Starting phenix.real_space_refine on Thu Jul 2 15:25:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tqd_26066/07_2026/7tqd_26066.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tqd_26066/07_2026/7tqd_26066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tqd_26066/07_2026/7tqd_26066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tqd_26066/07_2026/7tqd_26066.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tqd_26066/07_2026/7tqd_26066.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tqd_26066/07_2026/7tqd_26066.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tqd_26066/07_2026/7tqd_26066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tqd_26066/07_2026/7tqd_26066.map" } resolution = 2.9 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= -0.000 sd= 0.009 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 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 5503 2.51 5 N 1511 2.21 5 O 1640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8690 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 215} Chain: "B" Number of atoms: 3999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3999 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 484} Chain breaks: 4 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2878 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 83 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 1.45, per 1000 atoms: 0.17 Number of scatterers: 8690 At special positions: 0 Unit cell: (72.24, 100.8, 136.92, 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 28 16.00 P 6 15.00 Mg 2 11.99 O 1640 8.00 N 1511 7.00 C 5503 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 - 3.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 311.8 milliseconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 7 sheets defined 41.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.567A pdb=" N SER A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 4.079A pdb=" N HIS A 421 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.539A pdb=" N LEU A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.838A pdb=" N ALA A 524 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 577 Processing helix chain 'B' and resid 9 through 22 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 128 through 150 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 181 through 187 removed outlier: 3.512A pdb=" N TRP B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.707A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 269 Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 387 through 401 removed outlier: 3.662A pdb=" N SER B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 442 Processing helix chain 'B' and resid 460 through 469 Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.584A pdb=" N LEU B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 520 through 530 removed outlier: 3.839A pdb=" N ALA B 524 " --> pdb=" O PRO B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 577 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 17 through 38 Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 206 through 221 removed outlier: 3.948A pdb=" N GLN C 210 " --> pdb=" O HIS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 266 through 282 Processing helix chain 'C' and resid 282 through 288 Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.604A pdb=" N ALA C 306 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG C 307 " --> pdb=" O VAL C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 307' Processing helix chain 'C' and resid 309 through 333 removed outlier: 3.589A pdb=" N ALA C 332 " --> pdb=" O ARG C 328 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 3.919A pdb=" N LEU C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 448 through 452 removed outlier: 6.624A pdb=" N GLN A 405 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE A 452 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 407 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 382 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA4, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.624A pdb=" N ARG B 221 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER B 196 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE B 212 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE B 194 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N SER B 197 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR B 236 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N LEU B 294 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASN B 237 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 296 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 239 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLY B 298 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER B 241 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 311 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 11.311A pdb=" N ILE B 312 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ASN B 360 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TRP B 314 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR B 358 " --> pdb=" O TRP B 314 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA B 316 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG B 354 " --> pdb=" O ARG B 318 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N TRP B 355 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ARG B 357 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR B 171 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLN B 359 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 173 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU B 207 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL B 172 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU B 209 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLY B 174 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N GLU B 211 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 448 through 452 removed outlier: 6.607A pdb=" N VAL B 381 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU B 408 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE B 383 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 51 removed outlier: 6.728A pdb=" N VAL C 75 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR C 48 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 73 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU C 50 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP C 71 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 192 through 195 400 hydrogen bonds defined for protein. 1149 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: 0.86 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2843 1.34 - 1.46: 1677 1.46 - 1.58: 4328 1.58 - 1.69: 8 1.69 - 1.81: 46 Bond restraints: 8902 Sorted by residual: bond pdb=" CA ILE C 93 " pdb=" CB ILE C 93 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.66e+00 bond pdb=" C4 ADP C 405 " pdb=" C5 ADP C 405 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" C4 AMP C 401 " pdb=" C5 AMP C 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" CG PRO B 251 " pdb=" CD PRO B 251 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.10e+00 bond pdb=" C2' ADP C 405 " pdb=" C3' ADP C 405 " ideal model delta sigma weight residual 1.524 1.506 0.018 2.00e-02 2.50e+03 8.31e-01 ... (remaining 8897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 11890 1.46 - 2.92: 163 2.92 - 4.38: 41 4.38 - 5.84: 18 5.84 - 7.30: 2 Bond angle restraints: 12114 Sorted by residual: angle pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " pdb=" CG TRP C 24 " ideal model delta sigma weight residual 113.60 119.01 -5.41 1.90e+00 2.77e-01 8.12e+00 angle pdb=" CA ALA B 291 " pdb=" C ALA B 291 " pdb=" O ALA B 291 " ideal model delta sigma weight residual 119.13 121.16 -2.03 1.00e+00 1.00e+00 4.11e+00 angle pdb=" CA ALA B 291 " pdb=" C ALA B 291 " pdb=" N PRO B 292 " ideal model delta sigma weight residual 118.95 116.36 2.59 1.29e+00 6.01e-01 4.04e+00 angle pdb=" C ILE B 144 " pdb=" N ASP B 145 " pdb=" CA ASP B 145 " ideal model delta sigma weight residual 120.29 117.48 2.81 1.42e+00 4.96e-01 3.93e+00 angle pdb=" O1B ADP C 405 " pdb=" PB ADP C 405 " pdb=" O3B ADP C 405 " ideal model delta sigma weight residual 119.90 114.10 5.80 3.00e+00 1.11e-01 3.74e+00 ... (remaining 12109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 5225 34.65 - 69.30: 55 69.30 - 103.95: 0 103.95 - 138.60: 1 138.60 - 173.25: 2 Dihedral angle restraints: 5283 sinusoidal: 2112 harmonic: 3171 Sorted by residual: dihedral pdb=" O2A ADP C 405 " pdb=" O3A ADP C 405 " pdb=" PA ADP C 405 " pdb=" PB ADP C 405 " ideal model delta sinusoidal sigma weight residual 300.00 126.75 173.25 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' AMP C 401 " pdb=" O5' AMP C 401 " pdb=" P AMP C 401 " pdb=" O3P AMP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 150.14 149.87 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" O1B ADP C 405 " pdb=" O3A ADP C 405 " pdb=" PB ADP C 405 " pdb=" PA ADP C 405 " ideal model delta sinusoidal sigma weight residual -60.00 59.27 -119.27 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 5280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 847 0.028 - 0.056: 325 0.056 - 0.084: 74 0.084 - 0.113: 66 0.113 - 0.141: 18 Chirality restraints: 1330 Sorted by residual: chirality pdb=" C2' ADP C 405 " pdb=" C1' ADP C 405 " pdb=" C3' ADP C 405 " pdb=" O2' ADP C 405 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ILE C 127 " pdb=" N ILE C 127 " pdb=" C ILE C 127 " pdb=" CB ILE C 127 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1327 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 291 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C ALA B 291 " 0.034 2.00e-02 2.50e+03 pdb=" O ALA B 291 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO B 292 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 290 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C ARG B 290 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG B 290 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 291 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 49 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 50 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 50 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 50 " 0.027 5.00e-02 4.00e+02 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 20 2.55 - 3.14: 6196 3.14 - 3.72: 12740 3.72 - 4.31: 18284 4.31 - 4.90: 31305 Nonbonded interactions: 68545 Sorted by model distance: nonbonded pdb="MG MG C 403 " pdb=" O2B ATP C 404 " model vdw 1.960 2.170 nonbonded pdb=" OD2 ASP C 69 " pdb="MG MG C 402 " model vdw 1.995 2.170 nonbonded pdb=" OD2 ASP C 71 " pdb="MG MG C 403 " model vdw 2.254 2.170 nonbonded pdb=" O ARG B 468 " pdb=" NZ LYS B 495 " model vdw 2.276 3.120 nonbonded pdb=" OD1 ASN B 374 " pdb=" NH2 ARG B 377 " model vdw 2.314 3.120 ... (remaining 68540 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=0.50 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: 4.890 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: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.540 Find NCS groups from input model: 0.020 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:5.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 : 0.004 0.211 8903 Z= 0.264 Angle : 0.520 7.302 12114 Z= 0.262 Chirality : 0.039 0.141 1330 Planarity : 0.004 0.049 1551 Dihedral : 11.717 173.252 3217 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.95 (0.26), residues: 1078 helix: 2.65 (0.26), residues: 402 sheet: 0.52 (0.34), residues: 232 loop : -1.28 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 420 TYR 0.007 0.001 TYR C 225 PHE 0.009 0.001 PHE C 49 TRP 0.030 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 8902) covalent geometry : angle 0.51952 / 0.26 (12114) hydrogen bonds : bond 0.16953 / 11.63 ( 398) hydrogen bonds : angle 5.98035 / 4.34 ( 1149) Misc. bond : bond 0.21139 / 11.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7872 (mtm-85) REVERT: A 479 ASP cc_start: 0.7808 (t0) cc_final: 0.7472 (t0) REVERT: B 11 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8218 (tp30) REVERT: B 37 LYS cc_start: 0.9298 (mttt) cc_final: 0.8972 (mmmt) REVERT: B 73 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7397 (mmm160) REVERT: B 102 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7811 (tp30) REVERT: B 216 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8924 (mptt) REVERT: B 231 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8117 (pptt) REVERT: B 276 PHE cc_start: 0.7312 (m-80) cc_final: 0.7054 (m-80) REVERT: B 388 SER cc_start: 0.8518 (m) cc_final: 0.8267 (p) REVERT: B 507 GLU cc_start: 0.8605 (tt0) cc_final: 0.8027 (pt0) REVERT: B 527 ARG cc_start: 0.7413 (mmp80) cc_final: 0.5999 (mmm-85) REVERT: C 342 LEU cc_start: 0.8196 (mt) cc_final: 0.7914 (mm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.6517 time to fit residues: 107.2786 Evaluate side-chains 69 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 ASN B 178 GLN C 8 ASN C 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080574 restraints weight = 16378.704| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.09 r_work: 0.3117 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8903 Z= 0.156 Angle : 0.592 7.810 12114 Z= 0.291 Chirality : 0.041 0.166 1330 Planarity : 0.004 0.046 1551 Dihedral : 8.226 146.403 1193 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.87 % Allowed : 10.87 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.92 (0.26), residues: 1078 helix: 2.57 (0.26), residues: 408 sheet: 0.43 (0.32), residues: 236 loop : -1.27 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 450 TYR 0.007 0.001 TYR C 250 PHE 0.013 0.002 PHE A 510 TRP 0.024 0.001 TRP C 24 HIS 0.005 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 8902) covalent geometry : angle 0.59179 / 0.29 (12114) hydrogen bonds : bond 0.05025 / 3.46 ( 398) hydrogen bonds : angle 4.55104 / 3.31 ( 1149) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8276 (mtm180) cc_final: 0.7800 (mtm-85) REVERT: A 479 ASP cc_start: 0.7919 (t0) cc_final: 0.7622 (t0) REVERT: A 595 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7950 (tttp) REVERT: B 11 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8159 (tp30) REVERT: B 37 LYS cc_start: 0.9223 (mttt) cc_final: 0.8994 (mmmt) REVERT: B 102 GLU cc_start: 0.8681 (mt-10) cc_final: 0.7861 (tp30) REVERT: B 150 GLU cc_start: 0.7276 (tp30) cc_final: 0.6608 (tt0) REVERT: B 216 LYS cc_start: 0.9223 (mmtt) cc_final: 0.8904 (mptt) REVERT: B 231 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8052 (pptt) REVERT: B 259 GLN cc_start: 0.8149 (tp40) cc_final: 0.7641 (tm-30) REVERT: B 507 GLU cc_start: 0.8807 (tt0) cc_final: 0.8138 (pt0) REVERT: B 527 ARG cc_start: 0.7507 (mmp80) cc_final: 0.6077 (mmm-85) REVERT: C 325 GLU cc_start: 0.8611 (tt0) cc_final: 0.8316 (tp30) outliers start: 17 outliers final: 3 residues processed: 83 average time/residue: 0.5893 time to fit residues: 51.5715 Evaluate side-chains 62 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 103 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN A 561 GLN B 58 ASN B 561 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079439 restraints weight = 16761.631| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.09 r_work: 0.3125 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8903 Z= 0.148 Angle : 0.574 10.474 12114 Z= 0.278 Chirality : 0.041 0.155 1330 Planarity : 0.004 0.041 1551 Dihedral : 7.087 136.452 1193 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.98 % Allowed : 12.07 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.87 (0.26), residues: 1078 helix: 2.57 (0.26), residues: 408 sheet: 0.36 (0.32), residues: 236 loop : -1.31 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 450 TYR 0.010 0.001 TYR C 250 PHE 0.013 0.002 PHE A 510 TRP 0.022 0.001 TRP C 24 HIS 0.006 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 8902) covalent geometry : angle 0.57370 / 0.28 (12114) hydrogen bonds : bond 0.04732 / 3.25 ( 398) hydrogen bonds : angle 4.29519 / 3.16 ( 1149) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8245 (mtm180) cc_final: 0.7896 (ttp-110) REVERT: A 595 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8170 (tttp) REVERT: B 11 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8058 (tp30) REVERT: B 37 LYS cc_start: 0.9237 (mttt) cc_final: 0.9027 (mmmt) REVERT: B 216 LYS cc_start: 0.9236 (mmtt) cc_final: 0.8936 (mptt) REVERT: B 218 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7156 (ttpp) REVERT: B 231 LYS cc_start: 0.8727 (mtmt) cc_final: 0.8122 (pptt) REVERT: B 259 GLN cc_start: 0.8212 (tp40) cc_final: 0.7705 (tm-30) REVERT: B 267 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: B 507 GLU cc_start: 0.8817 (tt0) cc_final: 0.8175 (pt0) REVERT: B 527 ARG cc_start: 0.7853 (mmp80) cc_final: 0.6437 (mmm-85) REVERT: B 590 ASP cc_start: 0.8160 (p0) cc_final: 0.7922 (p0) outliers start: 18 outliers final: 7 residues processed: 78 average time/residue: 0.5614 time to fit residues: 46.3904 Evaluate side-chains 68 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.076701 restraints weight = 17339.264| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.11 r_work: 0.3069 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8903 Z= 0.182 Angle : 0.606 10.002 12114 Z= 0.293 Chirality : 0.042 0.164 1330 Planarity : 0.004 0.040 1551 Dihedral : 6.616 120.622 1193 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.41 % Allowed : 13.06 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.76 (0.26), residues: 1078 helix: 2.51 (0.26), residues: 407 sheet: 0.28 (0.32), residues: 237 loop : -1.39 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 281 TYR 0.011 0.001 TYR C 250 PHE 0.015 0.002 PHE A 489 TRP 0.022 0.001 TRP C 24 HIS 0.006 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 ( 8902) covalent geometry : angle 0.60595 / 0.29 (12114) hydrogen bonds : bond 0.05152 / 3.54 ( 398) hydrogen bonds : angle 4.36025 / 3.19 ( 1149) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8193 (mtm180) cc_final: 0.7832 (ttp-110) REVERT: A 595 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8219 (tttp) REVERT: B 11 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8060 (tp30) REVERT: B 37 LYS cc_start: 0.9301 (mttt) cc_final: 0.9052 (mmmt) REVERT: B 216 LYS cc_start: 0.9201 (mmtt) cc_final: 0.8939 (mptt) REVERT: B 231 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8486 (ptpp) REVERT: B 259 GLN cc_start: 0.8124 (tp40) cc_final: 0.7625 (tm-30) REVERT: B 267 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: B 507 GLU cc_start: 0.8826 (tt0) cc_final: 0.8118 (pt0) REVERT: B 527 ARG cc_start: 0.7929 (mmp80) cc_final: 0.6466 (mmm-85) REVERT: B 561 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7749 (mp10) outliers start: 22 outliers final: 8 residues processed: 78 average time/residue: 0.5688 time to fit residues: 47.0465 Evaluate side-chains 65 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN C 227 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.097418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.077050 restraints weight = 16789.605| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.96 r_work: 0.3082 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8903 Z= 0.131 Angle : 0.561 11.354 12114 Z= 0.266 Chirality : 0.040 0.150 1330 Planarity : 0.004 0.038 1551 Dihedral : 6.268 104.253 1193 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.87 % Allowed : 13.94 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.90 (0.26), residues: 1078 helix: 2.65 (0.26), residues: 407 sheet: 0.25 (0.32), residues: 238 loop : -1.27 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 281 TYR 0.009 0.001 TYR B 582 PHE 0.013 0.001 PHE A 510 TRP 0.020 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 8902) covalent geometry : angle 0.56079 / 0.27 (12114) hydrogen bonds : bond 0.04251 / 2.92 ( 398) hydrogen bonds : angle 4.14030 / 3.04 ( 1149) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8146 (mtm180) cc_final: 0.7830 (ttp-110) REVERT: A 380 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8194 (mtmt) REVERT: B 11 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8037 (tp30) REVERT: B 216 LYS cc_start: 0.9195 (mmtt) cc_final: 0.8964 (mptt) REVERT: B 259 GLN cc_start: 0.8068 (tp40) cc_final: 0.7610 (tm-30) REVERT: B 267 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7618 (mt0) REVERT: B 507 GLU cc_start: 0.8741 (tt0) cc_final: 0.8031 (pt0) REVERT: B 527 ARG cc_start: 0.7878 (mmp80) cc_final: 0.6429 (mmm-85) outliers start: 17 outliers final: 9 residues processed: 69 average time/residue: 0.5572 time to fit residues: 40.7886 Evaluate side-chains 63 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 61 optimal weight: 0.0050 chunk 75 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN B 178 GLN C 227 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.097954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.077633 restraints weight = 16680.534| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.96 r_work: 0.3089 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8903 Z= 0.112 Angle : 0.548 12.120 12114 Z= 0.258 Chirality : 0.040 0.151 1330 Planarity : 0.004 0.037 1551 Dihedral : 5.973 90.160 1193 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.76 % Allowed : 13.94 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 1.05 (0.26), residues: 1078 helix: 2.77 (0.26), residues: 408 sheet: 0.32 (0.32), residues: 238 loop : -1.19 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 450 TYR 0.010 0.001 TYR B 582 PHE 0.013 0.001 PHE A 510 TRP 0.020 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 8902) covalent geometry : angle 0.54847 / 0.26 (12114) hydrogen bonds : bond 0.03918 / 2.69 ( 398) hydrogen bonds : angle 3.97694 / 2.93 ( 1149) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8186 (mtm180) cc_final: 0.7875 (ttp-110) REVERT: A 380 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8191 (mtmt) REVERT: A 516 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6823 (mm-30) REVERT: B 11 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8074 (tp30) REVERT: B 216 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8940 (mptt) REVERT: B 507 GLU cc_start: 0.8712 (tt0) cc_final: 0.7949 (pt0) REVERT: B 527 ARG cc_start: 0.7873 (mmp80) cc_final: 0.6485 (mmm-85) REVERT: B 594 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7826 (mm-30) outliers start: 16 outliers final: 7 residues processed: 66 average time/residue: 0.5790 time to fit residues: 40.3752 Evaluate side-chains 61 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 76 optimal weight: 0.0170 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN C 107 GLN C 227 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.100269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078947 restraints weight = 17246.198| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.17 r_work: 0.3088 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8903 Z= 0.109 Angle : 0.533 12.030 12114 Z= 0.253 Chirality : 0.039 0.152 1330 Planarity : 0.004 0.036 1551 Dihedral : 5.795 81.252 1193 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.09 % Allowed : 14.05 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 (0.26), residues: 1078 helix: 2.83 (0.26), residues: 408 sheet: 0.31 (0.32), residues: 240 loop : -1.09 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 281 TYR 0.010 0.001 TYR B 582 PHE 0.013 0.001 PHE A 510 TRP 0.019 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8902) covalent geometry : angle 0.53312 / 0.25 (12114) hydrogen bonds : bond 0.03806 / 2.61 ( 398) hydrogen bonds : angle 3.90412 / 2.88 ( 1149) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8171 (mtm180) cc_final: 0.7834 (ttp-110) REVERT: A 380 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8131 (mtmt) REVERT: A 516 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6725 (mm-30) REVERT: B 11 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8013 (tp30) REVERT: B 216 LYS cc_start: 0.9187 (mmtt) cc_final: 0.8923 (mptt) REVERT: B 259 GLN cc_start: 0.8019 (tp40) cc_final: 0.7590 (tm-30) REVERT: B 507 GLU cc_start: 0.8686 (tt0) cc_final: 0.7898 (pt0) REVERT: B 527 ARG cc_start: 0.7840 (mmp80) cc_final: 0.6359 (mmm-85) REVERT: B 594 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: C 194 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7625 (pt) outliers start: 19 outliers final: 8 residues processed: 69 average time/residue: 0.5437 time to fit residues: 39.9843 Evaluate side-chains 62 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 194 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 73 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 0.0070 chunk 57 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN C 227 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.097756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.077330 restraints weight = 16737.582| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.97 r_work: 0.3086 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8903 Z= 0.117 Angle : 0.558 12.165 12114 Z= 0.261 Chirality : 0.040 0.148 1330 Planarity : 0.004 0.036 1551 Dihedral : 5.746 82.604 1193 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.65 % Allowed : 14.49 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 (0.26), residues: 1078 helix: 2.81 (0.26), residues: 408 sheet: 0.34 (0.32), residues: 239 loop : -1.07 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 82 TYR 0.009 0.001 TYR B 582 PHE 0.013 0.001 PHE A 510 TRP 0.023 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 8902) covalent geometry : angle 0.55766 / 0.26 (12114) hydrogen bonds : bond 0.03878 / 2.66 ( 398) hydrogen bonds : angle 3.90857 / 2.88 ( 1149) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7836 (ttp-110) REVERT: A 380 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8173 (mtmt) REVERT: A 516 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6761 (mm-30) REVERT: B 11 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7971 (tp30) REVERT: B 216 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8931 (mptt) REVERT: B 259 GLN cc_start: 0.8031 (tp40) cc_final: 0.7614 (tm-30) REVERT: B 484 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7289 (mttt) REVERT: B 507 GLU cc_start: 0.8679 (tt0) cc_final: 0.7877 (pt0) REVERT: B 527 ARG cc_start: 0.7793 (mmp80) cc_final: 0.6414 (mmm-85) REVERT: B 594 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7842 (mm-30) REVERT: C 194 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7673 (pt) outliers start: 15 outliers final: 8 residues processed: 64 average time/residue: 0.5622 time to fit residues: 38.2379 Evaluate side-chains 63 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 194 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 0.0010 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.076679 restraints weight = 16840.068| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.97 r_work: 0.3073 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8903 Z= 0.130 Angle : 0.553 12.196 12114 Z= 0.264 Chirality : 0.040 0.147 1330 Planarity : 0.004 0.036 1551 Dihedral : 5.712 83.805 1193 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.76 % Allowed : 14.38 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 1.11 (0.26), residues: 1078 helix: 2.77 (0.26), residues: 407 sheet: 0.36 (0.32), residues: 237 loop : -1.09 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 82 TYR 0.010 0.001 TYR B 582 PHE 0.013 0.001 PHE A 510 TRP 0.028 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 8902) covalent geometry : angle 0.55281 / 0.26 (12114) hydrogen bonds : bond 0.04127 / 2.83 ( 398) hydrogen bonds : angle 3.97282 / 2.92 ( 1149) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8189 (mtm180) cc_final: 0.7859 (ttp-110) REVERT: A 380 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8171 (mtmt) REVERT: A 516 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6858 (mm-30) REVERT: B 11 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7975 (tp30) REVERT: B 216 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8918 (mptt) REVERT: B 259 GLN cc_start: 0.8041 (tp40) cc_final: 0.7596 (tm-30) REVERT: B 527 ARG cc_start: 0.7831 (mmp80) cc_final: 0.6414 (mpt-90) REVERT: B 586 LYS cc_start: 0.8591 (tttt) cc_final: 0.8366 (ttpm) REVERT: B 594 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7833 (mm-30) outliers start: 16 outliers final: 9 residues processed: 64 average time/residue: 0.5637 time to fit residues: 38.2584 Evaluate side-chains 62 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.096631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.076165 restraints weight = 16957.924| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.98 r_work: 0.3063 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8903 Z= 0.142 Angle : 0.579 16.135 12114 Z= 0.274 Chirality : 0.041 0.148 1330 Planarity : 0.004 0.035 1551 Dihedral : 5.731 83.785 1193 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.43 % Allowed : 14.82 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 (0.26), residues: 1078 helix: 2.67 (0.26), residues: 407 sheet: 0.35 (0.32), residues: 237 loop : -1.08 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 281 TYR 0.011 0.001 TYR B 582 PHE 0.013 0.001 PHE A 510 TRP 0.031 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 8902) covalent geometry : angle 0.57909 / 0.27 (12114) hydrogen bonds : bond 0.04272 / 2.93 ( 398) hydrogen bonds : angle 4.05290 / 2.99 ( 1149) Misc. bond : bond 0.00046 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7849 (ttp-110) REVERT: A 380 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8178 (mtmt) REVERT: A 516 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6830 (mm-30) REVERT: B 11 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8004 (tp30) REVERT: B 216 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8902 (mptt) REVERT: B 507 GLU cc_start: 0.8689 (tt0) cc_final: 0.7890 (pt0) REVERT: B 586 LYS cc_start: 0.8592 (tttt) cc_final: 0.8347 (ttpm) REVERT: B 594 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7836 (mm-30) outliers start: 13 outliers final: 8 residues processed: 60 average time/residue: 0.5366 time to fit residues: 34.2090 Evaluate side-chains 59 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.094769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.074349 restraints weight = 16951.649| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.95 r_work: 0.3026 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8903 Z= 0.207 Angle : 0.621 13.725 12114 Z= 0.302 Chirality : 0.043 0.149 1330 Planarity : 0.004 0.036 1551 Dihedral : 5.871 79.432 1193 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.65 % Allowed : 14.93 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.78 (0.26), residues: 1078 helix: 2.37 (0.26), residues: 413 sheet: 0.29 (0.32), residues: 235 loop : -1.25 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 281 TYR 0.011 0.002 TYR C 250 PHE 0.018 0.002 PHE C 10 TRP 0.031 0.001 TRP C 24 HIS 0.005 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 ( 8902) covalent geometry : angle 0.62091 / 0.30 (12114) hydrogen bonds : bond 0.05163 / 3.54 ( 398) hydrogen bonds : angle 4.31603 / 3.16 ( 1149) Misc. bond : bond 0.00043 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.84 seconds wall clock time: 36 minutes 10.70 seconds (2170.70 seconds total)