Starting phenix.real_space_refine on Fri Sep 11 13:35:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8a1r_15084/09_2026/8a1r_15084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1r_15084/09_2026/8a1r_15084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a1r_15084/09_2026/8a1r_15084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1r_15084/09_2026/8a1r_15084.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a1r_15084/09_2026/8a1r_15084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1r_15084/09_2026/8a1r_15084.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8a1r_15084/09_2026/8a1r_15084.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8a1r_15084/09_2026/8a1r_15084.cif" } resolution = 3.6 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= 0.001 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 48 5.16 5 C 5894 2.51 5 N 1554 2.21 5 O 1786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 9286 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4530 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 571} Chain: "B" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4530 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 571} Chain: "A" Number of atoms: 113 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 83 Unusual residues: {'FAD': 1, 'KW2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Conformer: "B" Number of residues, atoms: 2, 83 Unusual residues: {'FAD': 1, 'KW2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} bond proxies already assigned to first conformer: 58 Chain: "B" Number of atoms: 113 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 83 Unusual residues: {'FAD': 1, 'KW2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Conformer: "B" Number of residues, atoms: 2, 83 Unusual residues: {'FAD': 1, 'KW2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} bond proxies already assigned to first conformer: 58 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AKW2 A 602 " occ=0.50 ... (58 atoms not shown) pdb=" O13BKW2 A 602 " occ=0.50 residue: pdb=" N AKW2 B 602 " occ=0.50 ... (58 atoms not shown) pdb=" O13BKW2 B 602 " occ=0.50 Time building chain proxies: 2.47, per 1000 atoms: 0.27 Number of scatterers: 9286 At special positions: 0 Unit cell: (101.905, 125.95, 92.745, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 4 15.00 O 1786 8.00 N 1554 7.00 C 5894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 31 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 31 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 291.8 milliseconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 15 sheets defined 39.6% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 Processing helix chain 'A' and resid 28 through 41 removed outlier: 3.594A pdb=" N LYS A 32 " --> pdb=" O CYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.532A pdb=" N LYS A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.950A pdb=" N VAL A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 181 removed outlier: 3.950A pdb=" N GLU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N HIS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.527A pdb=" N ILE A 190 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 219 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 295 through 307 Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 441 through 458 Processing helix chain 'A' and resid 485 through 494 Processing helix chain 'A' and resid 507 through 511 removed outlier: 3.682A pdb=" N THR A 511 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 543 through 557 removed outlier: 3.516A pdb=" N ILE A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N MET A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.589A pdb=" N GLU A 576 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A 577 " --> pdb=" O CYS A 574 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 581 " --> pdb=" O PHE A 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 18 Processing helix chain 'B' and resid 28 through 41 removed outlier: 3.700A pdb=" N LYS B 32 " --> pdb=" O CYS B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 84 through 95 Processing helix chain 'B' and resid 96 through 102 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.749A pdb=" N VAL B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 178 Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 193 through 219 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 441 through 458 Processing helix chain 'B' and resid 485 through 494 Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 543 through 557 removed outlier: 4.065A pdb=" N ILE B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET B 557 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 567 Processing helix chain 'B' and resid 574 through 581 removed outlier: 3.736A pdb=" N LEU B 581 " --> pdb=" O PHE B 578 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 removed outlier: 3.598A pdb=" N LEU A 22 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N MET A 75 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 224 removed outlier: 6.396A pdb=" N ASP A 109 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE A 254 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 111 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 224 removed outlier: 6.396A pdb=" N ASP A 109 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE A 254 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 111 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.696A pdb=" N VAL A 312 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 289 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N MET A 315 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 291 " --> pdb=" O MET A 315 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 290 " --> pdb=" O ILE A 388 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 356 removed outlier: 6.874A pdb=" N LYS A 371 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 352 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A 369 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN A 354 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU A 367 " --> pdb=" O GLN A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 473 removed outlier: 3.596A pdb=" N LYS A 523 " --> pdb=" O HIS A 538 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS A 520 " --> pdb=" O PHE A 505 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 498 through 499 Processing sheet with id=AA9, first strand: chain 'B' and resid 46 through 49 removed outlier: 7.359A pdb=" N MET B 75 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 82 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 222 through 224 removed outlier: 3.518A pdb=" N THR B 222 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 224 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA B 134 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 110 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU B 136 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 112 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP B 109 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 229 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 222 through 224 removed outlier: 3.518A pdb=" N THR B 222 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 224 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA B 134 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 110 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU B 136 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 112 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP B 109 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 260 through 261 Processing sheet with id=AB4, first strand: chain 'B' and resid 274 through 275 removed outlier: 6.745A pdb=" N ILE B 274 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 347 through 354 removed outlier: 5.563A pdb=" N HIS B 373 " --> pdb=" O PRO B 349 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 471 through 473 removed outlier: 6.515A pdb=" N VAL B 525 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 537 " --> pdb=" O LYS B 523 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS B 523 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL B 539 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR B 521 " --> pdb=" O VAL B 539 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1176 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: 1.49 Time building geometry restraints manager: 1.18 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: 2976 1.34 - 1.46: 1903 1.46 - 1.58: 4524 1.58 - 1.69: 17 1.69 - 1.81: 66 Bond restraints: 9486 Sorted by residual: bond pdb=" C12BKW2 B 602 " pdb=" C13BKW2 B 602 " ideal model delta sigma weight residual 1.551 1.228 0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" C12AKW2 A 602 " pdb=" C13AKW2 A 602 " ideal model delta sigma weight residual 1.551 1.229 0.322 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C12AKW2 B 602 " pdb=" C13AKW2 B 602 " ideal model delta sigma weight residual 1.551 1.229 0.322 2.00e-02 2.50e+03 2.59e+02 bond pdb=" C12BKW2 A 602 " pdb=" C13BKW2 A 602 " ideal model delta sigma weight residual 1.551 1.230 0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" C13BKW2 A 602 " pdb=" C14BKW2 A 602 " ideal model delta sigma weight residual 1.557 1.369 0.188 2.00e-02 2.50e+03 8.87e+01 ... (remaining 9481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 12837 4.70 - 9.41: 57 9.41 - 14.11: 0 14.11 - 18.81: 0 18.81 - 23.52: 4 Bond angle restraints: 12898 Sorted by residual: angle pdb=" C12BKW2 B 602 " pdb=" C13BKW2 B 602 " pdb=" C14BKW2 B 602 " ideal model delta sigma weight residual 85.19 108.71 -23.52 3.00e+00 1.11e-01 6.15e+01 angle pdb=" C12BKW2 A 602 " pdb=" C13BKW2 A 602 " pdb=" C14BKW2 A 602 " ideal model delta sigma weight residual 85.19 108.71 -23.52 3.00e+00 1.11e-01 6.14e+01 angle pdb=" C12AKW2 A 602 " pdb=" C13AKW2 A 602 " pdb=" C14AKW2 A 602 " ideal model delta sigma weight residual 85.19 108.62 -23.43 3.00e+00 1.11e-01 6.10e+01 angle pdb=" C12AKW2 B 602 " pdb=" C13AKW2 B 602 " pdb=" C14AKW2 B 602 " ideal model delta sigma weight residual 85.19 108.46 -23.27 3.00e+00 1.11e-01 6.02e+01 angle pdb=" CA CYS B 520 " pdb=" C CYS B 520 " pdb=" O CYS B 520 " ideal model delta sigma weight residual 121.55 117.92 3.63 1.06e+00 8.90e-01 1.17e+01 ... (remaining 12893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 5588 34.56 - 69.12: 127 69.12 - 103.68: 11 103.68 - 138.24: 4 138.24 - 172.80: 4 Dihedral angle restraints: 5734 sinusoidal: 2360 harmonic: 3374 Sorted by residual: dihedral pdb=" CB CYS B 154 " pdb=" SG CYS B 154 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual -86.00 -131.26 45.26 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -130.91 44.91 1 1.00e+01 1.00e-02 2.80e+01 dihedral pdb=" O5' FAD B 601 " pdb=" O3P FAD B 601 " pdb=" P FAD B 601 " pdb=" PA FAD B 601 " ideal model delta sinusoidal sigma weight residual -61.77 111.03 -172.80 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 5731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1423 0.111 - 0.221: 43 0.221 - 0.332: 0 0.332 - 0.442: 2 0.442 - 0.553: 10 Chirality restraints: 1478 Sorted by residual: chirality pdb=" C12AKW2 B 602 " pdb=" C13AKW2 B 602 " pdb=" C17AKW2 B 602 " pdb=" C18AKW2 B 602 " both_signs ideal model delta sigma weight residual False 3.20 2.65 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" C12AKW2 A 602 " pdb=" C13AKW2 A 602 " pdb=" C17AKW2 A 602 " pdb=" C18AKW2 A 602 " both_signs ideal model delta sigma weight residual False 3.20 2.65 0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" C12BKW2 B 602 " pdb=" C13BKW2 B 602 " pdb=" C17BKW2 B 602 " pdb=" C18BKW2 B 602 " both_signs ideal model delta sigma weight residual False 3.20 2.65 0.54 2.00e-01 2.50e+01 7.42e+00 ... (remaining 1475 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 142 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 143 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 590 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO B 591 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 591 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 591 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 232 " 0.031 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 233 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " 0.025 5.00e-02 4.00e+02 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 161 2.66 - 3.22: 9109 3.22 - 3.78: 15142 3.78 - 4.34: 20511 4.34 - 4.90: 32842 Nonbonded interactions: 77765 Sorted by model distance: nonbonded pdb=" OG1 THR B 573 " pdb=" OE1 GLU B 576 " model vdw 2.097 3.040 nonbonded pdb=" OG1 THR A 475 " pdb=" O LEU A 477 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR B 423 " pdb=" O VAL B 428 " model vdw 2.210 3.040 nonbonded pdb=" O ARG B 322 " pdb=" O1 BKW2 B 602 " model vdw 2.211 3.040 nonbonded pdb=" O ARG A 322 " pdb=" O1 BKW2 A 602 " model vdw 2.251 3.040 ... (remaining 77760 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 601) selection = (chain 'B' and resid 6 through 601) } 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.110 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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 : 0.011 0.323 9490 Z= 0.544 Angle : 0.859 23.517 12906 Z= 0.378 Chirality : 0.065 0.553 1478 Planarity : 0.004 0.052 1606 Dihedral : 16.262 172.797 3578 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.06 (0.25), residues: 1182 helix: 1.46 (0.27), residues: 400 sheet: -0.61 (0.35), residues: 238 loop : -0.86 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.017 0.001 TYR B 429 PHE 0.017 0.002 PHE B 578 TRP 0.008 0.001 TRP A 194 HIS 0.005 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.01087 / 0.54 ( 9486) covalent geometry : angle 0.85938 / 0.38 (12898) SS BOND : bond 0.00225 / 0.12 ( 4) SS BOND : angle 0.69178 / 0.35 ( 8) hydrogen bonds : bond 0.15107 / 10.15 ( 412) hydrogen bonds : angle 7.12871 / 5.16 ( 1176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 MET cc_start: 0.8239 (mpp) cc_final: 0.7874 (mpp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1042 time to fit residues: 13.4106 Evaluate side-chains 62 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN B 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.045169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.033221 restraints weight = 85358.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.034216 restraints weight = 58705.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.034866 restraints weight = 44804.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.035316 restraints weight = 37125.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.035620 restraints weight = 32419.988| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9490 Z= 0.131 Angle : 0.619 10.481 12906 Z= 0.308 Chirality : 0.045 0.139 1478 Planarity : 0.004 0.053 1606 Dihedral : 11.488 172.483 1478 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.61 % Allowed : 7.32 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.13 (0.25), residues: 1182 helix: 1.24 (0.26), residues: 404 sheet: -0.78 (0.34), residues: 256 loop : -0.69 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 78 TYR 0.015 0.001 TYR B 91 PHE 0.031 0.001 PHE A 304 TRP 0.008 0.001 TRP B 10 HIS 0.005 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9486) covalent geometry : angle 0.61936 / 0.31 (12898) SS BOND : bond 0.00240 / 0.13 ( 4) SS BOND : angle 0.48521 / 0.26 ( 8) hydrogen bonds : bond 0.03700 / 2.53 ( 412) hydrogen bonds : angle 5.63655 / 4.10 ( 1176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8632 (tpp) cc_final: 0.8206 (tpt) REVERT: B 165 MET cc_start: 0.9109 (ptm) cc_final: 0.8751 (ptm) REVERT: B 336 MET cc_start: 0.9278 (mpp) cc_final: 0.8837 (mpp) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.0924 time to fit residues: 10.5094 Evaluate side-chains 59 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 590 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 116 optimal weight: 0.0040 chunk 109 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 9 optimal weight: 0.0270 chunk 26 optimal weight: 0.0170 chunk 100 optimal weight: 0.0270 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 overall best weight: 0.1946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.045864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.034167 restraints weight = 77486.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.035132 restraints weight = 55167.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.035711 restraints weight = 42752.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.036140 restraints weight = 35887.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.036439 restraints weight = 31706.100| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9490 Z= 0.114 Angle : 0.596 9.259 12906 Z= 0.294 Chirality : 0.044 0.138 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.873 172.716 1478 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.91 % Allowed : 10.47 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.17 (0.25), residues: 1182 helix: 1.08 (0.26), residues: 406 sheet: -0.53 (0.33), residues: 260 loop : -0.77 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.023 0.001 TYR B 91 PHE 0.031 0.002 PHE B 304 TRP 0.008 0.001 TRP B 183 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9486) covalent geometry : angle 0.59650 / 0.29 (12898) SS BOND : bond 0.00423 / 0.21 ( 4) SS BOND : angle 0.56218 / 0.30 ( 8) hydrogen bonds : bond 0.03442 / 2.29 ( 412) hydrogen bonds : angle 5.36336 / 3.91 ( 1176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LEU cc_start: 0.9156 (mm) cc_final: 0.8533 (tp) REVERT: B 100 ILE cc_start: 0.9613 (pt) cc_final: 0.9283 (pt) REVERT: B 103 GLU cc_start: 0.9502 (tp30) cc_final: 0.9241 (pt0) outliers start: 9 outliers final: 4 residues processed: 74 average time/residue: 0.1021 time to fit residues: 10.8001 Evaluate side-chains 58 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 590 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 92 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 102 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.5568 > 50:) chunk 110 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 HIS A 156 ASN A 173 HIS A 339 HIS A 362 ASN A 422 GLN A 435 ASN A 468 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN B 225 ASN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.040656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.029627 restraints weight = 84681.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.030429 restraints weight = 59449.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.031020 restraints weight = 46999.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.031394 restraints weight = 38816.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.031540 restraints weight = 34678.580| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9490 Z= 0.327 Angle : 0.786 13.222 12906 Z= 0.401 Chirality : 0.046 0.172 1478 Planarity : 0.005 0.048 1606 Dihedral : 10.909 179.375 1478 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.44 % Allowed : 12.40 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.58 (0.25), residues: 1182 helix: 0.63 (0.25), residues: 406 sheet: -0.94 (0.33), residues: 246 loop : -0.80 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 229 TYR 0.017 0.002 TYR B 296 PHE 0.037 0.003 PHE B 304 TRP 0.016 0.002 TRP B 183 HIS 0.007 0.002 HIS B 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.33 ( 9486) covalent geometry : angle 0.78623 / 0.40 (12898) SS BOND : bond 0.00709 / 0.38 ( 4) SS BOND : angle 0.74393 / 0.44 ( 8) hydrogen bonds : bond 0.04109 / 2.75 ( 412) hydrogen bonds : angle 5.77515 / 4.14 ( 1176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.8636 (t-100) cc_final: 0.8346 (t-100) REVERT: B 100 ILE cc_start: 0.9619 (pt) cc_final: 0.9227 (pt) REVERT: B 103 GLU cc_start: 0.9501 (tp30) cc_final: 0.9230 (pt0) outliers start: 24 outliers final: 16 residues processed: 76 average time/residue: 0.0862 time to fit residues: 9.8504 Evaluate side-chains 68 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 10.0000 chunk 114 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 HIS B 209 ASN B 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.041418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.030168 restraints weight = 82912.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.031028 restraints weight = 58874.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.031641 restraints weight = 45928.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.031862 restraints weight = 37960.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.032135 restraints weight = 34256.334| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9490 Z= 0.190 Angle : 0.661 10.408 12906 Z= 0.333 Chirality : 0.045 0.155 1478 Planarity : 0.004 0.050 1606 Dihedral : 10.610 176.112 1478 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.63 % Allowed : 14.33 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.49 (0.25), residues: 1182 helix: 0.72 (0.25), residues: 406 sheet: -0.84 (0.33), residues: 240 loop : -0.81 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 414 TYR 0.014 0.002 TYR B 296 PHE 0.031 0.002 PHE B 304 TRP 0.013 0.001 TRP B 194 HIS 0.012 0.002 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 ( 9486) covalent geometry : angle 0.66074 / 0.33 (12898) SS BOND : bond 0.00383 / 0.21 ( 4) SS BOND : angle 0.84821 / 0.51 ( 8) hydrogen bonds : bond 0.03625 / 2.45 ( 412) hydrogen bonds : angle 5.54349 / 4.00 ( 1176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.9596 (m-80) cc_final: 0.9393 (t80) REVERT: A 210 TRP cc_start: 0.8559 (t-100) cc_final: 0.8290 (t-100) REVERT: B 23 PHE cc_start: 0.9493 (m-80) cc_final: 0.9235 (t80) REVERT: B 103 GLU cc_start: 0.9512 (tp30) cc_final: 0.9226 (pt0) outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.0851 time to fit residues: 9.2125 Evaluate side-chains 64 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 321 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.040814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.029726 restraints weight = 82688.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.030605 restraints weight = 58309.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.031157 restraints weight = 45088.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.031522 restraints weight = 37848.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.031685 restraints weight = 33705.464| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (13 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9490 Z= 0.213 Angle : 0.674 10.549 12906 Z= 0.342 Chirality : 0.045 0.178 1478 Planarity : 0.004 0.051 1606 Dihedral : 10.503 175.748 1478 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.93 % Allowed : 15.45 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.55 (0.25), residues: 1182 helix: 0.65 (0.25), residues: 408 sheet: -0.89 (0.33), residues: 240 loop : -0.81 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 414 TYR 0.015 0.002 TYR B 296 PHE 0.022 0.002 PHE B 304 TRP 0.010 0.001 TRP B 183 HIS 0.006 0.002 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 ( 9486) covalent geometry : angle 0.67392 / 0.34 (12898) SS BOND : bond 0.00447 / 0.24 ( 4) SS BOND : angle 0.83450 / 0.50 ( 8) hydrogen bonds : bond 0.03701 / 2.48 ( 412) hydrogen bonds : angle 5.60521 / 4.05 ( 1176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.8527 (t-100) cc_final: 0.8288 (t-100) REVERT: B 23 PHE cc_start: 0.9477 (m-80) cc_final: 0.9217 (t80) REVERT: B 103 GLU cc_start: 0.9534 (tp30) cc_final: 0.9209 (pt0) outliers start: 19 outliers final: 15 residues processed: 72 average time/residue: 0.0863 time to fit residues: 9.4564 Evaluate side-chains 69 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 555 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.041531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.030215 restraints weight = 88583.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.031143 restraints weight = 60496.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.031723 restraints weight = 46193.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.032146 restraints weight = 38372.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.032372 restraints weight = 33917.295| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9490 Z= 0.153 Angle : 0.636 10.087 12906 Z= 0.320 Chirality : 0.045 0.222 1478 Planarity : 0.004 0.052 1606 Dihedral : 10.367 175.155 1478 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.83 % Allowed : 16.16 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.44 (0.25), residues: 1182 helix: 0.77 (0.26), residues: 408 sheet: -0.89 (0.33), residues: 240 loop : -0.75 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.014 0.001 TYR B 551 PHE 0.029 0.002 PHE B 304 TRP 0.011 0.001 TRP B 194 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 9486) covalent geometry : angle 0.63620 / 0.32 (12898) SS BOND : bond 0.00273 / 0.15 ( 4) SS BOND : angle 0.79893 / 0.47 ( 8) hydrogen bonds : bond 0.03601 / 2.45 ( 412) hydrogen bonds : angle 5.48024 / 3.97 ( 1176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.8601 (t-100) cc_final: 0.8347 (t-100) outliers start: 18 outliers final: 12 residues processed: 74 average time/residue: 0.0926 time to fit residues: 10.0597 Evaluate side-chains 67 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 58 optimal weight: 0.0770 chunk 88 optimal weight: 0.8980 overall best weight: 1.0542 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.041842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.030786 restraints weight = 80570.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.031603 restraints weight = 56104.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.032112 restraints weight = 43888.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.032492 restraints weight = 37334.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.032690 restraints weight = 33303.095| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9490 Z= 0.136 Angle : 0.642 11.014 12906 Z= 0.317 Chirality : 0.045 0.275 1478 Planarity : 0.004 0.052 1606 Dihedral : 10.269 174.708 1478 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.93 % Allowed : 16.36 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.34 (0.25), residues: 1182 helix: 0.84 (0.26), residues: 408 sheet: -0.84 (0.33), residues: 240 loop : -0.67 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 78 TYR 0.012 0.001 TYR B 296 PHE 0.022 0.002 PHE A 304 TRP 0.012 0.001 TRP A 10 HIS 0.005 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 9486) covalent geometry : angle 0.64172 / 0.32 (12898) SS BOND : bond 0.00379 / 0.22 ( 4) SS BOND : angle 0.93487 / 0.50 ( 8) hydrogen bonds : bond 0.03576 / 2.44 ( 412) hydrogen bonds : angle 5.40010 / 3.91 ( 1176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.9457 (p0) cc_final: 0.8787 (m-30) REVERT: A 210 TRP cc_start: 0.8581 (t-100) cc_final: 0.8341 (t-100) REVERT: B 23 PHE cc_start: 0.9497 (m-80) cc_final: 0.9270 (t80) outliers start: 19 outliers final: 14 residues processed: 71 average time/residue: 0.0869 time to fit residues: 9.3857 Evaluate side-chains 71 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 0.0570 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.042468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.031156 restraints weight = 80931.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.032066 restraints weight = 57957.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.032609 restraints weight = 44843.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.033064 restraints weight = 37691.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.033344 restraints weight = 33508.516| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9490 Z= 0.121 Angle : 0.641 12.527 12906 Z= 0.316 Chirality : 0.045 0.292 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.134 174.117 1478 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.52 % Allowed : 17.38 % Favored : 81.10 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 9.52 % 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: -0.25 (0.25), residues: 1182 helix: 0.91 (0.26), residues: 404 sheet: -0.78 (0.33), residues: 240 loop : -0.60 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.011 0.001 TYR B 296 PHE 0.025 0.002 PHE A 304 TRP 0.011 0.001 TRP B 194 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9486) covalent geometry : angle 0.64118 / 0.32 (12898) SS BOND : bond 0.00245 / 0.14 ( 4) SS BOND : angle 0.73675 / 0.40 ( 8) hydrogen bonds : bond 0.03499 / 2.39 ( 412) hydrogen bonds : angle 5.31476 / 3.85 ( 1176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.9413 (p0) cc_final: 0.8709 (m-30) REVERT: A 210 TRP cc_start: 0.8572 (t-100) cc_final: 0.8330 (t-100) REVERT: B 23 PHE cc_start: 0.9504 (m-80) cc_final: 0.9262 (t80) REVERT: B 543 ASN cc_start: 0.8423 (t0) cc_final: 0.8219 (t0) outliers start: 15 outliers final: 12 residues processed: 72 average time/residue: 0.0845 time to fit residues: 9.2053 Evaluate side-chains 73 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.042468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.031199 restraints weight = 80953.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.032127 restraints weight = 56873.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.032692 restraints weight = 44092.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.032990 restraints weight = 37061.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.033283 restraints weight = 32707.012| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (16 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9490 Z= 0.124 Angle : 0.635 10.205 12906 Z= 0.315 Chirality : 0.045 0.217 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.080 173.606 1478 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.32 % Allowed : 17.58 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.25 (0.25), residues: 1182 helix: 0.93 (0.26), residues: 404 sheet: -0.79 (0.33), residues: 242 loop : -0.61 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.012 0.001 TYR B 296 PHE 0.023 0.002 PHE A 304 TRP 0.008 0.001 TRP B 194 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9486) covalent geometry : angle 0.63459 / 0.32 (12898) SS BOND : bond 0.00259 / 0.15 ( 4) SS BOND : angle 0.63560 / 0.34 ( 8) hydrogen bonds : bond 0.03468 / 2.37 ( 412) hydrogen bonds : angle 5.34220 / 3.87 ( 1176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.8506 (t-100) cc_final: 0.8279 (t-100) REVERT: B 23 PHE cc_start: 0.9507 (m-80) cc_final: 0.9295 (t80) REVERT: B 50 LEU cc_start: 0.9022 (mp) cc_final: 0.8714 (mp) outliers start: 13 outliers final: 13 residues processed: 72 average time/residue: 0.0885 time to fit residues: 9.5849 Evaluate side-chains 71 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 2 optimal weight: 0.3980 chunk 105 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 166 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.042312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.031180 restraints weight = 80648.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.032033 restraints weight = 57135.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.032603 restraints weight = 44851.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.032995 restraints weight = 37763.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.033226 restraints weight = 33307.246| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9490 Z= 0.129 Angle : 0.646 10.803 12906 Z= 0.324 Chirality : 0.046 0.287 1478 Planarity : 0.004 0.052 1606 Dihedral : 10.076 173.484 1478 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.73 % Allowed : 17.78 % Favored : 80.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 9.52 % 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: -0.27 (0.25), residues: 1182 helix: 0.88 (0.26), residues: 404 sheet: -0.75 (0.33), residues: 242 loop : -0.63 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.011 0.001 TYR B 296 PHE 0.077 0.002 PHE B 304 TRP 0.008 0.001 TRP B 194 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 9486) covalent geometry : angle 0.64558 / 0.32 (12898) SS BOND : bond 0.00272 / 0.16 ( 4) SS BOND : angle 0.67033 / 0.35 ( 8) hydrogen bonds : bond 0.03457 / 2.34 ( 412) hydrogen bonds : angle 5.40908 / 3.91 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.05 seconds wall clock time: 35 minutes 13.56 seconds (2113.56 seconds total)