) REVERT: B 321 MET cc_start: 0.7672 (mmt) cc_final: 0.7301 (mmt) REVERT: C 223 MET cc_start: 0.9252 (mmm) cc_final: 0.9049 (mmm) REVERT: C 264 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.7976 (t0) outliers start: 38 outliers final: 22 residues processed: 76 average time/residue: 0.2051 time to fit residues: 22.1397 Evaluate side-chains 63 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 40 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 C residue 140 LYS Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 186 VAL 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 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 90 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 132 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7253 Z= 0.230 Angle : 0.610 6.019 9813 Z= 0.314 Chirality : 0.042 0.207 1171 Planarity : 0.004 0.052 1282 Dihedral : 4.243 17.091 995 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.26 % Favored : 94.63 % Rotamer: Outliers : 6.67 % Allowed : 23.27 % 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: 0.12 (0.29), residues: 894 helix: 1.21 (0.25), residues: 435 sheet: -0.75 (0.58), residues: 77 loop : -1.04 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 246 HIS 0.006 0.001 HIS C 241 PHE 0.010 0.001 PHE B 234 TYR 0.009 0.001 TYR C 313 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 93 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 40 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6681 (tpt) cc_final: 0.5547 (tpt) REVERT: B 93 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9380 (mm) REVERT: B 113 MET cc_start: 0.8164 (pmm) cc_final: 0.7808 (pmm) REVERT: B 321 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7275 (mmt) REVERT: C 223 MET cc_start: 0.9284 (mmm) cc_final: 0.9083 (mmm) REVERT: C 264 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.7977 (t0) outliers start: 53 outliers final: 33 residues processed: 88 average time/residue: 0.2016 time to fit residues: 24.2957 Evaluate side-chains 74 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 38 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 39 THR 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 321 MET Chi-restraints excluded: chain C residue 36 ARG 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 186 VAL Chi-restraints excluded: chain C residue 194 SER 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 257 SER Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 299 VAL 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 90 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 132 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8307 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7253 Z= 0.205 Angle : 0.623 11.288 9813 Z= 0.311 Chirality : 0.041 0.152 1171 Planarity : 0.004 0.049 1282 Dihedral : 4.187 17.289 995 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.41 % Rotamer: Outliers : 5.66 % Allowed : 24.78 % Favored : 69.56 % 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: 0.15 (0.29), residues: 894 helix: 1.19 (0.25), residues: 437 sheet: -0.82 (0.56), residues: 77 loop : -0.97 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 246 HIS 0.006 0.001 HIS C 241 PHE 0.010 0.001 PHE B 234 TYR 0.007 0.001 TYR C 313 ARG 0.003 0.000 ARG C 247 *********************** 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 86 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 41 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6544 (tpt) cc_final: 0.5325 (tpt) REVERT: B 71 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7442 (tp) REVERT: B 93 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9414 (mm) REVERT: B 113 MET cc_start: 0.8257 (pmm) cc_final: 0.7954 (pmm) REVERT: C 223 MET cc_start: 0.9291 (mmm) cc_final: 0.9081 (mmm) REVERT: C 264 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8136 (t0) outliers start: 45 outliers final: 31 residues processed: 83 average time/residue: 0.1916 time to fit residues: 22.0189 Evaluate side-chains 71 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 37 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 43 ASN 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 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 186 VAL Chi-restraints excluded: chain C residue 194 SER 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 257 SER Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 299 VAL 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 90 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 132 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2569 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 : 0.652 12.149 9813 Z= 0.321 Chirality : 0.042 0.156 1171 Planarity : 0.005 0.119 1282 Dihedral : 4.181 17.244 995 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 4.40 % Allowed : 25.91 % Favored : 69.69 % 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: 0.20 (0.29), residues: 894 helix: 1.15 (0.25), residues: 438 sheet: -0.43 (0.62), residues: 67 loop : -0.90 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 246 HIS 0.006 0.001 HIS C 241 PHE 0.009 0.001 PHE B 234 TYR 0.008 0.001 TYR C 313 ARG 0.002 0.000 ARG C 60 *********************** 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 73 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 38 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6437 (tpt) cc_final: 0.5272 (tpt) REVERT: B 71 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7486 (tp) REVERT: B 93 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9380 (mm) REVERT: B 113 MET cc_start: 0.8190 (pmm) cc_final: 0.7924 (pmm) REVERT: B 330 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7721 (t80) REVERT: C 108 LYS cc_start: 0.9450 (mmtt) cc_final: 0.9148 (mmtm) REVERT: C 223 MET cc_start: 0.9290 (mmm) cc_final: 0.9060 (mmm) REVERT: C 264 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8085 (t0) outliers start: 35 outliers final: 22 residues processed: 71 average time/residue: 0.2008 time to fit residues: 19.6805 Evaluate side-chains 64 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 38 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 93 LEU 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 169 TRP Chi-restraints excluded: chain C residue 228 ARG 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 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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** A 542 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8307 moved from start: 0.2924 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= 0.204 Angle : 0.656 12.197 9813 Z= 0.326 Chirality : 0.042 0.162 1171 Planarity : 0.004 0.044 1282 Dihedral : 4.152 16.491 995 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.41 % Rotamer: Outliers : 4.28 % Allowed : 26.54 % Favored : 69.18 % 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: 0.22 (0.29), residues: 894 helix: 1.12 (0.25), residues: 439 sheet: -0.44 (0.63), residues: 68 loop : -0.84 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.009 0.001 PHE B 236 TYR 0.008 0.001 TYR C 313 ARG 0.004 0.000 ARG A 535 *********************** 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 73 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 39 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6824 (tpt) cc_final: 0.5673 (tpt) REVERT: B 93 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9363 (mm) REVERT: B 113 MET cc_start: 0.8281 (pmm) cc_final: 0.7991 (pmm) REVERT: B 330 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7675 (t80) REVERT: C 157 MET cc_start: 0.9038 (ptp) cc_final: 0.8764 (ptp) REVERT: D 98 ASP cc_start: 0.7419 (t0) cc_final: 0.7165 (t0) outliers start: 34 outliers final: 27 residues processed: 72 average time/residue: 0.1660 time to fit residues: 17.3205 Evaluate side-chains 66 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 37 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 93 LEU 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 194 SER Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ARG 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 60 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 132 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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: 0.3084 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= 0.189 Angle : 0.668 12.849 9813 Z= 0.329 Chirality : 0.042 0.174 1171 Planarity : 0.004 0.036 1282 Dihedral : 4.146 16.510 995 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 4.40 % Allowed : 26.29 % Favored : 69.31 % 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: 0.32 (0.29), residues: 894 helix: 1.20 (0.25), residues: 438 sheet: -0.36 (0.62), residues: 67 loop : -0.79 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 246 HIS 0.008 0.001 HIS C 241 PHE 0.009 0.001 PHE B 234 TYR 0.007 0.001 TYR C 313 ARG 0.004 0.000 ARG A 535 *********************** 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 73 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 38 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6978 (tpt) cc_final: 0.5836 (tpt) REVERT: B 93 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9354 (mm) REVERT: B 113 MET cc_start: 0.8175 (pmm) cc_final: 0.7892 (pmm) REVERT: B 330 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7739 (t80) REVERT: C 108 LYS cc_start: 0.9492 (mmtt) cc_final: 0.9177 (mmtm) REVERT: C 223 MET cc_start: 0.9250 (mmm) cc_final: 0.8745 (mmm) REVERT: D 98 ASP cc_start: 0.7382 (t0) cc_final: 0.7118 (t0) REVERT: F 75 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9070 (mp) outliers start: 35 outliers final: 30 residues processed: 72 average time/residue: 0.2000 time to fit residues: 20.4656 Evaluate side-chains 71 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 38 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 71 ILE 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 140 LYS Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ARG 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 60 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 82 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 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** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3179 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= 0.167 Angle : 0.673 13.516 9813 Z= 0.328 Chirality : 0.042 0.174 1171 Planarity : 0.004 0.034 1282 Dihedral : 4.122 16.684 995 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 3.65 % Allowed : 27.42 % Favored : 68.93 % 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: 0.40 (0.29), residues: 894 helix: 1.25 (0.25), residues: 438 sheet: -0.20 (0.65), residues: 60 loop : -0.75 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 246 HIS 0.009 0.001 HIS C 241 PHE 0.011 0.001 PHE B 234 TYR 0.006 0.001 TYR C 313 ARG 0.004 0.000 ARG A 535 *********************** 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 68 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 39 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6709 (tpt) cc_final: 0.5536 (tpt) REVERT: B 93 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9356 (mm) REVERT: B 113 MET cc_start: 0.8073 (pmm) cc_final: 0.7835 (pmm) REVERT: B 330 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7727 (t80) REVERT: C 108 LYS cc_start: 0.9492 (mmtt) cc_final: 0.9180 (mmtm) REVERT: C 157 MET cc_start: 0.8995 (ptp) cc_final: 0.8619 (ptp) REVERT: C 223 MET cc_start: 0.9219 (mmm) cc_final: 0.8751 (mmm) REVERT: D 98 ASP cc_start: 0.7579 (t0) cc_final: 0.7298 (t0) outliers start: 29 outliers final: 25 residues processed: 67 average time/residue: 0.1668 time to fit residues: 16.3085 Evaluate side-chains 65 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 38 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 ILE 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 52 GLN Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 218 CYS 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 E residue 60 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 132 MET 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 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: 6.9990 chunk 79 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8261 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7253 Z= 0.166 Angle : 0.686 13.102 9813 Z= 0.333 Chirality : 0.042 0.176 1171 Planarity : 0.004 0.036 1282 Dihedral : 4.067 16.334 995 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 3.65 % Allowed : 27.55 % Favored : 68.81 % 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: 0.52 (0.29), residues: 894 helix: 1.39 (0.25), residues: 434 sheet: -0.18 (0.64), residues: 60 loop : -0.71 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 246 HIS 0.010 0.001 HIS C 241 PHE 0.010 0.001 PHE B 234 TYR 0.005 0.001 TYR E 104 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 68 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 39 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6342 (tpt) cc_final: 0.4969 (tpt) REVERT: B 93 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9325 (mm) REVERT: C 157 MET cc_start: 0.8997 (ptp) cc_final: 0.8680 (ptp) REVERT: C 223 MET cc_start: 0.9209 (mmm) cc_final: 0.8762 (mmm) REVERT: D 98 ASP cc_start: 0.7520 (t0) cc_final: 0.7236 (t0) outliers start: 29 outliers final: 27 residues processed: 67 average time/residue: 0.1642 time to fit residues: 16.0342 Evaluate side-chains 65 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 37 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 71 ILE 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 194 SER Chi-restraints excluded: chain C residue 218 CYS 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 E residue 60 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 132 MET 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 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: 0.8980 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 70 optimal weight: 0.0470 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 0.0470 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 46 optimal weight: 0.0570 overall best weight: 0.3294 ------------------------------------------------------------------------------- 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** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** 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 = 0.3172 r_free = 0.3172 target = 0.034987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.026190 restraints weight = 99953.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.026689 restraints weight = 67043.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.026988 restraints weight = 50995.383| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7253 Z= 0.158 Angle : 0.688 14.091 9813 Z= 0.333 Chirality : 0.042 0.175 1171 Planarity : 0.004 0.036 1282 Dihedral : 3.992 16.379 995 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 2.39 % Allowed : 28.55 % Favored : 69.06 % 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: 0.58 (0.29), residues: 894 helix: 1.42 (0.25), residues: 433 sheet: -0.07 (0.63), residues: 60 loop : -0.66 (0.34), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 169 HIS 0.010 0.001 HIS C 241 PHE 0.012 0.001 PHE B 149 TYR 0.010 0.001 TYR C 179 ARG 0.005 0.000 ARG A 535 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.05 seconds wall clock time: 34 minutes 13.09 seconds (2053.09 seconds total)