Starting phenix.real_space_refine on Fri Sep 11 11:15:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tqd_26066/09_2026/7tqd_26066.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tqd_26066/09_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_26066/09_2026/7tqd_26066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tqd_26066/09_2026/7tqd_26066.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tqd_26066/09_2026/7tqd_26066.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tqd_26066/09_2026/7tqd_26066.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tqd_26066/09_2026/7tqd_26066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tqd_26066/09_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-2.2.1-6174/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: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 1.94, per 1000 atoms: 0.22 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: 0.80 Conformation dependent library (CDL) restraints added in 264.9 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: 0.25 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: 1.27 Time building geometry restraints manager: 1.02 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=" C4' AMP C 401 " pdb=" O4' AMP C 401 " ideal model delta sigma weight residual 1.426 1.453 -0.027 2.00e-02 2.50e+03 1.82e+00 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 ... (remaining 8897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 11951 1.91 - 3.82: 129 3.82 - 5.73: 29 5.73 - 7.64: 3 7.64 - 9.55: 2 Bond angle restraints: 12114 Sorted by residual: angle pdb=" C1' AMP C 401 " pdb=" C2' AMP C 401 " pdb=" C3' AMP C 401 " ideal model delta sigma weight residual 111.00 101.45 9.55 3.00e+00 1.11e-01 1.01e+01 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=" C2' AMP C 401 " pdb=" C3' AMP C 401 " pdb=" C4' AMP C 401 " ideal model delta sigma weight residual 111.00 102.84 8.16 3.00e+00 1.11e-01 7.39e+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 ... (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 - 0.048: 1092 0.048 - 0.095: 179 0.095 - 0.143: 58 0.143 - 0.190: 0 0.190 - 0.238: 1 Chirality restraints: 1330 Sorted by residual: chirality pdb=" C3' AMP C 401 " pdb=" C2' AMP C 401 " pdb=" C4' AMP C 401 " pdb=" O3' AMP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.41e+00 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 ... (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: 0.010 Normalize map: mean=0, sd=1: 7.930 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.890 ------------------------------------------------------------------------------- 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= 0.265 Angle : 0.541 9.548 12114 Z= 0.267 Chirality : 0.039 0.238 1330 Planarity : 0.004 0.049 1551 Dihedral : 11.738 173.252 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 0.00307 / 0.14 ( 8902) covalent geometry : angle 0.54067 / 0.27 (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 : 0.421 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: 0.7827 time to fit residues: 128.7436 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 : 0.298 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.101454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.080405 restraints weight = 16402.148| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.10 r_work: 0.3120 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 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 = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8903 Z= 0.147 Angle : 0.608 8.228 12114 Z= 0.294 Chirality : 0.041 0.167 1330 Planarity : 0.004 0.045 1551 Dihedral : 8.337 164.080 1193 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.65 % Allowed : 11.42 % Favored : 86.94 % 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: 0.86 (0.25), residues: 1078 helix: 2.51 (0.26), residues: 408 sheet: 0.39 (0.32), residues: 236 loop : -1.29 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 450 TYR 0.007 0.001 TYR C 250 PHE 0.011 0.002 PHE A 489 TRP 0.025 0.001 TRP C 24 HIS 0.006 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 8902) covalent geometry : angle 0.60819 / 0.29 (12114) hydrogen bonds : bond 0.04829 / 3.32 ( 398) hydrogen bonds : angle 4.46926 / 3.26 ( 1149) Misc. bond : bond 0.00051 / 0.03 ( 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 83 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.438 Fit side-chains REVERT: A 377 ARG cc_start: 0.8268 (mtm180) cc_final: 0.7783 (mtm-85) REVERT: A 479 ASP cc_start: 0.7938 (t0) cc_final: 0.7665 (t0) REVERT: A 595 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7938 (tttp) REVERT: B 11 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8091 (tp30) REVERT: B 37 LYS cc_start: 0.9225 (mttt) cc_final: 0.8996 (mmmt) REVERT: B 102 GLU cc_start: 0.8673 (mt-10) cc_final: 0.7844 (tp30) REVERT: B 150 GLU cc_start: 0.7285 (tp30) cc_final: 0.6626 (tt0) REVERT: B 216 LYS cc_start: 0.9222 (mmtt) cc_final: 0.8903 (mptt) REVERT: B 231 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8058 (pptt) REVERT: B 259 GLN cc_start: 0.8163 (tp40) cc_final: 0.7650 (tm-30) REVERT: B 507 GLU cc_start: 0.8787 (tt0) cc_final: 0.8109 (pt0) REVERT: B 527 ARG cc_start: 0.7572 (mmp80) cc_final: 0.6152 (mmm-85) outliers start: 15 outliers final: 2 residues processed: 77 average time/residue: 0.7641 time to fit residues: 62.0753 Evaluate side-chains 59 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 LYS 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: 3.9990 chunk 77 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 21 optimal weight: 0.8980 chunk 73 optimal weight: 0.0030 chunk 56 optimal weight: 1.9990 overall best weight: 0.4328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN B 58 ASN B 561 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.080666 restraints weight = 16187.568| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.09 r_work: 0.3116 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8903 Z= 0.109 Angle : 0.544 9.680 12114 Z= 0.257 Chirality : 0.039 0.151 1330 Planarity : 0.004 0.037 1551 Dihedral : 7.099 164.571 1193 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.32 % Allowed : 12.29 % Favored : 86.39 % 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: 2.75 (0.26), residues: 408 sheet: 0.36 (0.32), residues: 237 loop : -1.19 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 450 TYR 0.008 0.001 TYR C 250 PHE 0.011 0.001 PHE B 510 TRP 0.022 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8902) covalent geometry : angle 0.54432 / 0.26 (12114) hydrogen bonds : bond 0.04030 / 2.76 ( 398) hydrogen bonds : angle 4.07955 / 3.01 ( 1149) Misc. bond : bond 0.00021 / 0.01 ( 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 79 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8198 (mtm180) cc_final: 0.7887 (ttp-110) REVERT: A 479 ASP cc_start: 0.7901 (t0) cc_final: 0.7618 (t0) REVERT: B 11 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7995 (tp30) REVERT: B 37 LYS cc_start: 0.9218 (mttt) cc_final: 0.8975 (mmmt) REVERT: B 102 GLU cc_start: 0.8655 (mt-10) cc_final: 0.7835 (tp30) REVERT: B 216 LYS cc_start: 0.9212 (mmtt) cc_final: 0.8904 (mptt) REVERT: B 231 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8002 (pptt) REVERT: B 259 GLN cc_start: 0.8153 (tp40) cc_final: 0.7669 (tm-30) REVERT: B 267 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7471 (mp10) REVERT: B 507 GLU cc_start: 0.8770 (tt0) cc_final: 0.8072 (pt0) REVERT: B 527 ARG cc_start: 0.7693 (mmp80) cc_final: 0.6338 (mmm-85) REVERT: B 594 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7714 (mm-30) outliers start: 12 outliers final: 5 residues processed: 74 average time/residue: 0.7158 time to fit residues: 56.0286 Evaluate side-chains 66 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 267 GLN 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: 2.9990 chunk 16 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN A 561 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.076910 restraints weight = 17312.120| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.10 r_work: 0.3085 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- 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 = 0.43 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 = 0.60 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: 0.8346 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8903 Z= 0.190 Angle : 0.630 10.610 12114 Z= 0.303 Chirality : 0.043 0.162 1330 Planarity : 0.004 0.041 1551 Dihedral : 5.679 98.521 1193 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: 0.79 (0.26), residues: 1078 helix: 2.50 (0.26), residues: 407 sheet: 0.32 (0.32), residues: 237 loop : -1.35 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 281 TYR 0.012 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 0.00456 / 0.19 ( 8902) covalent geometry : angle 0.63032 / 0.30 (12114) hydrogen bonds : bond 0.05405 / 3.72 ( 398) hydrogen bonds : angle 4.40255 / 3.22 ( 1149) Misc. bond : bond 0.00078 / 0.04 ( 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 : 0.360 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7814 (ttp-110) REVERT: A 595 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8165 (tttp) REVERT: B 11 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8040 (tp30) REVERT: B 37 LYS cc_start: 0.9287 (mttt) cc_final: 0.9051 (mmmt) REVERT: B 216 LYS cc_start: 0.9203 (mmtt) cc_final: 0.8931 (mptt) REVERT: B 231 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8512 (ptpp) REVERT: B 259 GLN cc_start: 0.8105 (tp40) cc_final: 0.7603 (tm-30) REVERT: B 267 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7494 (mp10) REVERT: B 507 GLU cc_start: 0.8830 (tt0) cc_final: 0.8100 (pt0) REVERT: B 527 ARG cc_start: 0.7899 (mmp80) cc_final: 0.6449 (mmm-85) REVERT: B 561 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: B 594 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7826 (mm-30) outliers start: 22 outliers final: 5 residues processed: 78 average time/residue: 0.7244 time to fit residues: 59.7947 Evaluate side-chains 64 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 127 GLU 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 179 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 0.1980 chunk 79 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.077964 restraints weight = 17061.692| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.15 r_work: 0.3062 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8903 Z= 0.129 Angle : 0.570 11.607 12114 Z= 0.270 Chirality : 0.041 0.152 1330 Planarity : 0.004 0.039 1551 Dihedral : 5.127 72.181 1193 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.98 % Allowed : 14.05 % Favored : 83.97 % 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: 0.91 (0.26), residues: 1078 helix: 2.65 (0.26), residues: 407 sheet: 0.24 (0.32), residues: 237 loop : -1.23 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.010 0.001 TYR C 250 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 0.00306 / 0.13 ( 8902) covalent geometry : angle 0.56960 / 0.27 (12114) hydrogen bonds : bond 0.04351 / 2.99 ( 398) hydrogen bonds : angle 4.17888 / 3.06 ( 1149) Misc. bond : bond 0.00001 / 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: 18 poor density : 55 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8099 (mtm180) cc_final: 0.7741 (ttp-110) REVERT: A 380 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8149 (mtmt) REVERT: A 444 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8338 (pp) REVERT: A 595 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8196 (tttp) REVERT: B 11 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8051 (tp30) REVERT: B 37 LYS cc_start: 0.9306 (mttt) cc_final: 0.9052 (mmmt) REVERT: B 55 MET cc_start: 0.8094 (tpt) cc_final: 0.7807 (tpt) REVERT: B 150 GLU cc_start: 0.7306 (tp30) cc_final: 0.6482 (tt0) REVERT: B 216 LYS cc_start: 0.9216 (mmtt) cc_final: 0.8958 (mptt) REVERT: B 231 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8462 (ptpp) REVERT: B 259 GLN cc_start: 0.8082 (tp40) cc_final: 0.7577 (tm-30) REVERT: B 267 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: B 507 GLU cc_start: 0.8783 (tt0) cc_final: 0.8045 (pt0) REVERT: B 527 ARG cc_start: 0.7912 (mmp80) cc_final: 0.6500 (mmm-85) outliers start: 18 outliers final: 7 residues processed: 69 average time/residue: 0.6961 time to fit residues: 50.8533 Evaluate side-chains 64 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 444 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 595 LYS 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 179 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 96 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.097381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.077034 restraints weight = 16753.121| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.94 r_work: 0.3077 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- 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 = 0.76 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 = 0.77 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: 0.8335 moved from start: 0.3372 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= 0.129 Angle : 0.561 11.973 12114 Z= 0.264 Chirality : 0.040 0.154 1330 Planarity : 0.004 0.036 1551 Dihedral : 4.962 76.093 1193 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.76 % Allowed : 14.16 % Favored : 84.08 % 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: 1.00 (0.26), residues: 1078 helix: 2.69 (0.26), residues: 407 sheet: 0.31 (0.32), residues: 237 loop : -1.16 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.010 0.001 TYR C 250 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 0.00306 / 0.13 ( 8902) covalent geometry : angle 0.56051 / 0.26 (12114) hydrogen bonds : bond 0.04199 / 2.88 ( 398) hydrogen bonds : angle 4.05119 / 2.97 ( 1149) Misc. bond : bond 0.00008 / 0.00 ( 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 71 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8171 (mtm180) cc_final: 0.7825 (ttp-110) REVERT: A 380 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8194 (mtmt) REVERT: A 444 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8181 (pp) REVERT: A 595 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8206 (tttp) REVERT: B 11 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8060 (tp30) REVERT: B 55 MET cc_start: 0.8135 (tpt) cc_final: 0.7899 (tpt) REVERT: B 216 LYS cc_start: 0.9206 (mmtt) cc_final: 0.8960 (mptt) REVERT: B 259 GLN cc_start: 0.8065 (tp40) cc_final: 0.7580 (tm-30) REVERT: B 267 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7611 (mt0) REVERT: B 507 GLU cc_start: 0.8714 (tt0) cc_final: 0.7938 (pt0) REVERT: B 527 ARG cc_start: 0.7860 (mmp80) cc_final: 0.6480 (mmm-85) outliers start: 16 outliers final: 9 residues processed: 67 average time/residue: 0.7999 time to fit residues: 56.5898 Evaluate side-chains 64 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 444 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 595 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN C 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.101057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079864 restraints weight = 17119.745| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.15 r_work: 0.3101 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8903 Z= 0.097 Angle : 0.538 12.259 12114 Z= 0.251 Chirality : 0.039 0.151 1330 Planarity : 0.004 0.035 1551 Dihedral : 4.793 79.986 1193 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.65 % Allowed : 14.60 % 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: 1.20 (0.26), residues: 1078 helix: 2.87 (0.26), residues: 408 sheet: 0.33 (0.32), residues: 239 loop : -1.03 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 281 TYR 0.011 0.001 TYR B 582 PHE 0.012 0.001 PHE A 510 TRP 0.022 0.001 TRP C 24 HIS 0.003 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 8902) covalent geometry : angle 0.53802 / 0.25 (12114) hydrogen bonds : bond 0.03471 / 2.38 ( 398) hydrogen bonds : angle 3.84790 / 2.84 ( 1149) Misc. bond : bond 0.00014 / 0.01 ( 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 67 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8189 (mtm180) cc_final: 0.7850 (ttp-110) REVERT: A 380 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8132 (mtmt) REVERT: A 444 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7891 (pp) REVERT: A 446 ASP cc_start: 0.8486 (t0) cc_final: 0.8184 (m-30) REVERT: B 11 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8070 (tp30) REVERT: B 55 MET cc_start: 0.8030 (tpt) cc_final: 0.7797 (tpt) REVERT: B 216 LYS cc_start: 0.9201 (mmtt) cc_final: 0.8937 (mptt) REVERT: B 259 GLN cc_start: 0.8011 (tp40) cc_final: 0.7554 (tm-30) REVERT: B 507 GLU cc_start: 0.8707 (tt0) cc_final: 0.7941 (pt0) REVERT: B 527 ARG cc_start: 0.7811 (mmp80) cc_final: 0.6343 (mmm-85) REVERT: B 594 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7840 (mm-30) outliers start: 15 outliers final: 5 residues processed: 63 average time/residue: 0.7216 time to fit residues: 48.1429 Evaluate side-chains 57 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 444 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 179 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 73 optimal weight: 0.0370 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN B 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078355 restraints weight = 16951.813| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.12 r_work: 0.3069 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3537 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= 0.129 Angle : 0.562 12.161 12114 Z= 0.266 Chirality : 0.040 0.146 1330 Planarity : 0.004 0.035 1551 Dihedral : 4.863 81.159 1193 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.65 % Allowed : 14.71 % Favored : 83.64 % 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: 2.80 (0.26), residues: 408 sheet: 0.33 (0.32), residues: 238 loop : -1.07 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 281 TYR 0.009 0.001 TYR C 250 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 0.00306 / 0.13 ( 8902) covalent geometry : angle 0.56188 / 0.27 (12114) hydrogen bonds : bond 0.04064 / 2.79 ( 398) hydrogen bonds : angle 3.93849 / 2.90 ( 1149) Misc. bond : bond 0.00009 / 0.00 ( 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 : 0.365 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8145 (mtm180) cc_final: 0.7823 (ttp-110) REVERT: A 380 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8154 (mtmt) REVERT: A 444 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7911 (pp) REVERT: A 446 ASP cc_start: 0.8543 (t0) cc_final: 0.8235 (m-30) REVERT: B 11 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8018 (tp30) REVERT: B 55 MET cc_start: 0.8086 (tpt) cc_final: 0.7823 (tpt) REVERT: B 216 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8936 (mptt) REVERT: B 259 GLN cc_start: 0.8040 (tp40) cc_final: 0.7614 (tm-30) REVERT: B 507 GLU cc_start: 0.8697 (tt0) cc_final: 0.7877 (pt0) REVERT: B 527 ARG cc_start: 0.7820 (mmp80) cc_final: 0.6460 (mmm-85) REVERT: B 594 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7851 (mm-30) outliers start: 15 outliers final: 8 residues processed: 63 average time/residue: 0.7159 time to fit residues: 47.8337 Evaluate side-chains 61 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 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 444 LEU 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 179 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.099144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.078246 restraints weight = 17056.196| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.08 r_work: 0.3080 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8903 Z= 0.134 Angle : 0.563 12.242 12114 Z= 0.268 Chirality : 0.041 0.144 1330 Planarity : 0.004 0.035 1551 Dihedral : 4.927 82.522 1193 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.65 % Allowed : 14.38 % Favored : 83.97 % 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: 1.10 (0.26), residues: 1078 helix: 2.75 (0.26), residues: 407 sheet: 0.29 (0.32), residues: 238 loop : -1.04 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.011 0.001 TYR B 582 PHE 0.013 0.001 PHE A 510 TRP 0.029 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 8902) covalent geometry : angle 0.56333 / 0.27 (12114) hydrogen bonds : bond 0.04171 / 2.86 ( 398) hydrogen bonds : angle 3.98585 / 2.93 ( 1149) Misc. bond : bond 0.00011 / 0.01 ( 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 65 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8172 (mtm180) cc_final: 0.7846 (ttp-110) REVERT: A 380 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8149 (mtmt) REVERT: A 444 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7960 (pp) REVERT: A 446 ASP cc_start: 0.8555 (t0) cc_final: 0.8288 (m-30) REVERT: B 11 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8007 (tp30) REVERT: B 55 MET cc_start: 0.8139 (tpt) cc_final: 0.7847 (tpt) REVERT: B 216 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8938 (mptt) REVERT: B 507 GLU cc_start: 0.8665 (tt0) cc_final: 0.7861 (pt0) REVERT: B 527 ARG cc_start: 0.7854 (mmp80) cc_final: 0.6436 (mpt-90) REVERT: B 586 LYS cc_start: 0.8585 (tttt) cc_final: 0.8335 (ttpm) REVERT: B 594 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7840 (mm-30) outliers start: 15 outliers final: 7 residues processed: 62 average time/residue: 0.7132 time to fit residues: 46.9841 Evaluate side-chains 59 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 444 LEU Chi-restraints excluded: chain A residue 590 ASP 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 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 72 optimal weight: 0.0050 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.100759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079952 restraints weight = 17020.426| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.08 r_work: 0.3099 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8903 Z= 0.099 Angle : 0.537 12.535 12114 Z= 0.252 Chirality : 0.039 0.143 1330 Planarity : 0.004 0.034 1551 Dihedral : 4.817 87.023 1193 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.21 % Allowed : 15.04 % 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: 1.23 (0.26), residues: 1078 helix: 2.87 (0.26), residues: 408 sheet: 0.30 (0.32), residues: 240 loop : -0.95 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.013 0.001 TYR B 582 PHE 0.012 0.001 PHE A 510 TRP 0.029 0.001 TRP C 24 HIS 0.003 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 8902) covalent geometry : angle 0.53656 / 0.25 (12114) hydrogen bonds : bond 0.03503 / 2.40 ( 398) hydrogen bonds : angle 3.80606 / 2.80 ( 1149) Misc. bond : bond 0.00021 / 0.01 ( 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: 11 poor density : 51 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7860 (ttp-110) REVERT: A 444 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7791 (pp) REVERT: A 446 ASP cc_start: 0.8529 (t0) cc_final: 0.8264 (m-30) REVERT: B 11 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8003 (tp30) REVERT: B 216 LYS cc_start: 0.9195 (mmtt) cc_final: 0.8897 (mptt) REVERT: B 527 ARG cc_start: 0.7684 (mmp80) cc_final: 0.6279 (mpt-90) REVERT: B 586 LYS cc_start: 0.8569 (tttt) cc_final: 0.8326 (ttpm) REVERT: B 594 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7853 (mm-30) outliers start: 11 outliers final: 7 residues processed: 59 average time/residue: 0.6686 time to fit residues: 41.8419 Evaluate side-chains 59 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 590 ASP 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=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: 0.0670 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 82 optimal weight: 0.0020 chunk 65 optimal weight: 0.4980 chunk 14 optimal weight: 0.0070 chunk 15 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.2144 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.101503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.080849 restraints weight = 16750.446| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.06 r_work: 0.3151 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8903 Z= 0.092 Angle : 0.536 15.570 12114 Z= 0.249 Chirality : 0.039 0.144 1330 Planarity : 0.003 0.033 1551 Dihedral : 4.677 87.002 1193 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.77 % Allowed : 15.59 % Favored : 83.64 % 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: 1.28 (0.26), residues: 1078 helix: 2.85 (0.26), residues: 409 sheet: 0.36 (0.33), residues: 240 loop : -0.88 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 281 TYR 0.012 0.001 TYR B 582 PHE 0.011 0.001 PHE B 510 TRP 0.028 0.001 TRP C 24 HIS 0.003 0.000 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 8902) covalent geometry : angle 0.53594 / 0.25 (12114) hydrogen bonds : bond 0.03192 / 2.19 ( 398) hydrogen bonds : angle 3.71757 / 2.75 ( 1149) Misc. bond : bond 0.00021 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2574.80 seconds wall clock time: 44 minutes 50.28 seconds (2690.28 seconds total)