Starting phenix.real_space_refine on Sun Jul 21 08:36:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8f_42023/07_2024/8u8f_42023_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8f_42023/07_2024/8u8f_42023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8f_42023/07_2024/8u8f_42023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8f_42023/07_2024/8u8f_42023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8f_42023/07_2024/8u8f_42023_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8f_42023/07_2024/8u8f_42023_trim.cif" } resolution = 3.49 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= -0.003 sd= 0.065 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: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 4433 2.51 5 N 1209 2.21 5 O 1275 1.98 5 H 6925 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13891 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3800 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5094 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 871 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4094 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 1 Chain: "R" Number of atoms: 32 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 16 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 2 Conformer: "B" Number of residues, atoms: 1, 16 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" CA APLM R 401 " occ=0.68 ... (30 atoms not shown) pdb=" CF BPLM R 401 " occ=0.32 Time building chain proxies: 6.98, per 1000 atoms: 0.50 Number of scatterers: 13891 At special positions: 0 Unit cell: (78.26, 100.62, 126.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 O 1275 8.00 N 1209 7.00 C 4433 6.00 H 6925 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 177 " - pdb=" SG CYS R 184 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.21 Conformation dependent library (CDL) restraints added in 1.3 seconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 46.1% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.552A pdb=" N LYS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 279 removed outlier: 4.130A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.533A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.093A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.799A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.565A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 68 removed outlier: 3.691A pdb=" N CYS R 48 " --> pdb=" O ASP R 44 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU R 60 " --> pdb=" O CYS R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 101 removed outlier: 3.649A pdb=" N PHE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 140 removed outlier: 3.610A pdb=" N SER R 109 " --> pdb=" O SER R 105 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 146 removed outlier: 4.059A pdb=" N TYR R 145 " --> pdb=" O LEU R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 170 removed outlier: 4.035A pdb=" N LEU R 170 " --> pdb=" O GLY R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 230 removed outlier: 3.549A pdb=" N LEU R 229 " --> pdb=" O GLN R 225 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN R 230 " --> pdb=" O GLN R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 253 removed outlier: 3.655A pdb=" N VAL R 251 " --> pdb=" O ALA R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 270 Proline residue: R 262 - end of helix Processing helix chain 'R' and resid 275 through 282 removed outlier: 4.236A pdb=" N THR R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR R 280 " --> pdb=" O PRO R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 298 removed outlier: 3.772A pdb=" N ALA R 286 " --> pdb=" O THR R 282 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN R 289 " --> pdb=" O PRO R 285 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER R 290 " --> pdb=" O ALA R 286 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET R 291 " --> pdb=" O THR R 287 " (cutoff:3.500A) Proline residue: R 294 - end of helix Processing helix chain 'R' and resid 301 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.518A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 3.790A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.901A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.533A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.627A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.857A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.837A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.484A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1053 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: 5.43 Time building geometry restraints manager: 11.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6897 1.04 - 1.23: 246 1.23 - 1.43: 2748 1.43 - 1.63: 4065 1.63 - 1.83: 68 Bond restraints: 14024 Sorted by residual: bond pdb=" N VAL R 132 " pdb=" CA VAL R 132 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.90e+00 bond pdb=" N LEU R 136 " pdb=" H LEU R 136 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.83e+00 bond pdb=" N ALA R 129 " pdb=" H ALA R 129 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.74e+00 bond pdb=" N VAL R 155 " pdb=" H VAL R 155 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" N LEU R 78 " pdb=" H LEU R 78 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.70e+00 ... (remaining 14019 not shown) Histogram of bond angle deviations from ideal: 73.55 - 85.69: 3 85.69 - 97.84: 0 97.84 - 109.98: 11947 109.98 - 122.12: 11001 122.12 - 134.26: 2293 Bond angle restraints: 25244 Sorted by residual: angle pdb=" C ASN B 340 " pdb=" CA ASN B 340 " pdb=" HA ASN B 340 " ideal model delta sigma weight residual 109.00 73.55 35.45 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N ASN B 340 " pdb=" CA ASN B 340 " pdb=" HA ASN B 340 " ideal model delta sigma weight residual 110.00 74.70 35.30 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB ASN B 340 " pdb=" CA ASN B 340 " pdb=" HA ASN B 340 " ideal model delta sigma weight residual 109.00 79.73 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CA PRO G 49 " pdb=" N PRO G 49 " pdb=" CD PRO G 49 " ideal model delta sigma weight residual 112.00 104.99 7.01 1.40e+00 5.10e-01 2.51e+01 angle pdb=" N ASN B 313 " pdb=" CA ASN B 313 " pdb=" CB ASN B 313 " ideal model delta sigma weight residual 114.17 109.59 4.58 1.14e+00 7.69e-01 1.62e+01 ... (remaining 25239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5908 17.91 - 35.83: 502 35.83 - 53.74: 143 53.74 - 71.66: 36 71.66 - 89.57: 14 Dihedral angle restraints: 6603 sinusoidal: 3564 harmonic: 3039 Sorted by residual: dihedral pdb=" CB CYS R 177 " pdb=" SG CYS R 177 " pdb=" SG CYS R 184 " pdb=" CB CYS R 184 " ideal model delta sinusoidal sigma weight residual -86.00 -26.65 -59.35 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CA ASN R 176 " pdb=" C ASN R 176 " pdb=" N CYS R 177 " pdb=" CA CYS R 177 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA VAL R 187 " pdb=" C VAL R 187 " pdb=" N TYR R 188 " pdb=" CA TYR R 188 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 6600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1050 0.091 - 0.182: 53 0.182 - 0.273: 0 0.273 - 0.364: 0 0.364 - 0.455: 1 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CA ASN B 340 " pdb=" N ASN B 340 " pdb=" C ASN B 340 " pdb=" CB ASN B 340 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA VAL R 155 " pdb=" N VAL R 155 " pdb=" C VAL R 155 " pdb=" CB VAL R 155 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA LEU R 159 " pdb=" N LEU R 159 " pdb=" C LEU R 159 " pdb=" CB LEU R 159 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1101 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 152 " 0.447 9.50e-02 1.11e+02 1.51e-01 3.60e+01 pdb=" NE ARG R 152 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG R 152 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG R 152 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 152 " -0.005 2.00e-02 2.50e+03 pdb="HH11 ARG R 152 " -0.048 2.00e-02 2.50e+03 pdb="HH12 ARG R 152 " 0.051 2.00e-02 2.50e+03 pdb="HH21 ARG R 152 " 0.011 2.00e-02 2.50e+03 pdb="HH22 ARG R 152 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.085 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO G 49 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 136 " 0.013 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" N SER R 137 " -0.042 2.00e-02 2.50e+03 pdb=" CA SER R 137 " 0.011 2.00e-02 2.50e+03 pdb=" H SER R 137 " 0.018 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 912 2.20 - 2.80: 28548 2.80 - 3.40: 38690 3.40 - 4.00: 49337 4.00 - 4.60: 76825 Nonbonded interactions: 194312 Sorted by model distance: nonbonded pdb=" OD1 ASN R 176 " pdb=" H SER R 191 " model vdw 1.600 1.850 nonbonded pdb=" O ASN R 140 " pdb=" H TYR R 144 " model vdw 1.634 1.850 nonbonded pdb=" OD1 ASP R 179 " pdb=" H LEU R 181 " model vdw 1.662 1.850 nonbonded pdb="HH21 ARG A 38 " pdb=" OE2 GLU R 147 " model vdw 1.666 1.850 nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.666 1.850 ... (remaining 194307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.190 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 47.550 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 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 0.109 7099 Z= 0.206 Angle : 0.544 10.634 9616 Z= 0.326 Chirality : 0.042 0.455 1104 Planarity : 0.007 0.182 1219 Dihedral : 15.464 89.571 2563 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.51 % Favored : 97.37 % Rotamer: Outliers : 0.13 % Allowed : 19.46 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.30), residues: 875 helix: 2.63 (0.28), residues: 358 sheet: 0.14 (0.42), residues: 156 loop : -0.42 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.002 0.000 HIS R 223 PHE 0.013 0.001 PHE R 299 TYR 0.024 0.001 TYR R 139 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 139 average time/residue: 0.4591 time to fit residues: 82.6045 Evaluate side-chains 132 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.0000 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7099 Z= 0.167 Angle : 0.496 10.199 9616 Z= 0.265 Chirality : 0.041 0.445 1104 Planarity : 0.004 0.073 1219 Dihedral : 4.367 51.593 992 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.91 % Rotamer: Outliers : 1.74 % Allowed : 18.39 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.30), residues: 875 helix: 2.83 (0.27), residues: 362 sheet: -0.43 (0.42), residues: 163 loop : -0.44 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 63 HIS 0.004 0.001 HIS R 223 PHE 0.015 0.001 PHE A 246 TYR 0.011 0.001 TYR B 124 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 56 CYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6995 (m) outliers start: 13 outliers final: 8 residues processed: 148 average time/residue: 0.4664 time to fit residues: 89.5144 Evaluate side-chains 142 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 309 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7099 Z= 0.141 Angle : 0.471 10.313 9616 Z= 0.249 Chirality : 0.040 0.447 1104 Planarity : 0.004 0.065 1219 Dihedral : 4.178 49.902 992 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.68 % Allowed : 18.52 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.30), residues: 875 helix: 2.88 (0.27), residues: 363 sheet: -0.50 (0.42), residues: 167 loop : -0.41 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.003 0.001 HIS R 223 PHE 0.011 0.001 PHE A 246 TYR 0.013 0.001 TYR A 311 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 MET cc_start: 0.7259 (tpp) cc_final: 0.7031 (tpp) REVERT: R 56 CYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7026 (m) outliers start: 20 outliers final: 14 residues processed: 150 average time/residue: 0.4734 time to fit residues: 91.4252 Evaluate side-chains 148 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7099 Z= 0.254 Angle : 0.534 10.435 9616 Z= 0.288 Chirality : 0.042 0.442 1104 Planarity : 0.004 0.064 1219 Dihedral : 4.784 48.618 992 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.34 % Favored : 95.54 % Rotamer: Outliers : 2.82 % Allowed : 19.33 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.30), residues: 875 helix: 2.55 (0.27), residues: 367 sheet: -0.94 (0.41), residues: 172 loop : -0.68 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.004 0.001 HIS R 223 PHE 0.023 0.002 PHE B 241 TYR 0.009 0.001 TYR A 311 ARG 0.011 0.001 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 MET cc_start: 0.7388 (tpp) cc_final: 0.7171 (tpp) REVERT: R 56 CYS cc_start: 0.7342 (OUTLIER) cc_final: 0.7025 (m) outliers start: 21 outliers final: 17 residues processed: 144 average time/residue: 0.4903 time to fit residues: 90.6147 Evaluate side-chains 147 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 28 optimal weight: 0.4980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7099 Z= 0.162 Angle : 0.491 10.206 9616 Z= 0.261 Chirality : 0.041 0.444 1104 Planarity : 0.004 0.060 1219 Dihedral : 4.551 47.670 992 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.82 % Allowed : 19.87 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.30), residues: 875 helix: 2.64 (0.27), residues: 367 sheet: -0.97 (0.40), residues: 172 loop : -0.68 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.003 0.001 HIS R 223 PHE 0.013 0.001 PHE B 241 TYR 0.013 0.001 TYR A 311 ARG 0.006 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 TYR cc_start: 0.7684 (m-80) cc_final: 0.7442 (m-80) REVERT: B 44 GLN cc_start: 0.7399 (mt0) cc_final: 0.7056 (mt0) REVERT: R 56 CYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7053 (m) outliers start: 21 outliers final: 18 residues processed: 147 average time/residue: 0.4700 time to fit residues: 88.7361 Evaluate side-chains 150 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 309 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7099 Z= 0.215 Angle : 0.521 10.238 9616 Z= 0.279 Chirality : 0.041 0.441 1104 Planarity : 0.005 0.066 1219 Dihedral : 4.790 47.504 992 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.36 % Allowed : 19.73 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.29), residues: 875 helix: 2.50 (0.27), residues: 367 sheet: -1.18 (0.40), residues: 170 loop : -0.75 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 63 HIS 0.003 0.001 HIS R 223 PHE 0.019 0.002 PHE B 241 TYR 0.011 0.001 TYR A 311 ARG 0.010 0.001 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.6565 (t70) cc_final: 0.6303 (t0) REVERT: A 358 TYR cc_start: 0.7777 (m-80) cc_final: 0.7564 (m-80) REVERT: B 262 MET cc_start: 0.7365 (tpp) cc_final: 0.6969 (tpp) REVERT: R 56 CYS cc_start: 0.7343 (OUTLIER) cc_final: 0.7082 (m) REVERT: R 139 TYR cc_start: 0.7684 (t80) cc_final: 0.7434 (t80) outliers start: 25 outliers final: 19 residues processed: 150 average time/residue: 0.4879 time to fit residues: 94.9857 Evaluate side-chains 150 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 309 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7099 Z= 0.177 Angle : 0.506 10.191 9616 Z= 0.269 Chirality : 0.041 0.442 1104 Planarity : 0.004 0.069 1219 Dihedral : 4.667 46.530 992 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.09 % Allowed : 19.60 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.30), residues: 875 helix: 2.58 (0.27), residues: 367 sheet: -1.26 (0.39), residues: 170 loop : -0.78 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS R 223 PHE 0.014 0.001 PHE B 241 TYR 0.013 0.001 TYR A 311 ARG 0.010 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.6550 (t70) cc_final: 0.6293 (t0) REVERT: A 358 TYR cc_start: 0.7758 (m-80) cc_final: 0.7553 (m-80) REVERT: B 262 MET cc_start: 0.7291 (tpp) cc_final: 0.7012 (tpp) REVERT: R 56 CYS cc_start: 0.7276 (OUTLIER) cc_final: 0.7039 (m) REVERT: R 139 TYR cc_start: 0.7684 (t80) cc_final: 0.7416 (t80) outliers start: 23 outliers final: 16 residues processed: 145 average time/residue: 0.5078 time to fit residues: 93.9843 Evaluate side-chains 148 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7099 Z= 0.268 Angle : 0.557 10.269 9616 Z= 0.301 Chirality : 0.042 0.439 1104 Planarity : 0.005 0.070 1219 Dihedral : 5.083 46.399 992 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.17 % Favored : 93.71 % Rotamer: Outliers : 3.49 % Allowed : 19.46 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.29), residues: 875 helix: 2.33 (0.27), residues: 367 sheet: -1.52 (0.39), residues: 170 loop : -0.95 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 63 HIS 0.004 0.001 HIS B 62 PHE 0.023 0.002 PHE B 241 TYR 0.013 0.001 TYR A 311 ARG 0.010 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.6698 (t70) cc_final: 0.6424 (t0) REVERT: B 171 ILE cc_start: 0.7182 (mm) cc_final: 0.6916 (mm) REVERT: B 262 MET cc_start: 0.7336 (tpp) cc_final: 0.7003 (tpp) REVERT: R 56 CYS cc_start: 0.7255 (OUTLIER) cc_final: 0.7026 (m) REVERT: R 139 TYR cc_start: 0.7728 (t80) cc_final: 0.7444 (t80) outliers start: 26 outliers final: 20 residues processed: 147 average time/residue: 0.4841 time to fit residues: 90.8930 Evaluate side-chains 152 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 309 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7099 Z= 0.179 Angle : 0.513 10.169 9616 Z= 0.274 Chirality : 0.041 0.443 1104 Planarity : 0.004 0.077 1219 Dihedral : 4.823 45.633 992 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.34 % Favored : 95.54 % Rotamer: Outliers : 2.42 % Allowed : 21.34 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.29), residues: 875 helix: 2.47 (0.27), residues: 367 sheet: -1.47 (0.39), residues: 170 loop : -0.92 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 63 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.001 PHE B 241 TYR 0.011 0.001 TYR A 311 ARG 0.011 0.001 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.6673 (t70) cc_final: 0.6419 (t0) REVERT: B 171 ILE cc_start: 0.7079 (mm) cc_final: 0.6798 (mm) REVERT: B 262 MET cc_start: 0.7309 (tpp) cc_final: 0.6977 (tpp) REVERT: R 56 CYS cc_start: 0.7259 (OUTLIER) cc_final: 0.7010 (m) REVERT: R 139 TYR cc_start: 0.7705 (t80) cc_final: 0.7456 (t80) outliers start: 18 outliers final: 17 residues processed: 139 average time/residue: 0.4791 time to fit residues: 85.9745 Evaluate side-chains 144 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7099 Z= 0.172 Angle : 0.513 10.271 9616 Z= 0.274 Chirality : 0.041 0.444 1104 Planarity : 0.005 0.079 1219 Dihedral : 4.739 45.645 992 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.28 % Allowed : 21.07 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.29), residues: 875 helix: 2.54 (0.27), residues: 367 sheet: -1.49 (0.39), residues: 170 loop : -0.94 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS R 223 PHE 0.021 0.002 PHE A 290 TYR 0.012 0.001 TYR A 311 ARG 0.011 0.001 ARG R 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.6658 (t70) cc_final: 0.6409 (t0) REVERT: B 171 ILE cc_start: 0.7067 (mm) cc_final: 0.6788 (mm) REVERT: B 217 MET cc_start: 0.6876 (mtp) cc_final: 0.6419 (mmp) REVERT: B 262 MET cc_start: 0.7291 (tpp) cc_final: 0.7012 (tpp) REVERT: R 56 CYS cc_start: 0.7290 (OUTLIER) cc_final: 0.7054 (m) REVERT: R 139 TYR cc_start: 0.7702 (t80) cc_final: 0.7406 (t80) outliers start: 17 outliers final: 15 residues processed: 139 average time/residue: 0.5047 time to fit residues: 89.0097 Evaluate side-chains 142 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.188184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.152849 restraints weight = 24393.650| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 3.04 r_work: 0.3765 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7099 Z= 0.151 Angle : 0.501 10.227 9616 Z= 0.266 Chirality : 0.040 0.446 1104 Planarity : 0.004 0.080 1219 Dihedral : 4.559 45.364 992 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.15 % Allowed : 21.48 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.30), residues: 875 helix: 2.67 (0.27), residues: 368 sheet: -1.44 (0.39), residues: 170 loop : -0.90 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.003 0.001 HIS B 54 PHE 0.019 0.001 PHE A 290 TYR 0.011 0.001 TYR A 311 ARG 0.012 0.000 ARG R 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3853.27 seconds wall clock time: 67 minutes 37.20 seconds (4057.20 seconds total)