Starting phenix.real_space_refine on Sat Aug 3 06:33:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umd_42376/08_2024/8umd_42376.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umd_42376/08_2024/8umd_42376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umd_42376/08_2024/8umd_42376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umd_42376/08_2024/8umd_42376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umd_42376/08_2024/8umd_42376.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umd_42376/08_2024/8umd_42376.cif" } resolution = 3.6 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= 0.006 sd= 0.086 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 4528 2.51 5 N 1287 2.21 5 O 1359 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 PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D ASP 116": "OD1" <-> "OD2" Residue "D ASP 124": "OD1" <-> "OD2" Residue "E ASP 59": "OD1" <-> "OD2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ASP 124": "OD1" <-> "OD2" Residue "F ASP 59": "OD1" <-> "OD2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" 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: 7201 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 393 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2583 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 324} Chain: "C" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2348 Classifications: {'peptide': 290} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 267} Chain: "D" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 625 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "E" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 625 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 627 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Time building chain proxies: 6.56, per 1000 atoms: 0.91 Number of scatterers: 7201 At special positions: 0 Unit cell: (106.496, 109.824, 168.064, 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 1359 8.00 N 1287 7.00 C 4528 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: 2.92 Conformation dependent library (CDL) restraints added in 1.3 seconds 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 51.6% alpha, 23.7% 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 514 through 543 Processing helix chain 'A' and resid 543 through 558 Processing helix chain 'B' and resid 5 through 18 removed outlier: 3.832A pdb=" N GLY B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 48 through 67 Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.574A pdb=" N ARG B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLU B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N GLU B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG B 101 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.667A pdb=" N THR B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.635A pdb=" N HIS B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.610A 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 183 Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 207 through 222 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.517A pdb=" N LEU B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 242 through 252 removed outlier: 4.062A pdb=" N SER B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.647A pdb=" N LYS B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 297 through 318 removed outlier: 3.510A pdb=" N THR B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 74 Processing helix chain 'C' and resid 89 through 95 removed outlier: 3.619A pdb=" N ASN C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 131 Processing helix chain 'C' and resid 147 through 171 removed outlier: 4.016A pdb=" N ALA C 171 " --> pdb=" O ASP C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 227 through 233 removed outlier: 3.854A pdb=" N ASN C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'D' and resid 74 through 81 Processing helix chain 'D' and resid 127 through 134 Processing helix chain 'E' and resid 75 through 81 Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.630A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 130 through 135' Processing helix chain 'F' and resid 75 through 81 Processing helix chain 'F' and resid 127 through 136 Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36 removed outlier: 5.517A pdb=" N LEU E 105 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 101 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 107 " --> pdb=" O ILE E 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP E 98 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 86 through 92 removed outlier: 4.973A pdb=" N TYR F 118 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLN F 108 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE F 125 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ILE F 106 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE F 99 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN F 108 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU F 97 " --> pdb=" O GLN F 108 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL F 62 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG E 72 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU F 64 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG E 70 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL F 66 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL E 66 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP E 98 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 107 " --> pdb=" O ILE E 99 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 101 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU E 105 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 81 Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 81 removed outlier: 4.011A pdb=" N ARG C 181 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS C 106 " --> pdb=" O TYR C 179 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR C 179 " --> pdb=" O HIS C 106 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS C 108 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL C 177 " --> pdb=" O LYS C 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 283 through 284 removed outlier: 3.509A pdb=" N VAL D 120 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN D 108 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE D 125 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ILE D 106 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU D 105 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE D 101 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 107 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D 98 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL D 62 " --> pdb=" O PRO C 269 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU D 64 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP C 267 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL D 66 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA C 263 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG D 70 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU C 261 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE C 293 " --> pdb=" O ASN C 264 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL C 296 " --> pdb=" O PRO C 300 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL C 301 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU C 320 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR C 303 " --> pdb=" O GLU C 318 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR C 313 " --> pdb=" O LEU D 89 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1152 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: 2.23 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2499 1.34 - 1.46: 1323 1.46 - 1.58: 3415 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 7290 Sorted by residual: bond pdb=" N THR B 103 " pdb=" CA THR B 103 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.32e+00 bond pdb=" CB ASP E 59 " pdb=" CG ASP E 59 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.89e+00 bond pdb=" CA ASP D 116 " pdb=" CB ASP D 116 " ideal model delta sigma weight residual 1.530 1.553 -0.022 1.69e-02 3.50e+03 1.76e+00 bond pdb=" CA MET E 58 " pdb=" CB MET E 58 " ideal model delta sigma weight residual 1.537 1.560 -0.023 1.85e-02 2.92e+03 1.54e+00 bond pdb=" CB ASP D 116 " pdb=" CG ASP D 116 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.49e+00 ... (remaining 7285 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.35: 188 106.35 - 113.24: 4064 113.24 - 120.14: 2482 120.14 - 127.03: 3078 127.03 - 133.92: 53 Bond angle restraints: 9865 Sorted by residual: angle pdb=" CA MET E 58 " pdb=" CB MET E 58 " pdb=" CG MET E 58 " ideal model delta sigma weight residual 114.10 122.99 -8.89 2.00e+00 2.50e-01 1.97e+01 angle pdb=" CA MET D 132 " pdb=" CB MET D 132 " pdb=" CG MET D 132 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CA LEU A 549 " pdb=" CB LEU A 549 " pdb=" CG LEU A 549 " ideal model delta sigma weight residual 116.30 128.51 -12.21 3.50e+00 8.16e-02 1.22e+01 angle pdb=" C MET E 58 " pdb=" CA MET E 58 " pdb=" CB MET E 58 " ideal model delta sigma weight residual 109.80 114.97 -5.17 1.61e+00 3.86e-01 1.03e+01 angle pdb=" CA MET A 532 " pdb=" CB MET A 532 " pdb=" CG MET A 532 " ideal model delta sigma weight residual 114.10 120.23 -6.13 2.00e+00 2.50e-01 9.39e+00 ... (remaining 9860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3892 17.85 - 35.70: 492 35.70 - 53.55: 125 53.55 - 71.41: 21 71.41 - 89.26: 8 Dihedral angle restraints: 4538 sinusoidal: 1903 harmonic: 2635 Sorted by residual: dihedral pdb=" CA PRO C 234 " pdb=" C PRO C 234 " pdb=" N PRO C 235 " pdb=" CA PRO C 235 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LEU B 188 " pdb=" C LEU B 188 " pdb=" N LYS B 189 " pdb=" CA LYS B 189 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ILE E 125 " pdb=" C ILE E 125 " pdb=" N ILE E 126 " pdb=" CA ILE E 126 " ideal model delta harmonic sigma weight residual 180.00 158.13 21.87 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 4535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 879 0.043 - 0.087: 213 0.087 - 0.130: 78 0.130 - 0.173: 3 0.173 - 0.216: 3 Chirality restraints: 1176 Sorted by residual: chirality pdb=" CG LEU B 56 " pdb=" CB LEU B 56 " pdb=" CD1 LEU B 56 " pdb=" CD2 LEU B 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE A 536 " pdb=" CA ILE A 536 " pdb=" CG1 ILE A 536 " pdb=" CG2 ILE A 536 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB VAL C 251 " pdb=" CA VAL C 251 " pdb=" CG1 VAL C 251 " pdb=" CG2 VAL C 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 1173 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 102 " 0.023 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C ASP B 102 " -0.078 2.00e-02 2.50e+03 pdb=" O ASP B 102 " 0.030 2.00e-02 2.50e+03 pdb=" N THR B 103 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 234 " -0.049 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO C 235 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 235 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 235 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 116 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" C ASP D 116 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP D 116 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS D 117 " -0.014 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 124 2.66 - 3.22: 7181 3.22 - 3.78: 11179 3.78 - 4.34: 14252 4.34 - 4.90: 23009 Nonbonded interactions: 55745 Sorted by model distance: nonbonded pdb=" OG SER C 273 " pdb=" O MET D 58 " model vdw 2.098 3.040 nonbonded pdb=" O ILE B 97 " pdb=" OG1 THR B 100 " model vdw 2.119 3.040 nonbonded pdb=" NZ LYS E 76 " pdb=" O MET F 58 " model vdw 2.170 3.120 nonbonded pdb=" O GLY B 106 " pdb=" OG1 THR B 109 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR C 179 " pdb=" OG SER C 182 " model vdw 2.220 3.040 ... (remaining 55740 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 57 through 135) selection = (chain 'E' and resid 57 through 135) selection = (chain 'F' and resid 57 through 135) } 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: 7.090 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.420 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 0.047 7290 Z= 0.218 Angle : 0.722 12.213 9865 Z= 0.375 Chirality : 0.043 0.216 1176 Planarity : 0.005 0.073 1290 Dihedral : 16.777 89.258 2822 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.89 % Favored : 94.77 % Rotamer: Outliers : 0.50 % Allowed : 26.69 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.54 (0.29), residues: 899 helix: 1.56 (0.26), residues: 435 sheet: 0.15 (0.52), residues: 97 loop : -1.05 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 169 HIS 0.004 0.001 HIS C 295 PHE 0.018 0.002 PHE C 70 TYR 0.009 0.001 TYR D 118 ARG 0.010 0.001 ARG F 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.904 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: B 233 MET cc_start: 0.8573 (ttt) cc_final: 0.7989 (tpt) REVERT: B 270 LEU cc_start: 0.8772 (tp) cc_final: 0.8524 (mm) REVERT: C 67 MET cc_start: 0.9235 (mmt) cc_final: 0.8907 (mmm) REVERT: C 69 LEU cc_start: 0.9503 (mt) cc_final: 0.9272 (mt) REVERT: E 70 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7546 (ptp90) outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.2219 time to fit residues: 28.0647 Evaluate side-chains 64 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain E residue 74 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7290 Z= 0.185 Angle : 0.682 12.028 9865 Z= 0.344 Chirality : 0.044 0.172 1176 Planarity : 0.005 0.062 1290 Dihedral : 4.611 25.777 1003 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.34 % Favored : 95.33 % Rotamer: Outliers : 2.51 % Allowed : 24.19 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.62 (0.29), residues: 899 helix: 1.63 (0.25), residues: 437 sheet: 0.02 (0.54), residues: 92 loop : -0.97 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 169 HIS 0.002 0.001 HIS B 126 PHE 0.011 0.001 PHE C 215 TYR 0.006 0.001 TYR E 118 ARG 0.006 0.000 ARG E 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.8430 (ttt) cc_final: 0.7941 (tpt) REVERT: B 270 LEU cc_start: 0.8767 (tp) cc_final: 0.8509 (mm) REVERT: B 278 MET cc_start: 0.3078 (mmt) cc_final: 0.1666 (mmt) REVERT: C 67 MET cc_start: 0.9266 (mmt) cc_final: 0.8923 (mmm) REVERT: C 170 LYS cc_start: 0.9698 (tppp) cc_final: 0.9396 (tppp) REVERT: E 67 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7839 (tt0) REVERT: E 70 ARG cc_start: 0.8138 (mtm-85) cc_final: 0.7535 (ptp90) outliers start: 20 outliers final: 13 residues processed: 94 average time/residue: 0.1973 time to fit residues: 25.0296 Evaluate side-chains 76 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN C 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7290 Z= 0.188 Angle : 0.628 8.866 9865 Z= 0.322 Chirality : 0.042 0.173 1176 Planarity : 0.004 0.060 1290 Dihedral : 4.389 22.866 1000 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.89 % Favored : 94.77 % Rotamer: Outliers : 3.63 % Allowed : 23.06 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.71 (0.29), residues: 899 helix: 1.70 (0.26), residues: 436 sheet: 0.17 (0.56), residues: 91 loop : -0.94 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 554 HIS 0.003 0.001 HIS B 126 PHE 0.012 0.001 PHE C 65 TYR 0.006 0.001 TYR C 38 ARG 0.006 0.000 ARG E 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 63 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 LEU cc_start: 0.8696 (tp) cc_final: 0.8458 (mm) REVERT: B 278 MET cc_start: 0.3667 (mmt) cc_final: 0.2494 (mmt) REVERT: C 67 MET cc_start: 0.9273 (mmt) cc_final: 0.8939 (mmm) REVERT: C 170 LYS cc_start: 0.9698 (tppp) cc_final: 0.9426 (tppp) REVERT: E 67 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7999 (tt0) REVERT: E 70 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7594 (ptp90) outliers start: 29 outliers final: 21 residues processed: 88 average time/residue: 0.2004 time to fit residues: 23.9657 Evaluate side-chains 77 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 56 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 54 optimal weight: 0.2980 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7290 Z= 0.162 Angle : 0.610 10.891 9865 Z= 0.310 Chirality : 0.042 0.154 1176 Planarity : 0.004 0.058 1290 Dihedral : 4.265 22.430 1000 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.34 % Favored : 95.33 % Rotamer: Outliers : 3.88 % Allowed : 22.68 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.79 (0.29), residues: 899 helix: 1.74 (0.26), residues: 433 sheet: 0.03 (0.56), residues: 91 loop : -0.79 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 554 HIS 0.002 0.000 HIS B 126 PHE 0.011 0.001 PHE C 215 TYR 0.006 0.001 TYR C 165 ARG 0.003 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 64 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 270 LEU cc_start: 0.8692 (tp) cc_final: 0.8450 (mm) REVERT: B 278 MET cc_start: 0.3565 (mmt) cc_final: 0.2499 (mmt) REVERT: C 67 MET cc_start: 0.9243 (mmt) cc_final: 0.8918 (mmm) REVERT: C 170 LYS cc_start: 0.9687 (tppp) cc_final: 0.9387 (tppp) REVERT: F 73 MET cc_start: 0.8798 (ppp) cc_final: 0.8437 (ppp) outliers start: 31 outliers final: 20 residues processed: 89 average time/residue: 0.2104 time to fit residues: 25.1405 Evaluate side-chains 80 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 0.0980 chunk 35 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 0.0010 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7290 Z= 0.176 Angle : 0.617 8.375 9865 Z= 0.313 Chirality : 0.042 0.138 1176 Planarity : 0.004 0.058 1290 Dihedral : 4.230 22.161 1000 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.23 % Favored : 95.44 % Rotamer: Outliers : 3.51 % Allowed : 24.69 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.76 (0.30), residues: 899 helix: 1.68 (0.26), residues: 438 sheet: -0.14 (0.60), residues: 77 loop : -0.73 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 554 HIS 0.002 0.001 HIS B 126 PHE 0.013 0.001 PHE B 234 TYR 0.005 0.001 TYR F 104 ARG 0.002 0.000 ARG E 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 62 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 LEU cc_start: 0.8714 (tp) cc_final: 0.8470 (mm) REVERT: B 278 MET cc_start: 0.3681 (mmt) cc_final: 0.3034 (mmt) REVERT: C 67 MET cc_start: 0.9291 (mmt) cc_final: 0.8960 (mmm) outliers start: 28 outliers final: 21 residues processed: 87 average time/residue: 0.2065 time to fit residues: 24.4169 Evaluate side-chains 74 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 53 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7290 Z= 0.218 Angle : 0.644 8.943 9865 Z= 0.324 Chirality : 0.042 0.215 1176 Planarity : 0.004 0.058 1290 Dihedral : 4.307 22.921 1000 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.34 % Favored : 95.33 % Rotamer: Outliers : 3.76 % Allowed : 24.69 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.79 (0.30), residues: 899 helix: 1.72 (0.26), residues: 439 sheet: -0.20 (0.61), residues: 78 loop : -0.72 (0.35), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 554 HIS 0.003 0.001 HIS B 126 PHE 0.012 0.001 PHE B 66 TYR 0.010 0.001 TYR C 38 ARG 0.005 0.000 ARG E 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 55 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.8410 (ttt) cc_final: 0.8129 (tmm) REVERT: B 270 LEU cc_start: 0.8769 (tp) cc_final: 0.8510 (mm) REVERT: B 278 MET cc_start: 0.4170 (mmt) cc_final: 0.3394 (mmt) REVERT: C 67 MET cc_start: 0.9315 (mmt) cc_final: 0.8967 (mmm) REVERT: C 108 LYS cc_start: 0.9469 (mmtt) cc_final: 0.9170 (mmtt) REVERT: F 73 MET cc_start: 0.8940 (ppp) cc_final: 0.8005 (ppp) outliers start: 30 outliers final: 22 residues processed: 83 average time/residue: 0.2139 time to fit residues: 24.2176 Evaluate side-chains 74 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 52 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7290 Z= 0.167 Angle : 0.650 10.090 9865 Z= 0.323 Chirality : 0.042 0.181 1176 Planarity : 0.004 0.058 1290 Dihedral : 4.260 22.629 1000 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.34 % Favored : 95.33 % Rotamer: Outliers : 3.63 % Allowed : 25.44 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.75 (0.30), residues: 899 helix: 1.69 (0.26), residues: 438 sheet: -0.27 (0.62), residues: 73 loop : -0.72 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 554 HIS 0.003 0.001 HIS B 126 PHE 0.015 0.001 PHE C 131 TYR 0.007 0.001 TYR F 104 ARG 0.003 0.000 ARG A 535 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 55 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.8327 (tmm) cc_final: 0.8095 (tmm) REVERT: B 270 LEU cc_start: 0.8757 (tp) cc_final: 0.8510 (mm) REVERT: B 278 MET cc_start: 0.4067 (mmt) cc_final: 0.3249 (mmt) REVERT: C 67 MET cc_start: 0.9298 (mmt) cc_final: 0.8949 (mmm) REVERT: C 184 MET cc_start: 0.9199 (mmp) cc_final: 0.8984 (mmp) REVERT: F 73 MET cc_start: 0.8858 (ppp) cc_final: 0.7850 (ppp) outliers start: 29 outliers final: 23 residues processed: 82 average time/residue: 0.1932 time to fit residues: 21.9626 Evaluate side-chains 73 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 50 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 8 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7290 Z= 0.186 Angle : 0.661 11.886 9865 Z= 0.330 Chirality : 0.043 0.207 1176 Planarity : 0.004 0.058 1290 Dihedral : 4.256 22.664 1000 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.23 % Favored : 95.44 % Rotamer: Outliers : 3.51 % Allowed : 26.07 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.71 (0.30), residues: 899 helix: 1.60 (0.26), residues: 440 sheet: -0.27 (0.63), residues: 73 loop : -0.68 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.003 0.001 HIS C 106 PHE 0.018 0.001 PHE B 234 TYR 0.007 0.001 TYR D 118 ARG 0.003 0.000 ARG E 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 54 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 LEU cc_start: 0.8870 (tp) cc_final: 0.8590 (mm) REVERT: B 278 MET cc_start: 0.4231 (mmt) cc_final: 0.3384 (mmt) REVERT: C 67 MET cc_start: 0.9305 (mmt) cc_final: 0.8955 (mmm) REVERT: F 73 MET cc_start: 0.8840 (ppp) cc_final: 0.7843 (ppp) outliers start: 28 outliers final: 25 residues processed: 79 average time/residue: 0.1891 time to fit residues: 20.6661 Evaluate side-chains 77 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 52 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7290 Z= 0.171 Angle : 0.684 11.233 9865 Z= 0.340 Chirality : 0.043 0.178 1176 Planarity : 0.004 0.058 1290 Dihedral : 4.239 22.681 1000 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.12 % Favored : 95.55 % Rotamer: Outliers : 3.51 % Allowed : 25.94 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.62 (0.30), residues: 899 helix: 1.50 (0.26), residues: 441 sheet: -0.33 (0.61), residues: 74 loop : -0.69 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.003 0.001 HIS C 106 PHE 0.017 0.001 PHE B 234 TYR 0.006 0.001 TYR F 104 ARG 0.003 0.000 ARG E 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 54 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 LEU cc_start: 0.8867 (tp) cc_final: 0.8584 (mm) REVERT: B 278 MET cc_start: 0.4189 (mmt) cc_final: 0.3331 (mmt) REVERT: C 67 MET cc_start: 0.9296 (mmt) cc_final: 0.8945 (mmm) outliers start: 28 outliers final: 25 residues processed: 78 average time/residue: 0.1979 time to fit residues: 21.4022 Evaluate side-chains 78 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 53 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7290 Z= 0.177 Angle : 0.713 14.857 9865 Z= 0.352 Chirality : 0.043 0.173 1176 Planarity : 0.004 0.058 1290 Dihedral : 4.307 23.772 1000 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.23 % Favored : 95.44 % Rotamer: Outliers : 3.38 % Allowed : 26.19 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.65 (0.30), residues: 899 helix: 1.52 (0.26), residues: 435 sheet: -0.27 (0.62), residues: 74 loop : -0.65 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 246 HIS 0.002 0.000 HIS B 126 PHE 0.017 0.001 PHE B 234 TYR 0.006 0.001 TYR D 118 ARG 0.003 0.000 ARG E 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 54 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 LEU cc_start: 0.8870 (tp) cc_final: 0.8585 (mm) REVERT: B 278 MET cc_start: 0.4206 (mmt) cc_final: 0.3336 (mmt) REVERT: C 67 MET cc_start: 0.9294 (mmt) cc_final: 0.8943 (mmm) outliers start: 27 outliers final: 24 residues processed: 77 average time/residue: 0.1808 time to fit residues: 19.6414 Evaluate side-chains 78 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 54 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 73 optimal weight: 0.0570 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.044418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.033731 restraints weight = 61242.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.034516 restraints weight = 36390.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.035066 restraints weight = 25442.861| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7290 Z= 0.248 Angle : 0.756 15.516 9865 Z= 0.373 Chirality : 0.043 0.173 1176 Planarity : 0.004 0.057 1290 Dihedral : 4.486 24.400 1000 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.67 % Favored : 94.99 % Rotamer: Outliers : 3.38 % Allowed : 26.32 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.69 (0.30), residues: 899 helix: 1.49 (0.26), residues: 434 sheet: 0.28 (0.62), residues: 73 loop : -0.65 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 554 HIS 0.002 0.001 HIS B 136 PHE 0.017 0.002 PHE C 131 TYR 0.012 0.002 TYR C 38 ARG 0.004 0.000 ARG E 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.88 seconds wall clock time: 36 minutes 29.75 seconds (2189.75 seconds total)