Starting phenix.real_space_refine on Sat Aug 3 16:21:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urq_42497/08_2024/8urq_42497.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urq_42497/08_2024/8urq_42497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urq_42497/08_2024/8urq_42497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urq_42497/08_2024/8urq_42497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urq_42497/08_2024/8urq_42497.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urq_42497/08_2024/8urq_42497.cif" } resolution = 3.3 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= 0.001 sd= 0.083 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: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 5378 2.51 5 N 1463 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 25": "OE1" <-> "OE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 347": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8569 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 407 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 49} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1845 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2875 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 343} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2805 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 348} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 636 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.35, per 1000 atoms: 0.62 Number of scatterers: 8569 At special positions: 0 Unit cell: (69.16, 110.656, 135.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 31 15.00 Mg 1 11.99 O 1660 8.00 N 1463 7.00 C 5378 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: 3.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 26.7% alpha, 12.1% beta 5 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'F' and resid 13 through 21 removed outlier: 3.610A pdb=" N PHE F 17 " --> pdb=" O CYS F 13 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.624A pdb=" N SER F 28 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE F 29 " --> pdb=" O ARG F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 42 through 58 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 119 through 134 removed outlier: 3.824A pdb=" N ILE B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Proline residue: B 130 - end of helix Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.534A pdb=" N GLN B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 204 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 220 through 231 Processing helix chain 'B' and resid 236 through 241 removed outlier: 3.519A pdb=" N ILE B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 236 through 241' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 104 through 122 removed outlier: 3.535A pdb=" N CYS A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.606A pdb=" N ASN A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.787A pdb=" N VAL A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 292 through 302 removed outlier: 3.605A pdb=" N TYR A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.626A pdb=" N LEU A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.631A pdb=" N ILE A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 55 removed outlier: 3.784A pdb=" N ASP C 53 " --> pdb=" O ASN C 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.741A pdb=" N LEU B 47 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 49 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 146 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N GLU B 148 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.353A pdb=" N ARG A 25 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 70 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE A 27 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.512A pdb=" N THR A 128 " --> pdb=" O ILE A 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.540A pdb=" N CYS A 208 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 231 Processing sheet with id=AA6, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.602A pdb=" N LEU C 38 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL C 40 " --> pdb=" O TYR C 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 65 through 72 removed outlier: 3.957A pdb=" N HIS C 67 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.961A pdb=" N GLU C 110 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 99 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE C 108 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.950A pdb=" N LEU C 141 " --> pdb=" O TRP C 153 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N THR C 150 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR C 178 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE C 152 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 210 through 211 removed outlier: 3.592A pdb=" N ILE C 211 " --> pdb=" O TYR C 221 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR C 221 " --> pdb=" O ILE C 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 236 through 241 removed outlier: 3.507A pdb=" N SER C 238 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 248 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE C 260 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY C 272 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 294 through 298 removed outlier: 3.620A pdb=" N SER C 298 " --> pdb=" O CYS C 307 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS C 307 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 306 " --> pdb=" O TRP C 318 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 357 through 362 removed outlier: 3.965A pdb=" N ASP C 359 " --> pdb=" O VAL C 382 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 543 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.52: 5914 1.52 - 1.85: 2888 1.85 - 2.18: 0 2.18 - 2.52: 0 2.52 - 2.85: 1 Bond restraints: 8803 Sorted by residual: bond pdb=" C LEU B 12 " pdb=" N SER B 28 " ideal model delta sigma weight residual 1.329 2.851 -1.522 1.40e-02 5.10e+03 1.18e+04 bond pdb=" CA PRO A 96 " pdb=" C PRO A 96 " ideal model delta sigma weight residual 1.526 1.479 0.047 9.80e-03 1.04e+04 2.27e+01 bond pdb=" N ASP C 18 " pdb=" CA ASP C 18 " ideal model delta sigma weight residual 1.457 1.516 -0.058 1.29e-02 6.01e+03 2.04e+01 bond pdb=" C GLY A 257 " pdb=" O GLY A 257 " ideal model delta sigma weight residual 1.232 1.188 0.044 1.03e-02 9.43e+03 1.85e+01 bond pdb=" C TYR A 292 " pdb=" O TYR A 292 " ideal model delta sigma weight residual 1.237 1.183 0.054 1.36e-02 5.41e+03 1.55e+01 ... (remaining 8798 not shown) Histogram of bond angle deviations from ideal: 64.53 - 85.61: 2 85.61 - 106.70: 433 106.70 - 127.78: 11469 127.78 - 148.87: 118 148.87 - 169.95: 1 Bond angle restraints: 12023 Sorted by residual: angle pdb=" O LEU B 12 " pdb=" C LEU B 12 " pdb=" N SER B 28 " ideal model delta sigma weight residual 122.20 64.53 57.67 1.34e+00 5.57e-01 1.85e+03 angle pdb=" CA LEU B 12 " pdb=" C LEU B 12 " pdb=" N SER B 28 " ideal model delta sigma weight residual 117.06 169.95 -52.89 1.53e+00 4.27e-01 1.20e+03 angle pdb=" C LEU B 12 " pdb=" N SER B 28 " pdb=" CA SER B 28 " ideal model delta sigma weight residual 121.70 85.35 36.35 1.80e+00 3.09e-01 4.08e+02 angle pdb=" N ILE A 353 " pdb=" CA ILE A 353 " pdb=" C ILE A 353 " ideal model delta sigma weight residual 111.90 101.91 9.99 8.10e-01 1.52e+00 1.52e+02 angle pdb=" N LYS A 258 " pdb=" CA LYS A 258 " pdb=" C LYS A 258 " ideal model delta sigma weight residual 111.28 123.48 -12.20 1.09e+00 8.42e-01 1.25e+02 ... (remaining 12018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4120 17.38 - 34.75: 666 34.75 - 52.13: 308 52.13 - 69.50: 82 69.50 - 86.88: 18 Dihedral angle restraints: 5194 sinusoidal: 2287 harmonic: 2907 Sorted by residual: dihedral pdb=" CA MET A 253 " pdb=" C MET A 253 " pdb=" N LEU A 254 " pdb=" CA LEU A 254 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PRO B 247 " pdb=" C PRO B 247 " pdb=" N PRO B 248 " pdb=" CA PRO B 248 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" C LYS A 258 " pdb=" N LYS A 258 " pdb=" CA LYS A 258 " pdb=" CB LYS A 258 " ideal model delta harmonic sigma weight residual -122.60 -132.04 9.44 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 5191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1274 0.103 - 0.206: 81 0.206 - 0.308: 12 0.308 - 0.411: 0 0.411 - 0.514: 1 Chirality restraints: 1368 Sorted by residual: chirality pdb=" CA LYS A 258 " pdb=" N LYS A 258 " pdb=" C LYS A 258 " pdb=" CB LYS A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" CA PHE F 22 " pdb=" N PHE F 22 " pdb=" C PHE F 22 " pdb=" CB PHE F 22 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA GLN A 343 " pdb=" N GLN A 343 " pdb=" C GLN A 343 " pdb=" CB GLN A 343 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1365 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 12 " 0.052 2.00e-02 2.50e+03 5.21e-02 2.71e+01 pdb=" C LEU B 12 " -0.086 2.00e-02 2.50e+03 pdb=" O LEU B 12 " 0.008 2.00e-02 2.50e+03 pdb=" N SER B 28 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC D 41 " -0.049 2.00e-02 2.50e+03 2.89e-02 1.88e+01 pdb=" N1 DC D 41 " 0.069 2.00e-02 2.50e+03 pdb=" C2 DC D 41 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DC D 41 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DC D 41 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC D 41 " -0.009 2.00e-02 2.50e+03 pdb=" N4 DC D 41 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC D 41 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DC D 41 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 169 " -0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO A 170 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.047 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 33 2.40 - 3.02: 4835 3.02 - 3.65: 12661 3.65 - 4.27: 18672 4.27 - 4.90: 31171 Nonbonded interactions: 67372 Sorted by model distance: nonbonded pdb=" OD2 ASP A 288 " pdb="MG MG A 501 " model vdw 1.769 2.170 nonbonded pdb=" OD2 ASP A 290 " pdb="MG MG A 501 " model vdw 1.915 2.170 nonbonded pdb=" O HIS A 97 " pdb=" ND1 HIS A 97 " model vdw 2.129 3.120 nonbonded pdb=" O GLU A 235 " pdb=" OG1 THR A 239 " model vdw 2.225 3.040 nonbonded pdb=" O THR B 9 " pdb=" OG1 THR B 9 " model vdw 2.229 3.040 ... (remaining 67367 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 ========== 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=1.00 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.730 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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 : 0.017 1.522 8803 Z= 1.291 Angle : 1.247 57.670 12023 Z= 0.810 Chirality : 0.057 0.514 1368 Planarity : 0.006 0.087 1407 Dihedral : 21.281 86.876 3290 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.81 % Favored : 88.88 % Rotamer: Outliers : 4.61 % Allowed : 32.25 % Favored : 63.15 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.94 % 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: -3.76 (0.24), residues: 953 helix: -1.21 (0.32), residues: 263 sheet: -3.08 (0.35), residues: 180 loop : -3.04 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 129 HIS 0.004 0.001 HIS A 63 PHE 0.026 0.002 PHE C 288 TYR 0.031 0.002 TYR C 56 ARG 0.005 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 124 time to evaluate : 0.886 Fit side-chains REVERT: F 15 GLN cc_start: 0.6237 (OUTLIER) cc_final: 0.5572 (pp30) REVERT: F 21 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: F 40 ARG cc_start: 0.7241 (tpp80) cc_final: 0.7007 (mtp85) REVERT: A 183 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: A 199 LYS cc_start: 0.7459 (pttt) cc_final: 0.7242 (ptmt) REVERT: A 200 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6225 (mt0) REVERT: A 206 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7708 (mttp) REVERT: A 214 GLN cc_start: 0.6909 (tp-100) cc_final: 0.6469 (mp10) REVERT: C 18 ASP cc_start: 0.6368 (OUTLIER) cc_final: 0.5735 (p0) REVERT: C 295 MET cc_start: 0.7044 (mmt) cc_final: 0.6161 (mmm) outliers start: 41 outliers final: 23 residues processed: 158 average time/residue: 0.2488 time to fit residues: 51.4480 Evaluate side-chains 135 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 123 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 86 HIS A 101 HIS A 102 GLN A 144 GLN A 370 ASN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8803 Z= 0.179 Angle : 0.624 6.680 12023 Z= 0.334 Chirality : 0.043 0.204 1368 Planarity : 0.004 0.058 1407 Dihedral : 19.447 85.056 1457 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.53 % Favored : 90.37 % Rotamer: Outliers : 6.07 % Allowed : 28.54 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -3.44 (0.25), residues: 955 helix: -0.74 (0.32), residues: 257 sheet: -2.96 (0.33), residues: 212 loop : -2.86 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 129 HIS 0.005 0.001 HIS C 66 PHE 0.014 0.001 PHE C 257 TYR 0.015 0.001 TYR A 300 ARG 0.006 0.001 ARG B 245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 114 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7961 (mt) cc_final: 0.7356 (tt) REVERT: B 144 TYR cc_start: 0.6008 (m-80) cc_final: 0.5679 (m-10) REVERT: A 206 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7431 (mtmm) REVERT: A 267 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7170 (tp) REVERT: C 21 SER cc_start: 0.7908 (m) cc_final: 0.7695 (m) REVERT: C 41 TRP cc_start: 0.8034 (OUTLIER) cc_final: 0.7827 (m100) REVERT: C 295 MET cc_start: 0.7219 (mmt) cc_final: 0.6291 (mmt) REVERT: C 343 LEU cc_start: 0.5197 (OUTLIER) cc_final: 0.4797 (tt) outliers start: 54 outliers final: 29 residues processed: 161 average time/residue: 0.2198 time to fit residues: 47.5760 Evaluate side-chains 136 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 246 HIS ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8803 Z= 0.295 Angle : 0.679 7.426 12023 Z= 0.362 Chirality : 0.045 0.201 1368 Planarity : 0.004 0.049 1407 Dihedral : 19.135 87.090 1412 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 5.62 % Allowed : 29.55 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -3.36 (0.25), residues: 955 helix: -0.84 (0.31), residues: 265 sheet: -2.83 (0.33), residues: 201 loop : -2.79 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 129 HIS 0.010 0.001 HIS C 66 PHE 0.018 0.002 PHE B 63 TYR 0.025 0.002 TYR A 300 ARG 0.005 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 105 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6897 (tpt170) REVERT: B 114 LYS cc_start: 0.8454 (ttpp) cc_final: 0.8073 (tttm) REVERT: B 144 TYR cc_start: 0.6028 (m-10) cc_final: 0.5733 (m-10) REVERT: A 90 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6805 (t70) REVERT: A 161 SER cc_start: 0.8340 (t) cc_final: 0.8121 (m) REVERT: A 206 LYS cc_start: 0.7839 (mmtp) cc_final: 0.7516 (mtmm) REVERT: A 267 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7442 (tp) REVERT: C 21 SER cc_start: 0.8076 (m) cc_final: 0.7837 (m) REVERT: C 81 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5650 (tt) REVERT: C 295 MET cc_start: 0.7269 (mmt) cc_final: 0.6385 (mmt) outliers start: 50 outliers final: 35 residues processed: 151 average time/residue: 0.2254 time to fit residues: 45.5828 Evaluate side-chains 132 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 93 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 0.0050 chunk 80 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 HIS A 246 HIS A 323 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8803 Z= 0.253 Angle : 0.644 6.776 12023 Z= 0.342 Chirality : 0.043 0.158 1368 Planarity : 0.004 0.048 1407 Dihedral : 19.024 89.077 1408 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 6.97 % Allowed : 28.31 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -3.24 (0.25), residues: 955 helix: -0.67 (0.32), residues: 261 sheet: -2.77 (0.33), residues: 201 loop : -2.74 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 129 HIS 0.011 0.002 HIS C 156 PHE 0.014 0.001 PHE B 63 TYR 0.022 0.002 TYR A 300 ARG 0.005 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 112 time to evaluate : 0.940 Fit side-chains REVERT: B 35 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6775 (tpt170) REVERT: A 105 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8084 (mp) REVERT: A 161 SER cc_start: 0.8314 (t) cc_final: 0.8091 (m) REVERT: A 206 LYS cc_start: 0.7678 (mmtp) cc_final: 0.7325 (mtmm) REVERT: A 214 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6272 (mp10) REVERT: C 21 SER cc_start: 0.8037 (m) cc_final: 0.7766 (m) REVERT: C 41 TRP cc_start: 0.8119 (OUTLIER) cc_final: 0.7870 (m100) REVERT: C 240 LYS cc_start: 0.7554 (mmtt) cc_final: 0.6921 (mmtt) REVERT: C 295 MET cc_start: 0.7291 (mmt) cc_final: 0.6481 (mmt) outliers start: 62 outliers final: 43 residues processed: 166 average time/residue: 0.2159 time to fit residues: 48.4752 Evaluate side-chains 145 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 98 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN A 246 HIS C 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8803 Z= 0.193 Angle : 0.628 14.592 12023 Z= 0.328 Chirality : 0.042 0.176 1368 Planarity : 0.005 0.120 1407 Dihedral : 18.861 89.643 1407 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 6.52 % Allowed : 28.54 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -3.06 (0.26), residues: 955 helix: -0.50 (0.33), residues: 264 sheet: -2.62 (0.35), residues: 194 loop : -2.69 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 129 HIS 0.007 0.001 HIS C 156 PHE 0.013 0.001 PHE F 17 TYR 0.017 0.001 TYR A 300 ARG 0.021 0.001 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 109 time to evaluate : 0.927 Fit side-chains REVERT: F 41 ILE cc_start: 0.7476 (mt) cc_final: 0.7104 (tt) REVERT: B 35 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6598 (tpt170) REVERT: B 114 LYS cc_start: 0.8337 (ttpp) cc_final: 0.8042 (tttm) REVERT: A 107 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6869 (ptm160) REVERT: A 161 SER cc_start: 0.8380 (t) cc_final: 0.8162 (m) REVERT: A 200 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6273 (mt0) REVERT: A 206 LYS cc_start: 0.7566 (mmtp) cc_final: 0.7210 (mtmm) REVERT: A 214 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6197 (mp10) REVERT: C 21 SER cc_start: 0.7906 (OUTLIER) cc_final: 0.7663 (m) REVERT: C 41 TRP cc_start: 0.8087 (OUTLIER) cc_final: 0.7877 (m100) REVERT: C 81 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5581 (tt) REVERT: C 173 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.5999 (mp) REVERT: C 295 MET cc_start: 0.7250 (mmt) cc_final: 0.6458 (mmt) outliers start: 58 outliers final: 38 residues processed: 157 average time/residue: 0.2281 time to fit residues: 47.8536 Evaluate side-chains 138 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 92 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8803 Z= 0.203 Angle : 0.620 12.234 12023 Z= 0.325 Chirality : 0.042 0.162 1368 Planarity : 0.005 0.097 1407 Dihedral : 18.774 89.791 1402 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 6.18 % Allowed : 29.10 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -2.99 (0.26), residues: 955 helix: -0.42 (0.33), residues: 261 sheet: -2.53 (0.34), residues: 216 loop : -2.63 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 129 HIS 0.006 0.001 HIS C 66 PHE 0.017 0.001 PHE C 257 TYR 0.018 0.001 TYR A 300 ARG 0.008 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 103 time to evaluate : 0.852 Fit side-chains REVERT: F 41 ILE cc_start: 0.7337 (mt) cc_final: 0.6968 (tt) REVERT: B 35 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.6470 (tpt170) REVERT: B 114 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8044 (tttm) REVERT: A 90 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6736 (t0) REVERT: A 161 SER cc_start: 0.8397 (t) cc_final: 0.8148 (m) REVERT: A 200 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6224 (mt0) REVERT: A 206 LYS cc_start: 0.7564 (mmtp) cc_final: 0.7192 (mtmm) REVERT: A 214 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6155 (mp10) REVERT: C 21 SER cc_start: 0.7973 (OUTLIER) cc_final: 0.7729 (m) REVERT: C 41 TRP cc_start: 0.8078 (OUTLIER) cc_final: 0.7870 (m100) REVERT: C 56 TYR cc_start: 0.7308 (m-10) cc_final: 0.7098 (m-10) REVERT: C 81 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5617 (tt) REVERT: C 173 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.5924 (mp) REVERT: C 295 MET cc_start: 0.7236 (mmt) cc_final: 0.6430 (mmt) REVERT: C 343 LEU cc_start: 0.5171 (OUTLIER) cc_final: 0.4722 (tt) outliers start: 55 outliers final: 38 residues processed: 150 average time/residue: 0.2113 time to fit residues: 43.2605 Evaluate side-chains 142 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 95 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.0370 chunk 81 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8803 Z= 0.176 Angle : 0.603 11.234 12023 Z= 0.317 Chirality : 0.042 0.175 1368 Planarity : 0.004 0.041 1407 Dihedral : 18.686 88.833 1398 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 6.18 % Allowed : 29.55 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -2.87 (0.26), residues: 955 helix: -0.38 (0.33), residues: 266 sheet: -2.44 (0.34), residues: 213 loop : -2.55 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 129 HIS 0.005 0.001 HIS C 156 PHE 0.017 0.001 PHE F 17 TYR 0.017 0.001 TYR A 275 ARG 0.006 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 108 time to evaluate : 0.921 Fit side-chains REVERT: F 40 ARG cc_start: 0.7657 (mtp85) cc_final: 0.7433 (mtp85) REVERT: F 41 ILE cc_start: 0.7241 (mt) cc_final: 0.6861 (tt) REVERT: B 35 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6425 (tpt170) REVERT: B 114 LYS cc_start: 0.8289 (ttpp) cc_final: 0.8050 (tttm) REVERT: A 107 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6761 (ptm160) REVERT: A 161 SER cc_start: 0.8412 (t) cc_final: 0.8171 (m) REVERT: A 200 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6302 (mt0) REVERT: A 203 PHE cc_start: 0.8266 (m-80) cc_final: 0.8037 (m-80) REVERT: A 206 LYS cc_start: 0.7468 (mmtp) cc_final: 0.7199 (mtmm) REVERT: A 214 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6221 (mp10) REVERT: C 21 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.7715 (m) REVERT: C 41 TRP cc_start: 0.8042 (OUTLIER) cc_final: 0.7817 (m100) REVERT: C 81 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5547 (tt) REVERT: C 173 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5861 (mp) REVERT: C 295 MET cc_start: 0.7246 (mmt) cc_final: 0.6456 (mmt) REVERT: C 333 CYS cc_start: 0.5800 (OUTLIER) cc_final: 0.5353 (p) REVERT: C 343 LEU cc_start: 0.5181 (OUTLIER) cc_final: 0.4962 (tt) outliers start: 55 outliers final: 39 residues processed: 155 average time/residue: 0.2138 time to fit residues: 44.8293 Evaluate side-chains 147 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 98 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8803 Z= 0.204 Angle : 0.625 10.211 12023 Z= 0.329 Chirality : 0.042 0.161 1368 Planarity : 0.004 0.039 1407 Dihedral : 18.668 88.672 1394 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 5.96 % Allowed : 30.22 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -2.89 (0.26), residues: 955 helix: -0.35 (0.33), residues: 263 sheet: -2.45 (0.33), residues: 215 loop : -2.58 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 129 HIS 0.006 0.001 HIS C 66 PHE 0.037 0.002 PHE A 156 TYR 0.017 0.001 TYR A 300 ARG 0.005 0.000 ARG B 245 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 93 time to evaluate : 0.920 Fit side-chains REVERT: F 40 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7381 (mtp85) REVERT: F 41 ILE cc_start: 0.7219 (mt) cc_final: 0.6851 (tt) REVERT: B 35 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.6391 (tpt170) REVERT: B 114 LYS cc_start: 0.8279 (ttpp) cc_final: 0.8024 (tttm) REVERT: A 90 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6742 (t0) REVERT: A 107 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6739 (ptm160) REVERT: A 161 SER cc_start: 0.8153 (t) cc_final: 0.7881 (m) REVERT: A 200 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6322 (mm-40) REVERT: A 206 LYS cc_start: 0.7591 (mmtp) cc_final: 0.7240 (mptt) REVERT: A 214 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6228 (mp10) REVERT: C 21 SER cc_start: 0.8005 (OUTLIER) cc_final: 0.7777 (m) REVERT: C 41 TRP cc_start: 0.8086 (OUTLIER) cc_final: 0.7803 (m100) REVERT: C 81 LEU cc_start: 0.5803 (OUTLIER) cc_final: 0.5572 (tt) REVERT: C 173 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.5968 (mp) REVERT: C 295 MET cc_start: 0.7308 (mmt) cc_final: 0.6407 (mmt) REVERT: C 333 CYS cc_start: 0.5768 (OUTLIER) cc_final: 0.5306 (p) REVERT: C 343 LEU cc_start: 0.5251 (OUTLIER) cc_final: 0.5021 (tt) outliers start: 53 outliers final: 36 residues processed: 140 average time/residue: 0.2143 time to fit residues: 41.1902 Evaluate side-chains 136 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 89 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8803 Z= 0.215 Angle : 0.634 10.159 12023 Z= 0.333 Chirality : 0.043 0.179 1368 Planarity : 0.004 0.041 1407 Dihedral : 18.655 88.151 1394 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 5.73 % Allowed : 30.45 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -2.85 (0.26), residues: 955 helix: -0.34 (0.33), residues: 260 sheet: -2.36 (0.34), residues: 210 loop : -2.59 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 129 HIS 0.006 0.001 HIS C 66 PHE 0.030 0.002 PHE A 156 TYR 0.018 0.001 TYR A 300 ARG 0.006 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 93 time to evaluate : 0.925 Fit side-chains REVERT: F 41 ILE cc_start: 0.7229 (mt) cc_final: 0.6847 (tt) REVERT: B 35 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6396 (tpt170) REVERT: B 114 LYS cc_start: 0.8277 (ttpp) cc_final: 0.8021 (tttm) REVERT: A 90 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6741 (t0) REVERT: A 102 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7528 (tp40) REVERT: A 107 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6767 (ptm160) REVERT: A 161 SER cc_start: 0.8324 (t) cc_final: 0.8020 (m) REVERT: A 200 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6240 (mm-40) REVERT: A 206 LYS cc_start: 0.7585 (mmtp) cc_final: 0.7235 (mptt) REVERT: A 214 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.6433 (mp10) REVERT: C 21 SER cc_start: 0.7987 (OUTLIER) cc_final: 0.7757 (m) REVERT: C 41 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7814 (m100) REVERT: C 173 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6238 (mp) REVERT: C 295 MET cc_start: 0.7318 (mmt) cc_final: 0.6432 (mmt) REVERT: C 333 CYS cc_start: 0.5852 (OUTLIER) cc_final: 0.5423 (p) outliers start: 51 outliers final: 35 residues processed: 138 average time/residue: 0.2118 time to fit residues: 39.9762 Evaluate side-chains 133 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 88 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.0370 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8803 Z= 0.184 Angle : 0.628 9.905 12023 Z= 0.329 Chirality : 0.042 0.197 1368 Planarity : 0.004 0.044 1407 Dihedral : 18.576 88.226 1394 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 4.83 % Allowed : 31.01 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -2.77 (0.26), residues: 955 helix: -0.22 (0.34), residues: 259 sheet: -2.29 (0.34), residues: 210 loop : -2.58 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 129 HIS 0.005 0.001 HIS C 66 PHE 0.028 0.002 PHE A 156 TYR 0.015 0.001 TYR A 275 ARG 0.006 0.000 ARG A 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 92 time to evaluate : 0.855 Fit side-chains REVERT: F 41 ILE cc_start: 0.7024 (mt) cc_final: 0.6718 (tt) REVERT: B 35 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6389 (tpt170) REVERT: B 114 LYS cc_start: 0.8306 (ttpp) cc_final: 0.8093 (tttm) REVERT: A 107 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6717 (ptm160) REVERT: A 161 SER cc_start: 0.8187 (t) cc_final: 0.7844 (m) REVERT: A 206 LYS cc_start: 0.7427 (mmtp) cc_final: 0.7148 (mptt) REVERT: A 214 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6397 (mp10) REVERT: C 21 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7711 (m) REVERT: C 41 TRP cc_start: 0.8050 (OUTLIER) cc_final: 0.7774 (m100) REVERT: C 295 MET cc_start: 0.7321 (mmt) cc_final: 0.6446 (mmt) REVERT: C 333 CYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5456 (p) outliers start: 43 outliers final: 33 residues processed: 129 average time/residue: 0.2180 time to fit residues: 38.4723 Evaluate side-chains 130 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 91 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.214774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.179920 restraints weight = 11138.534| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.27 r_work: 0.4085 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8803 Z= 0.299 Angle : 0.696 10.767 12023 Z= 0.367 Chirality : 0.045 0.196 1368 Planarity : 0.004 0.049 1407 Dihedral : 18.639 88.011 1391 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 4.94 % Allowed : 30.67 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -3.06 (0.26), residues: 955 helix: -0.62 (0.32), residues: 261 sheet: -2.49 (0.34), residues: 205 loop : -2.65 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 129 HIS 0.009 0.001 HIS C 66 PHE 0.024 0.002 PHE A 156 TYR 0.024 0.002 TYR A 300 ARG 0.007 0.001 ARG A 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2046.17 seconds wall clock time: 37 minutes 9.40 seconds (2229.40 seconds total)