Starting phenix.real_space_refine on Thu Jul 2 12:45:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6i_33641/07_2026/7y6i_33641_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6i_33641/07_2026/7y6i_33641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6i_33641/07_2026/7y6i_33641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6i_33641/07_2026/7y6i_33641.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6i_33641/07_2026/7y6i_33641_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6i_33641/07_2026/7y6i_33641_neut.cif" } resolution = 2.85 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= 0.102 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: 7 Type Number sf(0) Gaussians P 17 5.49 5 S 42 5.16 5 Cl 4 4.86 5 Na 4 4.78 5 C 5544 2.51 5 N 1137 2.21 5 O 1428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 8176 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3564 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 450} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3564 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 450} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 515 Ad-hoc single atom residues: {' CL': 2, ' NA': 2} Unusual residues: {'LPE': 4, 'NAG': 1, 'POV': 5, 'Y01': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 463 Ad-hoc single atom residues: {' CL': 2, ' NA': 2} Unusual residues: {'LPE': 4, 'NAG': 1, 'POV': 4, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 10} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 1.57, per 1000 atoms: 0.19 Number of scatterers: 8176 At special positions: 0 Unit cell: (80.542, 109.83, 94.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 42 16.00 P 17 15.00 Na 4 11.00 O 1428 8.00 N 1137 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 421 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 436 " distance=2.04 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 421 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 436 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1117 " - " ASN A 406 " " NAG B1116 " - " ASN B 406 " " NAG C 1 " - " ASN A 426 " " NAG D 1 " - " ASN B 426 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 275.7 milliseconds 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 158 through 194 removed outlier: 6.786A pdb=" N ILE A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N VAL A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 212 through 249 removed outlier: 3.718A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 277 removed outlier: 3.600A pdb=" N ILE A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 306 removed outlier: 3.547A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 321 through 329 Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.644A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.212A pdb=" N GLY A 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 358 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 395 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.559A pdb=" N CYS A 421 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 453 through 486 removed outlier: 3.758A pdb=" N ILE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 removed outlier: 3.645A pdb=" N PHE A 494 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 496 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS A 497 " --> pdb=" O PHE A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 521 Processing helix chain 'A' and resid 524 through 553 Proline residue: A 530 - end of helix Processing helix chain 'A' and resid 566 through 585 removed outlier: 3.628A pdb=" N THR A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 605 removed outlier: 3.611A pdb=" N ALA A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 151 removed outlier: 4.504A pdb=" N ILE B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ARG B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 removed outlier: 4.105A pdb=" N TYR B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 166 Processing helix chain 'B' and resid 167 through 194 removed outlier: 3.528A pdb=" N VAL B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 212 through 249 removed outlier: 3.760A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 277 Processing helix chain 'B' and resid 281 through 306 removed outlier: 4.696A pdb=" N VAL B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 321 through 330 removed outlier: 4.211A pdb=" N VAL B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 348 removed outlier: 3.627A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 366 through 394 Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 418 through 424 Processing helix chain 'B' and resid 428 through 434 Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.692A pdb=" N MET B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 486 removed outlier: 3.841A pdb=" N ILE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 521 Processing helix chain 'B' and resid 524 through 553 Proline residue: B 530 - end of helix Processing helix chain 'B' and resid 566 through 585 removed outlier: 3.631A pdb=" N THR B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 605 removed outlier: 3.618A pdb=" N ALA B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1515 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: 0.99 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1120 1.28 - 1.41: 2011 1.41 - 1.54: 5101 1.54 - 1.68: 58 1.68 - 1.81: 63 Bond restraints: 8353 Sorted by residual: bond pdb="C310 POV A1116 " pdb="C311 POV A1116 " ideal model delta sigma weight residual 1.523 1.375 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C31 POV B1115 " pdb=" O31 POV B1115 " ideal model delta sigma weight residual 1.327 1.471 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C31 POV B1101 " pdb=" O31 POV B1101 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C21 POV A1116 " pdb=" O21 POV A1116 " ideal model delta sigma weight residual 1.330 1.464 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C21 POV B1102 " pdb=" O21 POV B1102 " ideal model delta sigma weight residual 1.330 1.464 -0.134 2.00e-02 2.50e+03 4.49e+01 ... (remaining 8348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.21: 10978 5.21 - 10.41: 205 10.41 - 15.62: 76 15.62 - 20.82: 22 20.82 - 26.03: 10 Bond angle restraints: 11291 Sorted by residual: angle pdb=" O32 LPE B1110 " pdb=" P LPE B1110 " pdb=" O33 LPE B1110 " ideal model delta sigma weight residual 110.64 84.61 26.03 3.00e+00 1.11e-01 7.53e+01 angle pdb=" O11 POV A1116 " pdb=" P POV A1116 " pdb=" O12 POV A1116 " ideal model delta sigma weight residual 97.67 123.02 -25.35 3.00e+00 1.11e-01 7.14e+01 angle pdb=" C37 POV A1116 " pdb=" C38 POV A1116 " pdb=" C39 POV A1116 " ideal model delta sigma weight residual 113.94 89.39 24.55 3.00e+00 1.11e-01 6.70e+01 angle pdb=" C27 POV B1115 " pdb=" C28 POV B1115 " pdb=" C29 POV B1115 " ideal model delta sigma weight residual 112.18 87.68 24.50 3.00e+00 1.11e-01 6.67e+01 angle pdb=" O3 LPE B1110 " pdb=" P LPE B1110 " pdb=" O32 LPE B1110 " ideal model delta sigma weight residual 103.09 126.46 -23.37 3.00e+00 1.11e-01 6.07e+01 ... (remaining 11286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 4818 26.67 - 53.35: 456 53.35 - 80.02: 67 80.02 - 106.70: 37 106.70 - 133.37: 7 Dihedral angle restraints: 5385 sinusoidal: 2711 harmonic: 2674 Sorted by residual: dihedral pdb=" CB CYS B 416 " pdb=" SG CYS B 416 " pdb=" SG CYS B 421 " pdb=" CB CYS B 421 " ideal model delta sinusoidal sigma weight residual 93.00 151.35 -58.35 1 1.00e+01 1.00e-02 4.56e+01 dihedral pdb=" C39 POV A1112 " pdb="C310 POV A1112 " pdb="C311 POV A1112 " pdb="C312 POV A1112 " ideal model delta sinusoidal sigma weight residual 180.49 47.12 133.37 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" C39 POV A1116 " pdb="C310 POV A1116 " pdb="C311 POV A1116 " pdb="C312 POV A1116 " ideal model delta sinusoidal sigma weight residual 180.49 47.43 133.06 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 5382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 1260 0.164 - 0.328: 8 0.328 - 0.492: 1 0.492 - 0.656: 1 0.656 - 0.820: 1 Chirality restraints: 1271 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 426 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb=" C2 LPE B1111 " pdb=" C1 LPE B1111 " pdb=" C3 LPE B1111 " pdb=" O2H LPE B1111 " both_signs ideal model delta sigma weight residual False 2.43 1.86 0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" CA ARG B 334 " pdb=" N ARG B 334 " pdb=" C ARG B 334 " pdb=" CB ARG B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 1268 not shown) Planarity restraints: 1271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.336 2.00e-02 2.50e+03 2.89e-01 1.05e+03 pdb=" C7 NAG D 1 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.504 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1117 " -0.176 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" C7 NAG A1117 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG A1117 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG A1117 " 0.239 2.00e-02 2.50e+03 pdb=" O7 NAG A1117 " -0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.112 2.00e-02 2.50e+03 9.26e-02 1.07e+02 pdb=" C7 NAG D 2 " -0.031 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.084 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.148 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.017 2.00e-02 2.50e+03 ... (remaining 1268 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 81 2.60 - 3.18: 6983 3.18 - 3.75: 13049 3.75 - 4.33: 19250 4.33 - 4.90: 31498 Nonbonded interactions: 70861 Sorted by model distance: nonbonded pdb=" O2H LPE B1110 " pdb=" O31 LPE B1110 " model vdw 2.025 3.040 nonbonded pdb=" O SER A 345 " pdb=" OG SER A 533 " model vdw 2.222 3.040 nonbonded pdb=" O SER B 345 " pdb=" OG SER B 533 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 156 " pdb=" OG SER A 296 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR B 156 " pdb=" OG SER B 296 " model vdw 2.234 3.040 ... (remaining 70856 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 137 through 605 or resid 1103 through 1104 or resid 1107 o \ r resid 1110 through 1111 or resid 1114 through 1115)) selection = (chain 'B' and (resid 137 through 605 or resid 1103 through 1104 or resid 1107 o \ r resid 1110 through 1111 or resid 1114 through 1115)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.420 Find NCS groups from input model: 0.140 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:5.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.015 0.148 8363 Z= 0.782 Angle : 2.020 26.030 11317 Z= 0.757 Chirality : 0.054 0.820 1271 Planarity : 0.010 0.289 1267 Dihedral : 20.978 133.370 3673 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.21 % Favored : 96.68 % Rotamer: Outliers : 1.06 % Allowed : 19.28 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 934 helix: 1.65 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 559 TYR 0.017 0.001 TYR B 320 PHE 0.011 0.001 PHE B 494 TRP 0.016 0.001 TRP A 161 HIS 0.002 0.000 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.01547 / 0.78 ( 8353) covalent geometry : angle 2.01515 / 0.76 (11291) SS BOND : bond 0.00499 / 0.31 ( 4) SS BOND : angle 0.77202 / 0.40 ( 8) hydrogen bonds : bond 0.13169 / 9.30 ( 520) hydrogen bonds : angle 5.22888 / 3.68 ( 1515) link_BETA1-4 : bond 0.01471 / 0.83 ( 2) link_BETA1-4 : angle 2.97374 / 1.53 ( 6) link_NAG-ASN : bond 0.01238 / 0.77 ( 4) link_NAG-ASN : angle 4.63220 / 2.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 497 LYS cc_start: 0.7538 (ptmt) cc_final: 0.6013 (mmtm) REVERT: A 581 MET cc_start: 0.8921 (ttm) cc_final: 0.8645 (ttm) outliers start: 8 outliers final: 5 residues processed: 82 average time/residue: 0.3368 time to fit residues: 30.0587 Evaluate side-chains 73 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain B residue 292 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.166547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129062 restraints weight = 7456.732| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.58 r_work: 0.3262 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8363 Z= 0.147 Angle : 0.612 7.290 11317 Z= 0.288 Chirality : 0.042 0.237 1271 Planarity : 0.004 0.047 1267 Dihedral : 20.570 141.395 2212 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.79 % Allowed : 17.95 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.28), residues: 934 helix: 1.61 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.57 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.010 0.001 TYR A 204 PHE 0.016 0.002 PHE A 545 TRP 0.013 0.001 TRP B 425 HIS 0.008 0.002 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 8353) covalent geometry : angle 0.60232 / 0.29 (11291) SS BOND : bond 0.00381 / 0.23 ( 4) SS BOND : angle 1.01465 / 0.53 ( 8) hydrogen bonds : bond 0.04355 / 2.97 ( 520) hydrogen bonds : angle 4.27715 / 3.07 ( 1515) link_BETA1-4 : bond 0.00061 / 0.04 ( 2) link_BETA1-4 : angle 0.86348 / 0.43 ( 6) link_NAG-ASN : bond 0.00575 / 0.32 ( 4) link_NAG-ASN : angle 3.36385 / 1.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.176 Fit side-chains REVERT: A 447 MET cc_start: 0.8368 (ttt) cc_final: 0.8142 (ttt) REVERT: A 497 LYS cc_start: 0.7590 (ptmt) cc_final: 0.5973 (mmtm) REVERT: A 581 MET cc_start: 0.8810 (ttm) cc_final: 0.8544 (ttm) REVERT: B 248 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6659 (pp20) REVERT: B 492 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7220 (pp) outliers start: 21 outliers final: 9 residues processed: 86 average time/residue: 0.3210 time to fit residues: 30.0966 Evaluate side-chains 76 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 561 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.161951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121242 restraints weight = 7468.856| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.73 r_work: 0.3131 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8363 Z= 0.152 Angle : 0.557 7.512 11317 Z= 0.273 Chirality : 0.041 0.187 1271 Planarity : 0.004 0.046 1267 Dihedral : 18.738 131.760 2208 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.06 % Allowed : 18.09 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 934 helix: 1.61 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.52 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.011 0.001 TYR A 204 PHE 0.012 0.002 PHE A 545 TRP 0.010 0.001 TRP A 425 HIS 0.005 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 8353) covalent geometry : angle 0.55046 / 0.27 (11291) SS BOND : bond 0.00339 / 0.20 ( 4) SS BOND : angle 1.03958 / 0.54 ( 8) hydrogen bonds : bond 0.04205 / 2.87 ( 520) hydrogen bonds : angle 4.16945 / 2.99 ( 1515) link_BETA1-4 : bond 0.00473 / 0.28 ( 2) link_BETA1-4 : angle 1.00390 / 0.52 ( 6) link_NAG-ASN : bond 0.00562 / 0.31 ( 4) link_NAG-ASN : angle 2.58225 / 1.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 LYS cc_start: 0.7633 (ptmt) cc_final: 0.5969 (mmtm) REVERT: A 581 MET cc_start: 0.8671 (ttm) cc_final: 0.8431 (ttm) REVERT: B 248 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6640 (pp20) REVERT: B 343 MET cc_start: 0.8807 (mmt) cc_final: 0.8291 (mmt) REVERT: B 405 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8007 (mp) REVERT: B 559 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6997 (mmt180) REVERT: B 598 PHE cc_start: 0.7664 (t80) cc_final: 0.7424 (t80) outliers start: 23 outliers final: 9 residues processed: 88 average time/residue: 0.3103 time to fit residues: 29.9819 Evaluate side-chains 79 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 561 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.0270 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.0670 chunk 62 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 149 ASN B 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.165183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124577 restraints weight = 7589.233| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.74 r_work: 0.3223 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8363 Z= 0.111 Angle : 0.494 5.473 11317 Z= 0.246 Chirality : 0.039 0.224 1271 Planarity : 0.004 0.047 1267 Dihedral : 17.700 127.879 2207 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.93 % Allowed : 19.15 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.34 (0.28), residues: 934 helix: 1.80 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.45 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.008 0.001 TYR A 204 PHE 0.017 0.001 PHE B 494 TRP 0.010 0.001 TRP A 161 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8353) covalent geometry : angle 0.48606 / 0.24 (11291) SS BOND : bond 0.00358 / 0.22 ( 4) SS BOND : angle 0.87632 / 0.46 ( 8) hydrogen bonds : bond 0.03660 / 2.47 ( 520) hydrogen bonds : angle 3.97019 / 2.84 ( 1515) link_BETA1-4 : bond 0.00563 / 0.33 ( 2) link_BETA1-4 : angle 1.36934 / 0.71 ( 6) link_NAG-ASN : bond 0.00483 / 0.27 ( 4) link_NAG-ASN : angle 2.57520 / 1.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ILE cc_start: 0.7854 (mt) cc_final: 0.7600 (mm) REVERT: A 320 TYR cc_start: 0.8395 (m-80) cc_final: 0.8147 (m-80) REVERT: A 497 LYS cc_start: 0.7497 (ptmt) cc_final: 0.5937 (mmtm) REVERT: B 248 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6682 (pp20) REVERT: B 343 MET cc_start: 0.8764 (mmt) cc_final: 0.8406 (mmt) REVERT: B 405 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7877 (mp) REVERT: B 559 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.6999 (mtt180) REVERT: B 598 PHE cc_start: 0.7871 (t80) cc_final: 0.7576 (t80) outliers start: 22 outliers final: 10 residues processed: 88 average time/residue: 0.3773 time to fit residues: 36.2178 Evaluate side-chains 84 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 561 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN A 299 ASN B 566 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.163265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.125202 restraints weight = 7459.549| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.58 r_work: 0.3179 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8363 Z= 0.180 Angle : 0.561 5.457 11317 Z= 0.278 Chirality : 0.042 0.205 1271 Planarity : 0.004 0.048 1267 Dihedral : 17.624 119.667 2207 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.66 % Allowed : 19.95 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.28), residues: 934 helix: 1.55 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.52 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 158 TYR 0.013 0.001 TYR A 204 PHE 0.016 0.002 PHE B 494 TRP 0.010 0.001 TRP B 281 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 8353) covalent geometry : angle 0.55345 / 0.28 (11291) SS BOND : bond 0.00552 / 0.33 ( 4) SS BOND : angle 1.48608 / 0.78 ( 8) hydrogen bonds : bond 0.04364 / 2.97 ( 520) hydrogen bonds : angle 4.19957 / 3.01 ( 1515) link_BETA1-4 : bond 0.00498 / 0.29 ( 2) link_BETA1-4 : angle 1.32821 / 0.67 ( 6) link_NAG-ASN : bond 0.00490 / 0.27 ( 4) link_NAG-ASN : angle 2.47865 / 1.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7782 (mm) REVERT: A 497 LYS cc_start: 0.7606 (ptmt) cc_final: 0.5999 (mmtm) REVERT: B 248 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6776 (pp20) REVERT: B 320 TYR cc_start: 0.8094 (m-80) cc_final: 0.7796 (m-80) REVERT: B 405 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7985 (mp) REVERT: B 488 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8300 (mp) REVERT: B 559 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7167 (mmt180) REVERT: B 566 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8108 (t0) outliers start: 20 outliers final: 9 residues processed: 85 average time/residue: 0.3663 time to fit residues: 33.7461 Evaluate side-chains 87 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 566 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 566 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.164815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127203 restraints weight = 7362.681| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.56 r_work: 0.3203 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8363 Z= 0.141 Angle : 0.517 5.616 11317 Z= 0.258 Chirality : 0.040 0.198 1271 Planarity : 0.004 0.048 1267 Dihedral : 17.393 118.550 2207 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.93 % Allowed : 19.68 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 934 helix: 1.62 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.53 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 399 TYR 0.010 0.001 TYR A 204 PHE 0.017 0.002 PHE B 494 TRP 0.011 0.001 TRP B 568 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 8353) covalent geometry : angle 0.51005 / 0.26 (11291) SS BOND : bond 0.00362 / 0.21 ( 4) SS BOND : angle 1.27449 / 0.68 ( 8) hydrogen bonds : bond 0.04025 / 2.73 ( 520) hydrogen bonds : angle 4.09465 / 2.93 ( 1515) link_BETA1-4 : bond 0.00399 / 0.23 ( 2) link_BETA1-4 : angle 1.44151 / 0.72 ( 6) link_NAG-ASN : bond 0.00477 / 0.26 ( 4) link_NAG-ASN : angle 2.25562 / 1.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 LYS cc_start: 0.7620 (ptmt) cc_final: 0.6001 (mmtm) REVERT: B 405 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7905 (OUTLIER) REVERT: B 559 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7120 (mmt180) REVERT: B 566 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.8032 (t0) outliers start: 22 outliers final: 11 residues processed: 89 average time/residue: 0.3320 time to fit residues: 32.3020 Evaluate side-chains 83 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 566 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 566 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125691 restraints weight = 7431.799| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.57 r_work: 0.3108 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8363 Z= 0.135 Angle : 0.515 6.625 11317 Z= 0.258 Chirality : 0.039 0.192 1271 Planarity : 0.004 0.047 1267 Dihedral : 17.173 116.417 2207 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.93 % Allowed : 20.35 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 934 helix: 1.66 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.54 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 145 TYR 0.010 0.001 TYR A 204 PHE 0.017 0.001 PHE B 494 TRP 0.010 0.001 TRP A 161 HIS 0.003 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 8353) covalent geometry : angle 0.50822 / 0.26 (11291) SS BOND : bond 0.00334 / 0.20 ( 4) SS BOND : angle 1.17053 / 0.63 ( 8) hydrogen bonds : bond 0.03942 / 2.67 ( 520) hydrogen bonds : angle 4.06198 / 2.91 ( 1515) link_BETA1-4 : bond 0.00420 / 0.25 ( 2) link_BETA1-4 : angle 1.47316 / 0.74 ( 6) link_NAG-ASN : bond 0.00470 / 0.26 ( 4) link_NAG-ASN : angle 2.23031 / 1.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 LYS cc_start: 0.7563 (ptmt) cc_final: 0.5923 (mmtm) REVERT: B 405 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7813 (OUTLIER) REVERT: B 559 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7136 (mmt180) REVERT: B 566 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.7995 (t0) REVERT: B 598 PHE cc_start: 0.7777 (t80) cc_final: 0.7468 (t80) outliers start: 22 outliers final: 11 residues processed: 87 average time/residue: 0.3332 time to fit residues: 31.7029 Evaluate side-chains 83 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 566 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 45 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 566 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.165459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127925 restraints weight = 7375.845| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.56 r_work: 0.3186 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8363 Z= 0.136 Angle : 0.512 5.750 11317 Z= 0.256 Chirality : 0.040 0.187 1271 Planarity : 0.004 0.047 1267 Dihedral : 16.905 114.408 2205 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.93 % Allowed : 20.35 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.28), residues: 934 helix: 1.82 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.66 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 145 TYR 0.011 0.001 TYR A 204 PHE 0.018 0.002 PHE B 494 TRP 0.010 0.001 TRP A 161 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8353) covalent geometry : angle 0.50492 / 0.25 (11291) SS BOND : bond 0.00346 / 0.21 ( 4) SS BOND : angle 1.13051 / 0.61 ( 8) hydrogen bonds : bond 0.03917 / 2.66 ( 520) hydrogen bonds : angle 4.05077 / 2.90 ( 1515) link_BETA1-4 : bond 0.00448 / 0.27 ( 2) link_BETA1-4 : angle 1.47031 / 0.74 ( 6) link_NAG-ASN : bond 0.00471 / 0.26 ( 4) link_NAG-ASN : angle 2.22532 / 1.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7655 (mt) REVERT: A 497 LYS cc_start: 0.7631 (ptmt) cc_final: 0.5992 (mmtm) REVERT: A 566 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8184 (t0) REVERT: B 559 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7081 (mmt180) REVERT: B 566 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7928 (t0) REVERT: B 598 PHE cc_start: 0.7823 (t80) cc_final: 0.7535 (t80) outliers start: 22 outliers final: 12 residues processed: 84 average time/residue: 0.3546 time to fit residues: 32.4158 Evaluate side-chains 83 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 566 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 57 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 566 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.165320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127704 restraints weight = 7439.849| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.56 r_work: 0.3185 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8363 Z= 0.137 Angle : 0.511 5.791 11317 Z= 0.256 Chirality : 0.039 0.193 1271 Planarity : 0.004 0.047 1267 Dihedral : 16.662 112.678 2205 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.06 % Allowed : 20.35 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 934 helix: 1.85 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 145 TYR 0.011 0.001 TYR A 204 PHE 0.019 0.002 PHE B 494 TRP 0.010 0.001 TRP A 161 HIS 0.003 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8353) covalent geometry : angle 0.50464 / 0.25 (11291) SS BOND : bond 0.00320 / 0.19 ( 4) SS BOND : angle 1.10806 / 0.59 ( 8) hydrogen bonds : bond 0.03905 / 2.65 ( 520) hydrogen bonds : angle 4.04453 / 2.90 ( 1515) link_BETA1-4 : bond 0.00372 / 0.22 ( 2) link_BETA1-4 : angle 1.47452 / 0.73 ( 6) link_NAG-ASN : bond 0.00465 / 0.26 ( 4) link_NAG-ASN : angle 2.24524 / 1.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7763 (mm) REVERT: A 320 TYR cc_start: 0.8339 (m-80) cc_final: 0.8084 (m-80) REVERT: A 371 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7608 (mt) REVERT: A 497 LYS cc_start: 0.7633 (ptmt) cc_final: 0.5984 (mmtm) REVERT: A 566 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8175 (t0) REVERT: B 559 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7075 (mmt180) REVERT: B 566 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7982 (t0) outliers start: 23 outliers final: 13 residues processed: 83 average time/residue: 0.3573 time to fit residues: 32.3023 Evaluate side-chains 85 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 566 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 566 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125636 restraints weight = 7427.572| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.56 r_work: 0.3182 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8363 Z= 0.141 Angle : 0.526 9.288 11317 Z= 0.260 Chirality : 0.040 0.317 1271 Planarity : 0.004 0.047 1267 Dihedral : 16.519 111.310 2205 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.93 % Allowed : 20.35 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.28), residues: 934 helix: 1.85 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 145 TYR 0.011 0.001 TYR A 204 PHE 0.019 0.002 PHE B 494 TRP 0.009 0.001 TRP B 568 HIS 0.003 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 8353) covalent geometry : angle 0.51013 / 0.26 (11291) SS BOND : bond 0.00328 / 0.20 ( 4) SS BOND : angle 1.11266 / 0.60 ( 8) hydrogen bonds : bond 0.03932 / 2.67 ( 520) hydrogen bonds : angle 4.04996 / 2.90 ( 1515) link_BETA1-4 : bond 0.00438 / 0.26 ( 2) link_BETA1-4 : angle 1.48015 / 0.74 ( 6) link_NAG-ASN : bond 0.00454 / 0.25 ( 4) link_NAG-ASN : angle 3.77790 / 1.91 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 TYR cc_start: 0.8417 (m-80) cc_final: 0.8042 (m-80) REVERT: A 497 LYS cc_start: 0.7647 (ptmt) cc_final: 0.6002 (mmtm) REVERT: A 566 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8200 (t0) REVERT: B 559 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7076 (mmt180) REVERT: B 566 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7964 (t0) outliers start: 22 outliers final: 14 residues processed: 83 average time/residue: 0.3464 time to fit residues: 31.2395 Evaluate side-chains 84 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 566 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 74 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 359 ASN B 566 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.160069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120290 restraints weight = 7520.031| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.66 r_work: 0.3134 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8363 Z= 0.122 Angle : 0.505 8.144 11317 Z= 0.251 Chirality : 0.039 0.315 1271 Planarity : 0.004 0.047 1267 Dihedral : 16.301 110.763 2205 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.19 % Allowed : 20.35 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.28), residues: 934 helix: 1.92 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 145 TYR 0.010 0.001 TYR A 204 PHE 0.019 0.001 PHE B 494 TRP 0.012 0.001 TRP A 161 HIS 0.003 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8353) covalent geometry : angle 0.49161 / 0.25 (11291) SS BOND : bond 0.00303 / 0.18 ( 4) SS BOND : angle 1.05856 / 0.57 ( 8) hydrogen bonds : bond 0.03777 / 2.56 ( 520) hydrogen bonds : angle 3.99769 / 2.86 ( 1515) link_BETA1-4 : bond 0.00463 / 0.28 ( 2) link_BETA1-4 : angle 1.46737 / 0.73 ( 6) link_NAG-ASN : bond 0.00494 / 0.27 ( 4) link_NAG-ASN : angle 3.39255 / 1.75 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.73 seconds wall clock time: 36 minutes 30.75 seconds (2190.75 seconds total)