Starting phenix.real_space_refine on Tue Mar 3 17:31:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8djm_27461/03_2026/8djm_27461.cif Found real_map, /net/cci-nas-00/data/ceres_data/8djm_27461/03_2026/8djm_27461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8djm_27461/03_2026/8djm_27461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8djm_27461/03_2026/8djm_27461.map" model { file = "/net/cci-nas-00/data/ceres_data/8djm_27461/03_2026/8djm_27461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8djm_27461/03_2026/8djm_27461.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4601 2.51 5 N 1114 2.21 5 O 1281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7032 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1871 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 7, 'TRANS': 229} Chain breaks: 3 Chain: "B" Number of atoms: 2152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2152 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain breaks: 2 Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 944 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 930 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "A" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 214 Unusual residues: {'AJP': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'AJP': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 19 Time building chain proxies: 1.65, per 1000 atoms: 0.23 Number of scatterers: 7032 At special positions: 0 Unit cell: (113.67, 101.04, 106.934, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1281 8.00 N 1114 7.00 C 4601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.72 Conformation dependent library (CDL) restraints added in 261.7 milliseconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 67.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 0 through 16 Processing helix chain 'A' and resid 16 through 33 removed outlier: 3.689A pdb=" N VAL A 20 " --> pdb=" O HIS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 85 removed outlier: 3.734A pdb=" N ILE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 113 removed outlier: 4.281A pdb=" N LEU A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.700A pdb=" N LEU A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.712A pdb=" N ALA A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 181 removed outlier: 4.468A pdb=" N ARG A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Proline residue: A 166 - end of helix removed outlier: 3.568A pdb=" N ASP A 171 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 187 through 223 removed outlier: 3.572A pdb=" N CYS A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 235 through 247 removed outlier: 4.716A pdb=" N VAL A 241 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 273 removed outlier: 3.759A pdb=" N MET A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.979A pdb=" N ALA B 52 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 77 removed outlier: 4.615A pdb=" N THR B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 80 through 106 removed outlier: 3.720A pdb=" N LEU B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 85 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 153 removed outlier: 4.021A pdb=" N VAL B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B 132 " --> pdb=" O PRO B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.300A pdb=" N TYR B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 208 removed outlier: 3.852A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Proline residue: B 196 - end of helix Processing helix chain 'B' and resid 212 through 218 removed outlier: 4.016A pdb=" N VAL B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 218 " --> pdb=" O PRO B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.539A pdb=" N GLU B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 253 through 279 Proline residue: B 268 - end of helix removed outlier: 3.527A pdb=" N THR B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 288 Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 310 through 330 Processing helix chain 'C' and resid 265 through 286 Processing helix chain 'C' and resid 288 through 309 removed outlier: 4.255A pdb=" N VAL C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 315 removed outlier: 3.713A pdb=" N GLU C 315 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 346 Processing helix chain 'C' and resid 350 through 367 Processing helix chain 'C' and resid 367 through 383 removed outlier: 4.023A pdb=" N SER C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 382 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 102 removed outlier: 4.094A pdb=" N ILE L 102 " --> pdb=" O SER L 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 84 removed outlier: 3.863A pdb=" N LYS H 84 " --> pdb=" O GLN H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 106 through 109 Processing sheet with id=AA1, first strand: chain 'L' and resid 23 through 25 Processing sheet with id=AA2, first strand: chain 'L' and resid 38 through 39 Processing sheet with id=AA3, first strand: chain 'L' and resid 72 through 73 removed outlier: 6.803A pdb=" N TRP L 54 " --> pdb=" O VAL L 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA5, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.493A pdb=" N GLU H 29 " --> pdb=" O THR H 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.940A pdb=" N SER H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER H 59 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR H 128 " --> pdb=" O ARG H 117 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1188 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: 1.02 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.20: 12 1.20 - 1.40: 2776 1.40 - 1.60: 4287 1.60 - 1.81: 110 1.81 - 2.01: 21 Bond restraints: 7206 Sorted by residual: bond pdb=" C07 AJP B 402 " pdb=" C08 AJP B 402 " ideal model delta sigma weight residual 1.550 2.008 -0.458 2.00e-02 2.50e+03 5.25e+02 bond pdb=" C07 AJP A 405 " pdb=" C08 AJP A 405 " ideal model delta sigma weight residual 1.550 2.003 -0.453 2.00e-02 2.50e+03 5.13e+02 bond pdb=" C01 AJP B 402 " pdb=" C02 AJP B 402 " ideal model delta sigma weight residual 1.521 1.959 -0.438 2.00e-02 2.50e+03 4.79e+02 bond pdb=" C01 AJP A 405 " pdb=" C02 AJP A 405 " ideal model delta sigma weight residual 1.521 1.954 -0.433 2.00e-02 2.50e+03 4.69e+02 bond pdb=" C02 AJP A 405 " pdb=" C03 AJP A 405 " ideal model delta sigma weight residual 1.525 1.103 0.422 2.00e-02 2.50e+03 4.44e+02 ... (remaining 7201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 9687 4.64 - 9.27: 128 9.27 - 13.91: 11 13.91 - 18.54: 3 18.54 - 23.18: 3 Bond angle restraints: 9832 Sorted by residual: angle pdb=" C TRP L 113 " pdb=" CA TRP L 113 " pdb=" CB TRP L 113 " ideal model delta sigma weight residual 108.68 85.50 23.18 1.39e+00 5.18e-01 2.78e+02 angle pdb=" C SER L 26 " pdb=" N PRO L 27 " pdb=" CA PRO L 27 " ideal model delta sigma weight residual 120.51 104.02 16.49 1.26e+00 6.30e-01 1.71e+02 angle pdb=" N SER L 26 " pdb=" CA SER L 26 " pdb=" C SER L 26 " ideal model delta sigma weight residual 109.81 128.99 -19.18 2.21e+00 2.05e-01 7.53e+01 angle pdb=" N PRO L 27 " pdb=" CA PRO L 27 " pdb=" C PRO L 27 " ideal model delta sigma weight residual 112.01 100.76 11.25 1.84e+00 2.95e-01 3.74e+01 angle pdb=" N ILE C 368 " pdb=" CA ILE C 368 " pdb=" C ILE C 368 " ideal model delta sigma weight residual 110.23 116.10 -5.87 1.04e+00 9.25e-01 3.18e+01 ... (remaining 9827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 4395 35.59 - 71.19: 206 71.19 - 106.78: 112 106.78 - 142.37: 70 142.37 - 177.96: 21 Dihedral angle restraints: 4804 sinusoidal: 2311 harmonic: 2493 Sorted by residual: dihedral pdb=" C TRP L 113 " pdb=" N TRP L 113 " pdb=" CA TRP L 113 " pdb=" CB TRP L 113 " ideal model delta harmonic sigma weight residual -122.60 -95.39 -27.21 0 2.50e+00 1.60e-01 1.18e+02 dihedral pdb=" N SER L 26 " pdb=" C SER L 26 " pdb=" CA SER L 26 " pdb=" CB SER L 26 " ideal model delta harmonic sigma weight residual 122.80 138.69 -15.89 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" C SER L 26 " pdb=" N SER L 26 " pdb=" CA SER L 26 " pdb=" CB SER L 26 " ideal model delta harmonic sigma weight residual -122.60 -137.67 15.07 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 4801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.148: 1124 1.148 - 2.295: 0 2.295 - 3.443: 0 3.443 - 4.590: 5 4.590 - 5.738: 46 Chirality restraints: 1175 Sorted by residual: chirality pdb=" C20 AJP A 405 " pdb=" C15 AJP A 405 " pdb=" C19 AJP A 405 " pdb=" C21 AJP A 405 " both_signs ideal model delta sigma weight residual False 2.96 -2.78 5.74 2.00e-01 2.50e+01 8.23e+02 chirality pdb=" C20 AJP B 402 " pdb=" C15 AJP B 402 " pdb=" C19 AJP B 402 " pdb=" C21 AJP B 402 " both_signs ideal model delta sigma weight residual False 2.96 -2.76 5.72 2.00e-01 2.50e+01 8.18e+02 chirality pdb=" C16 AJP A 405 " pdb=" C11 AJP A 405 " pdb=" C15 AJP A 405 " pdb=" C17 AJP A 405 " both_signs ideal model delta sigma weight residual False -2.70 2.87 -5.57 2.00e-01 2.50e+01 7.75e+02 ... (remaining 1172 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP L 113 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C TRP L 113 " 0.044 2.00e-02 2.50e+03 pdb=" O TRP L 113 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO L 114 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 367 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C TYR C 367 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR C 367 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE C 368 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO L 27 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C PRO L 27 " -0.028 2.00e-02 2.50e+03 pdb=" O PRO L 27 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA L 28 " 0.010 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 8 2.45 - 3.07: 3841 3.07 - 3.68: 10424 3.68 - 4.29: 14629 4.29 - 4.90: 25443 Nonbonded interactions: 54345 Sorted by model distance: nonbonded pdb=" N PRO B 309 " pdb=" O VAL C 383 " model vdw 1.844 3.120 nonbonded pdb=" CA PRO B 309 " pdb=" O VAL C 383 " model vdw 2.320 3.470 nonbonded pdb=" C04 AJP A 405 " pdb=" C85 AJP A 405 " model vdw 2.408 3.072 nonbonded pdb=" C04 AJP B 402 " pdb=" C85 AJP B 402 " model vdw 2.416 3.072 nonbonded pdb=" C03 AJP B 402 " pdb=" O84 AJP B 402 " model vdw 2.440 2.752 ... (remaining 54340 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 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 : 0.029 0.458 7208 Z= 1.509 Angle : 1.526 23.179 9836 Z= 0.875 Chirality : 1.041 5.738 1175 Planarity : 0.004 0.038 1172 Dihedral : 32.650 177.962 3192 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.82 % Allowed : 3.70 % Favored : 95.47 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.25), residues: 842 helix: -0.85 (0.19), residues: 501 sheet: -3.36 (0.36), residues: 110 loop : -1.49 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 7 TYR 0.014 0.002 TYR B 150 PHE 0.014 0.002 PHE B 256 TRP 0.010 0.001 TRP H 66 HIS 0.004 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.02898 ( 7206) covalent geometry : angle 1.52598 ( 9832) SS BOND : bond 0.00327 ( 2) SS BOND : angle 0.81940 ( 4) hydrogen bonds : bond 0.21774 ( 418) hydrogen bonds : angle 7.56211 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.7902 (mmm) cc_final: 0.7561 (tpp) REVERT: B 325 PHE cc_start: 0.7150 (m-10) cc_final: 0.6947 (m-10) REVERT: C 342 LEU cc_start: 0.8466 (tt) cc_final: 0.8212 (pp) REVERT: L 43 ARG cc_start: 0.7443 (ttp-170) cc_final: 0.6648 (ttm-80) REVERT: H 42 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7633 (tttp) REVERT: H 51 TYR cc_start: 0.8871 (m-80) cc_final: 0.8591 (m-80) REVERT: H 86 LYS cc_start: 0.7613 (ptpt) cc_final: 0.7295 (ptpt) REVERT: H 88 THR cc_start: 0.7242 (p) cc_final: 0.6880 (p) REVERT: H 101 GLU cc_start: 0.7664 (tt0) cc_final: 0.7253 (tt0) outliers start: 6 outliers final: 4 residues processed: 99 average time/residue: 0.1011 time to fit residues: 13.0092 Evaluate side-chains 82 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain H residue 121 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN B 95 HIS B 316 ASN C 272 ASN C 277 ASN C 279 ASN C 337 GLN C 380 GLN L 25 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.194511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135175 restraints weight = 7868.184| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.14 r_work: 0.3349 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7208 Z= 0.166 Angle : 1.421 35.068 9836 Z= 0.520 Chirality : 0.137 2.057 1175 Planarity : 0.004 0.036 1172 Dihedral : 23.438 179.086 1675 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.37 % Allowed : 8.09 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.29), residues: 842 helix: 1.29 (0.23), residues: 504 sheet: -2.15 (0.40), residues: 124 loop : -1.09 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 118 TYR 0.014 0.001 TYR B 174 PHE 0.012 0.001 PHE B 107 TRP 0.014 0.001 TRP C 273 HIS 0.002 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 7206) covalent geometry : angle 1.42080 ( 9832) SS BOND : bond 0.00368 ( 2) SS BOND : angle 0.74644 ( 4) hydrogen bonds : bond 0.04174 ( 418) hydrogen bonds : angle 4.44981 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7919 (mp) REVERT: A 152 GLU cc_start: 0.6792 (tp30) cc_final: 0.6370 (tp30) REVERT: A 218 LEU cc_start: 0.8294 (tp) cc_final: 0.8057 (mp) REVERT: C 342 LEU cc_start: 0.8419 (tt) cc_final: 0.8173 (pp) REVERT: L 43 ARG cc_start: 0.7646 (ttp-170) cc_final: 0.7043 (ttm-80) REVERT: H 42 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7734 (tttm) REVERT: H 86 LYS cc_start: 0.8237 (ptpt) cc_final: 0.7962 (ptpt) outliers start: 10 outliers final: 9 residues processed: 94 average time/residue: 0.0768 time to fit residues: 9.8990 Evaluate side-chains 91 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 121 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 77 optimal weight: 0.0470 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.195858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.128817 restraints weight = 7716.905| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.51 r_work: 0.3420 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7208 Z= 0.125 Angle : 1.337 33.774 9836 Z= 0.482 Chirality : 0.135 2.006 1175 Planarity : 0.004 0.034 1172 Dihedral : 22.949 178.831 1673 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.51 % Allowed : 8.92 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.30), residues: 842 helix: 1.79 (0.23), residues: 504 sheet: -1.50 (0.46), residues: 121 loop : -1.07 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 96 TYR 0.014 0.001 TYR H 79 PHE 0.010 0.001 PHE B 213 TRP 0.025 0.001 TRP C 273 HIS 0.002 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7206) covalent geometry : angle 1.33738 ( 9832) SS BOND : bond 0.00231 ( 2) SS BOND : angle 0.48349 ( 4) hydrogen bonds : bond 0.03542 ( 418) hydrogen bonds : angle 4.01149 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.7646 (mtt) cc_final: 0.7228 (tmm) REVERT: A 100 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7874 (mp) REVERT: A 152 GLU cc_start: 0.6735 (tp30) cc_final: 0.6316 (tp30) REVERT: C 342 LEU cc_start: 0.8376 (tt) cc_final: 0.8137 (pp) REVERT: L 43 ARG cc_start: 0.7562 (ttp-170) cc_final: 0.6924 (ttm-80) REVERT: H 86 LYS cc_start: 0.8242 (ptpt) cc_final: 0.7955 (ptpt) outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 0.0865 time to fit residues: 11.5626 Evaluate side-chains 94 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain H residue 121 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.0980 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 50.0000 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.190847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136087 restraints weight = 7934.636| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.71 r_work: 0.3198 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7208 Z= 0.177 Angle : 1.360 34.507 9836 Z= 0.496 Chirality : 0.135 2.011 1175 Planarity : 0.004 0.035 1172 Dihedral : 22.869 179.815 1673 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.47 % Allowed : 9.33 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.30), residues: 842 helix: 1.66 (0.23), residues: 504 sheet: -1.31 (0.46), residues: 121 loop : -0.97 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.017 0.002 TYR H 79 PHE 0.014 0.001 PHE B 213 TRP 0.017 0.001 TRP C 273 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 7206) covalent geometry : angle 1.36017 ( 9832) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.64675 ( 4) hydrogen bonds : bond 0.03963 ( 418) hydrogen bonds : angle 4.06013 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.278 Fit side-chains REVERT: A 8 MET cc_start: 0.7668 (mtt) cc_final: 0.7303 (ttt) REVERT: A 100 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8017 (mp) REVERT: A 152 GLU cc_start: 0.6781 (tp30) cc_final: 0.6392 (tp30) REVERT: A 154 ARG cc_start: 0.6906 (mtt180) cc_final: 0.6454 (mtt90) REVERT: C 304 LEU cc_start: 0.7998 (tp) cc_final: 0.7627 (mm) REVERT: C 342 LEU cc_start: 0.8237 (tt) cc_final: 0.8018 (pp) REVERT: C 370 LYS cc_start: 0.5470 (pptt) cc_final: 0.4789 (ptpt) REVERT: L 43 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.7059 (ttm-80) outliers start: 18 outliers final: 15 residues processed: 102 average time/residue: 0.0955 time to fit residues: 12.9465 Evaluate side-chains 105 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 121 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 0.0770 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.194576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139794 restraints weight = 7853.579| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.43 r_work: 0.3270 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7208 Z= 0.116 Angle : 1.325 33.684 9836 Z= 0.475 Chirality : 0.135 1.998 1175 Planarity : 0.004 0.036 1172 Dihedral : 22.614 178.835 1673 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.65 % Allowed : 10.56 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.30), residues: 842 helix: 1.82 (0.23), residues: 512 sheet: -1.19 (0.47), residues: 122 loop : -0.87 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.017 0.001 TYR H 79 PHE 0.010 0.001 PHE B 213 TRP 0.030 0.001 TRP C 273 HIS 0.002 0.000 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7206) covalent geometry : angle 1.32562 ( 9832) SS BOND : bond 0.00239 ( 2) SS BOND : angle 0.43744 ( 4) hydrogen bonds : bond 0.03155 ( 418) hydrogen bonds : angle 3.79334 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.7654 (mtt) cc_final: 0.7230 (ttt) REVERT: A 100 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7942 (mp) REVERT: A 152 GLU cc_start: 0.6702 (tp30) cc_final: 0.6340 (tp30) REVERT: B 50 VAL cc_start: 0.8087 (OUTLIER) cc_final: 0.7855 (t) REVERT: C 342 LEU cc_start: 0.8233 (tt) cc_final: 0.8024 (pp) REVERT: L 43 ARG cc_start: 0.7554 (ttp-170) cc_final: 0.6933 (ttm-80) REVERT: H 86 LYS cc_start: 0.8318 (ptpt) cc_final: 0.7909 (ptpt) outliers start: 12 outliers final: 8 residues processed: 103 average time/residue: 0.0797 time to fit residues: 11.2476 Evaluate side-chains 97 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.192732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137736 restraints weight = 7957.825| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.51 r_work: 0.3245 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7208 Z= 0.136 Angle : 1.336 34.147 9836 Z= 0.481 Chirality : 0.135 2.007 1175 Planarity : 0.004 0.039 1172 Dihedral : 22.550 179.515 1673 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.33 % Allowed : 11.11 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.30), residues: 842 helix: 1.90 (0.23), residues: 504 sheet: -1.06 (0.47), residues: 122 loop : -0.80 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.018 0.001 TYR H 79 PHE 0.012 0.001 PHE B 213 TRP 0.019 0.001 TRP C 273 HIS 0.002 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7206) covalent geometry : angle 1.33620 ( 9832) SS BOND : bond 0.00277 ( 2) SS BOND : angle 0.56041 ( 4) hydrogen bonds : bond 0.03427 ( 418) hydrogen bonds : angle 3.84337 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.251 Fit side-chains REVERT: A 8 MET cc_start: 0.7712 (mtt) cc_final: 0.7260 (ttt) REVERT: A 100 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7984 (mp) REVERT: A 152 GLU cc_start: 0.6724 (tp30) cc_final: 0.6361 (tp30) REVERT: B 50 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7900 (t) REVERT: C 304 LEU cc_start: 0.8011 (tp) cc_final: 0.7678 (mm) REVERT: C 370 LYS cc_start: 0.5380 (pptt) cc_final: 0.4799 (ptpt) REVERT: L 43 ARG cc_start: 0.7556 (ttp-170) cc_final: 0.6940 (ttm-80) outliers start: 17 outliers final: 10 residues processed: 94 average time/residue: 0.0800 time to fit residues: 10.3671 Evaluate side-chains 94 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 72 optimal weight: 0.0000 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.192877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137138 restraints weight = 7908.701| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.44 r_work: 0.3240 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7208 Z= 0.137 Angle : 1.339 34.080 9836 Z= 0.482 Chirality : 0.135 2.001 1175 Planarity : 0.004 0.039 1172 Dihedral : 22.490 179.445 1671 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.19 % Allowed : 11.39 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.30), residues: 842 helix: 1.85 (0.23), residues: 512 sheet: -1.13 (0.47), residues: 124 loop : -0.71 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.018 0.001 TYR H 79 PHE 0.012 0.001 PHE B 213 TRP 0.020 0.001 TRP C 273 HIS 0.002 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7206) covalent geometry : angle 1.33959 ( 9832) SS BOND : bond 0.00287 ( 2) SS BOND : angle 0.52623 ( 4) hydrogen bonds : bond 0.03397 ( 418) hydrogen bonds : angle 3.83500 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.263 Fit side-chains REVERT: A 100 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8054 (mp) REVERT: A 152 GLU cc_start: 0.6715 (tp30) cc_final: 0.6379 (tp30) REVERT: B 50 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7895 (t) REVERT: C 304 LEU cc_start: 0.8020 (tp) cc_final: 0.7696 (mm) REVERT: C 370 LYS cc_start: 0.5203 (pptt) cc_final: 0.4559 (ptpt) REVERT: L 29 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9002 (mt) REVERT: L 43 ARG cc_start: 0.7546 (ttp-170) cc_final: 0.6963 (ttm-80) outliers start: 16 outliers final: 13 residues processed: 94 average time/residue: 0.0809 time to fit residues: 10.4676 Evaluate side-chains 97 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 0.0670 chunk 13 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.194673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137918 restraints weight = 7916.830| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.44 r_work: 0.3252 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7208 Z= 0.113 Angle : 1.330 33.727 9836 Z= 0.475 Chirality : 0.135 2.001 1175 Planarity : 0.004 0.040 1172 Dihedral : 22.369 178.738 1671 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.92 % Allowed : 11.93 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.30), residues: 842 helix: 1.97 (0.24), residues: 512 sheet: -1.01 (0.47), residues: 122 loop : -0.71 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.017 0.001 TYR H 79 PHE 0.011 0.001 PHE B 213 TRP 0.022 0.001 TRP C 273 HIS 0.001 0.000 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7206) covalent geometry : angle 1.33042 ( 9832) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.46242 ( 4) hydrogen bonds : bond 0.03043 ( 418) hydrogen bonds : angle 3.72953 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.6650 (tp30) cc_final: 0.6341 (tp30) REVERT: B 50 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7887 (t) REVERT: C 299 MET cc_start: 0.7153 (mmp) cc_final: 0.6845 (mtp) REVERT: C 370 LYS cc_start: 0.5206 (pptt) cc_final: 0.4574 (ptpt) REVERT: L 29 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8981 (mt) REVERT: L 43 ARG cc_start: 0.7543 (ttp-170) cc_final: 0.6979 (ttm-80) REVERT: L 80 ARG cc_start: 0.7968 (ptp-170) cc_final: 0.7700 (ptp-170) outliers start: 14 outliers final: 9 residues processed: 94 average time/residue: 0.0849 time to fit residues: 10.8449 Evaluate side-chains 92 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.194582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139509 restraints weight = 7916.828| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.58 r_work: 0.3253 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7208 Z= 0.122 Angle : 1.339 33.921 9836 Z= 0.480 Chirality : 0.136 2.004 1175 Planarity : 0.004 0.040 1172 Dihedral : 22.366 178.993 1671 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.51 % Allowed : 12.21 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.30), residues: 842 helix: 1.97 (0.23), residues: 512 sheet: -1.04 (0.47), residues: 124 loop : -0.64 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.017 0.001 TYR H 79 PHE 0.011 0.001 PHE B 213 TRP 0.022 0.001 TRP C 273 HIS 0.002 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7206) covalent geometry : angle 1.33963 ( 9832) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.45908 ( 4) hydrogen bonds : bond 0.03181 ( 418) hydrogen bonds : angle 3.78871 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.6667 (tp30) cc_final: 0.6352 (tp30) REVERT: B 50 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7880 (t) REVERT: C 299 MET cc_start: 0.7149 (mmp) cc_final: 0.6902 (mtp) REVERT: C 370 LYS cc_start: 0.5251 (pptt) cc_final: 0.4570 (ptpt) REVERT: L 29 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8987 (mt) REVERT: L 43 ARG cc_start: 0.7533 (ttp-170) cc_final: 0.6952 (ttm-80) REVERT: L 80 ARG cc_start: 0.7949 (ptp-170) cc_final: 0.7699 (ptp-170) outliers start: 11 outliers final: 9 residues processed: 89 average time/residue: 0.0817 time to fit residues: 9.8063 Evaluate side-chains 92 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 69 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.0060 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 0.0050 chunk 54 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 overall best weight: 0.5410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.194832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.137941 restraints weight = 7842.529| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.44 r_work: 0.3267 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7208 Z= 0.115 Angle : 1.335 33.773 9836 Z= 0.479 Chirality : 0.136 2.003 1175 Planarity : 0.004 0.040 1172 Dihedral : 22.326 178.744 1671 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.37 % Allowed : 12.62 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.30), residues: 842 helix: 2.02 (0.23), residues: 512 sheet: -1.01 (0.47), residues: 124 loop : -0.63 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 96 TYR 0.015 0.001 TYR H 79 PHE 0.011 0.001 PHE B 213 TRP 0.022 0.001 TRP C 273 HIS 0.002 0.000 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7206) covalent geometry : angle 1.33491 ( 9832) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.44980 ( 4) hydrogen bonds : bond 0.03051 ( 418) hydrogen bonds : angle 3.75391 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.6600 (tp30) cc_final: 0.6334 (tp30) REVERT: B 50 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7895 (t) REVERT: L 29 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8988 (mt) REVERT: L 43 ARG cc_start: 0.7498 (ttp-170) cc_final: 0.6908 (ttm-80) REVERT: L 80 ARG cc_start: 0.7976 (ptp-170) cc_final: 0.7669 (ptp-170) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 0.0872 time to fit residues: 10.5171 Evaluate side-chains 87 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 79 optimal weight: 0.0980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.194826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138005 restraints weight = 7848.797| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.78 r_work: 0.3214 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7208 Z= 0.120 Angle : 1.336 33.882 9836 Z= 0.479 Chirality : 0.136 2.005 1175 Planarity : 0.004 0.040 1172 Dihedral : 22.336 178.944 1671 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.23 % Allowed : 12.62 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.30), residues: 842 helix: 2.02 (0.23), residues: 512 sheet: -1.00 (0.47), residues: 124 loop : -0.60 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 96 TYR 0.014 0.001 TYR H 79 PHE 0.011 0.001 PHE B 213 TRP 0.021 0.001 TRP C 273 HIS 0.002 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7206) covalent geometry : angle 1.33671 ( 9832) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.45537 ( 4) hydrogen bonds : bond 0.03129 ( 418) hydrogen bonds : angle 3.76888 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1851.89 seconds wall clock time: 32 minutes 21.54 seconds (1941.54 seconds total)