Starting phenix.real_space_refine on Wed Sep 17 16:03:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1r_15084/09_2025/8a1r_15084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1r_15084/09_2025/8a1r_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_2025/8a1r_15084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1r_15084/09_2025/8a1r_15084.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a1r_15084/09_2025/8a1r_15084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1r_15084/09_2025/8a1r_15084.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 2.39, per 1000 atoms: 0.26 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: 0.98 Conformation dependent library (CDL) restraints added in 258.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.48 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: 1.51 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: 5657 34.56 - 69.12: 144 69.12 - 103.68: 11 103.68 - 138.24: 4 138.24 - 172.80: 4 Dihedral angle restraints: 5820 sinusoidal: 2446 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 5817 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: 0.02 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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.940 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 16.562 172.797 3664 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 aren 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 covalent geometry : bond 0.01087 ( 9486) covalent geometry : angle 0.85938 (12898) SS BOND : bond 0.00225 ( 4) SS BOND : angle 0.69178 ( 8) hydrogen bonds : bond 0.15107 ( 412) hydrogen bonds : angle 7.12871 ( 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 : 0.395 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: 0.1100 time to fit residues: 13.8611 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 : 0.360 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3503 r_free = 0.3503 target = 0.045211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.033239 restraints weight = 86410.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.034263 restraints weight = 59464.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.034859 restraints weight = 45173.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.035355 restraints weight = 37641.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.035670 restraints weight = 32780.409| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 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 = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1324 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= 0.133 Angle : 0.624 10.431 12906 Z= 0.309 Chirality : 0.045 0.149 1478 Planarity : 0.004 0.053 1606 Dihedral : 12.596 175.056 1564 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.61 % Allowed : 7.62 % Favored : 91.77 % 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 aren not related in a simple way. whole: -0.12 (0.25), residues: 1182 helix: 1.25 (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 0.003 0.001 ARG B 78 TYR 0.016 0.001 TYR B 91 PHE 0.030 0.001 PHE A 304 TRP 0.010 0.001 TRP B 10 HIS 0.005 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9486) covalent geometry : angle 0.62394 (12898) SS BOND : bond 0.00223 ( 4) SS BOND : angle 0.46501 ( 8) hydrogen bonds : bond 0.03785 ( 412) hydrogen bonds : angle 5.66859 ( 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 78 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8648 (tpp) cc_final: 0.8171 (tpt) REVERT: A 336 MET cc_start: 0.9119 (mmm) cc_final: 0.8506 (mpp) REVERT: B 165 MET cc_start: 0.9103 (ptm) cc_final: 0.8743 (ptm) REVERT: B 328 MET cc_start: 0.9337 (mtt) cc_final: 0.9125 (mtp) REVERT: B 336 MET cc_start: 0.9288 (mpp) cc_final: 0.8849 (mpp) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 0.1003 time to fit residues: 10.7845 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 : 0.281 ------------------------------------------------------------------------------- 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: 0.0670 chunk 109 optimal weight: 0.0050 chunk 44 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS B 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.043975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.032449 restraints weight = 78861.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.033391 restraints weight = 56429.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.033985 restraints weight = 43859.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.034235 restraints weight = 36481.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.034519 restraints weight = 33057.765| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9490 Z= 0.149 Angle : 0.601 8.896 12906 Z= 0.301 Chirality : 0.044 0.139 1478 Planarity : 0.004 0.051 1606 Dihedral : 12.024 177.997 1564 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.02 % Allowed : 11.08 % Favored : 87.91 % 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 aren not related in a simple way. whole: -0.15 (0.25), residues: 1182 helix: 1.06 (0.26), residues: 406 sheet: -0.83 (0.34), residues: 246 loop : -0.54 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 78 TYR 0.016 0.001 TYR B 91 PHE 0.029 0.002 PHE B 304 TRP 0.011 0.001 TRP B 183 HIS 0.005 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9486) covalent geometry : angle 0.60121 (12898) SS BOND : bond 0.00318 ( 4) SS BOND : angle 0.58301 ( 8) hydrogen bonds : bond 0.03465 ( 412) hydrogen bonds : angle 5.43893 ( 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 72 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 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: 0.9246 (mm) cc_final: 0.8582 (tp) REVERT: B 100 ILE cc_start: 0.9602 (pt) cc_final: 0.9280 (pt) REVERT: B 103 GLU cc_start: 0.9468 (tp30) cc_final: 0.9215 (pt0) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.0916 time to fit residues: 9.6585 Evaluate side-chains 58 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 92 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 156 ASN A 173 HIS A 422 GLN A 435 ASN A 468 ASN B 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.041194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.029985 restraints weight = 83286.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.030840 restraints weight = 58851.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.031408 restraints weight = 45651.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.031793 restraints weight = 38326.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.032025 restraints weight = 33962.499| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 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 = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9490 Z= 0.258 Angle : 0.695 11.424 12906 Z= 0.353 Chirality : 0.045 0.151 1478 Planarity : 0.005 0.050 1606 Dihedral : 11.677 177.906 1564 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.13 % Allowed : 12.50 % Favored : 85.37 % 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 aren not related in a simple way. whole: -0.40 (0.25), residues: 1182 helix: 0.81 (0.26), residues: 406 sheet: -0.99 (0.32), residues: 246 loop : -0.63 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 78 TYR 0.022 0.002 TYR A 91 PHE 0.037 0.002 PHE B 304 TRP 0.013 0.001 TRP B 183 HIS 0.006 0.002 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 9486) covalent geometry : angle 0.69471 (12898) SS BOND : bond 0.00593 ( 4) SS BOND : angle 0.75831 ( 8) hydrogen bonds : bond 0.03820 ( 412) hydrogen bonds : angle 5.61164 ( 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: 21 poor density : 59 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.8603 (t-100) cc_final: 0.8330 (t-100) REVERT: B 100 ILE cc_start: 0.9619 (pt) cc_final: 0.9221 (pt) REVERT: B 103 GLU cc_start: 0.9506 (tp30) cc_final: 0.9235 (pt0) REVERT: B 486 GLU cc_start: 0.8358 (pt0) cc_final: 0.8112 (pt0) REVERT: B 557 MET cc_start: 0.9508 (ppp) cc_final: 0.9271 (ppp) outliers start: 21 outliers final: 15 residues processed: 75 average time/residue: 0.0796 time to fit residues: 9.0930 Evaluate side-chains 68 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 173 HIS Chi-restraints excluded: chain A residue 255 LEU 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: 7.9990 chunk 114 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3419 r_free = 0.3419 target = 0.042285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.030912 restraints weight = 82001.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.031861 restraints weight = 56953.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.032463 restraints weight = 43334.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.032859 restraints weight = 36806.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.033025 restraints weight = 32662.520| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2748 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= 0.144 Angle : 0.610 9.665 12906 Z= 0.307 Chirality : 0.044 0.180 1478 Planarity : 0.004 0.052 1606 Dihedral : 11.334 176.477 1564 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.63 % Allowed : 14.43 % Favored : 83.94 % 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 aren not related in a simple way. whole: -0.35 (0.25), residues: 1182 helix: 0.85 (0.25), residues: 406 sheet: -0.88 (0.33), residues: 240 loop : -0.66 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.037 0.001 TYR A 91 PHE 0.034 0.002 PHE B 304 TRP 0.008 0.001 TRP B 183 HIS 0.012 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9486) covalent geometry : angle 0.61010 (12898) SS BOND : bond 0.00299 ( 4) SS BOND : angle 0.82201 ( 8) hydrogen bonds : bond 0.03459 ( 412) hydrogen bonds : angle 5.41314 ( 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 72 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.279 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: 0.8557 (t-100) cc_final: 0.8303 (t-100) REVERT: B 23 PHE cc_start: 0.9499 (m-80) cc_final: 0.9255 (t80) REVERT: B 103 GLU cc_start: 0.9528 (tp30) cc_final: 0.9248 (pt0) REVERT: B 557 MET cc_start: 0.9451 (ppp) cc_final: 0.9159 (ppp) outliers start: 16 outliers final: 8 residues processed: 68 average time/residue: 0.0777 time to fit residues: 7.9919 Evaluate side-chains 64 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 210 TRP 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: 9.9990 chunk 103 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 173 HIS A 435 ASN B 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.040009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.028848 restraints weight = 84841.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.029676 restraints weight = 59569.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.030175 restraints weight = 46135.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.030551 restraints weight = 39224.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.030725 restraints weight = 34976.191| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 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 = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 9490 Z= 0.324 Angle : 0.765 12.444 12906 Z= 0.391 Chirality : 0.046 0.156 1478 Planarity : 0.005 0.050 1606 Dihedral : 11.332 176.199 1564 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.34 % Allowed : 14.94 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.74 (0.25), residues: 1182 helix: 0.50 (0.25), residues: 410 sheet: -1.07 (0.32), residues: 244 loop : -0.89 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 229 TYR 0.041 0.003 TYR A 91 PHE 0.031 0.003 PHE B 304 TRP 0.012 0.002 TRP B 194 HIS 0.008 0.002 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00648 ( 9486) covalent geometry : angle 0.76521 (12898) SS BOND : bond 0.00596 ( 4) SS BOND : angle 0.80403 ( 8) hydrogen bonds : bond 0.04100 ( 412) hydrogen bonds : angle 5.88694 ( 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 77 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.8626 (t-100) cc_final: 0.8397 (t-100) REVERT: B 23 PHE cc_start: 0.9436 (m-80) cc_final: 0.9179 (t80) REVERT: B 103 GLU cc_start: 0.9548 (tp30) cc_final: 0.9196 (pt0) REVERT: B 328 MET cc_start: 0.9493 (mtt) cc_final: 0.9280 (mtt) REVERT: B 486 GLU cc_start: 0.8295 (pt0) cc_final: 0.7930 (pt0) outliers start: 23 outliers final: 15 residues processed: 74 average time/residue: 0.0810 time to fit residues: 8.9514 Evaluate side-chains 66 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 255 LEU Chi-restraints excluded: chain A residue 370 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 0.1980 chunk 85 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 435 ASN B 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.041909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.030293 restraints weight = 90733.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.031184 restraints weight = 61325.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.031876 restraints weight = 47088.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.032297 restraints weight = 38644.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.032492 restraints weight = 33990.143| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 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 = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9490 Z= 0.129 Angle : 0.640 10.634 12906 Z= 0.320 Chirality : 0.046 0.289 1478 Planarity : 0.004 0.052 1606 Dihedral : 11.106 175.014 1564 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.63 % Allowed : 16.67 % 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 aren not related in a simple way. whole: -0.41 (0.25), residues: 1182 helix: 0.84 (0.25), residues: 408 sheet: -0.88 (0.33), residues: 240 loop : -0.76 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.039 0.002 TYR A 91 PHE 0.035 0.002 PHE B 578 TRP 0.009 0.001 TRP A 194 HIS 0.006 0.001 HIS B 502 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9486) covalent geometry : angle 0.63867 (12898) SS BOND : bond 0.00280 ( 4) SS BOND : angle 1.69911 ( 8) hydrogen bonds : bond 0.03474 ( 412) hydrogen bonds : angle 5.52650 ( 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 74 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.8609 (t-100) cc_final: 0.8360 (t-100) REVERT: B 486 GLU cc_start: 0.8364 (pt0) cc_final: 0.7985 (pt0) outliers start: 16 outliers final: 11 residues processed: 70 average time/residue: 0.0886 time to fit residues: 9.0824 Evaluate side-chains 65 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 210 TRP Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 584 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 5 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.041657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.030419 restraints weight = 80128.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.031309 restraints weight = 56628.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.031873 restraints weight = 44097.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.032323 restraints weight = 37089.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.032477 restraints weight = 32736.869| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9490 Z= 0.139 Angle : 0.629 10.578 12906 Z= 0.317 Chirality : 0.045 0.194 1478 Planarity : 0.004 0.052 1606 Dihedral : 10.969 175.193 1564 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.22 % Allowed : 17.38 % Favored : 81.40 % 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 aren not related in a simple way. whole: -0.36 (0.25), residues: 1182 helix: 0.83 (0.25), residues: 408 sheet: -0.81 (0.33), residues: 240 loop : -0.70 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.038 0.002 TYR A 91 PHE 0.027 0.002 PHE B 578 TRP 0.012 0.001 TRP A 10 HIS 0.005 0.001 HIS B 502 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9486) covalent geometry : angle 0.62803 (12898) SS BOND : bond 0.00242 ( 4) SS BOND : angle 1.62815 ( 8) hydrogen bonds : bond 0.03444 ( 412) hydrogen bonds : angle 5.45048 ( 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 67 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.8534 (t-100) cc_final: 0.8312 (t-100) REVERT: B 23 PHE cc_start: 0.9517 (m-80) cc_final: 0.9267 (t80) outliers start: 12 outliers final: 10 residues processed: 63 average time/residue: 0.0756 time to fit residues: 7.3638 Evaluate side-chains 63 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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 210 TRP Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 584 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.042161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.030812 restraints weight = 80684.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.031686 restraints weight = 56514.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.032338 restraints weight = 43589.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.032735 restraints weight = 36368.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.032940 restraints weight = 32113.402| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 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 = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9490 Z= 0.125 Angle : 0.631 10.562 12906 Z= 0.321 Chirality : 0.046 0.205 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.901 175.651 1564 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.42 % Allowed : 17.99 % Favored : 80.59 % 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 aren not related in a simple way. whole: -0.30 (0.25), residues: 1182 helix: 0.87 (0.25), residues: 408 sheet: -0.75 (0.33), residues: 240 loop : -0.68 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.041 0.001 TYR A 91 PHE 0.026 0.002 PHE B 578 TRP 0.010 0.001 TRP A 10 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9486) covalent geometry : angle 0.63003 (12898) SS BOND : bond 0.00178 ( 4) SS BOND : angle 1.35010 ( 8) hydrogen bonds : bond 0.03455 ( 412) hydrogen bonds : angle 5.45564 ( 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 67 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 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 210 TRP cc_start: 0.8532 (t-100) cc_final: 0.8299 (t-100) REVERT: B 23 PHE cc_start: 0.9508 (m-80) cc_final: 0.9260 (t80) outliers start: 14 outliers final: 10 residues processed: 63 average time/residue: 0.0850 time to fit residues: 8.1530 Evaluate side-chains 63 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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 210 TRP Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 584 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 72 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.041655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.030474 restraints weight = 83931.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.031322 restraints weight = 57922.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.031930 restraints weight = 45268.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.032317 restraints weight = 37565.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.032454 restraints weight = 33477.825| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9490 Z= 0.151 Angle : 0.642 10.699 12906 Z= 0.325 Chirality : 0.046 0.292 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.858 176.085 1564 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.22 % Allowed : 18.29 % Favored : 80.49 % 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 aren not related in a simple way. whole: -0.28 (0.25), residues: 1182 helix: 0.86 (0.25), residues: 408 sheet: -0.72 (0.33), residues: 240 loop : -0.66 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.042 0.001 TYR A 91 PHE 0.025 0.002 PHE A 304 TRP 0.008 0.001 TRP B 183 HIS 0.004 0.001 HIS B 502 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9486) covalent geometry : angle 0.64122 (12898) SS BOND : bond 0.00262 ( 4) SS BOND : angle 1.26199 ( 8) hydrogen bonds : bond 0.03460 ( 412) hydrogen bonds : angle 5.51393 ( 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 66 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.8577 (t-100) cc_final: 0.8335 (t-100) REVERT: B 23 PHE cc_start: 0.9521 (m-80) cc_final: 0.9280 (t80) outliers start: 12 outliers final: 9 residues processed: 62 average time/residue: 0.0848 time to fit residues: 7.9889 Evaluate side-chains 63 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 210 TRP Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.042206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.030911 restraints weight = 79157.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.031781 restraints weight = 57408.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.032302 restraints weight = 44625.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.032743 restraints weight = 37597.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.033044 restraints weight = 33274.716| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 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 = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9490 Z= 0.127 Angle : 0.634 10.839 12906 Z= 0.319 Chirality : 0.046 0.281 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.752 176.295 1564 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.02 % Allowed : 18.29 % Favored : 80.69 % 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 aren not related in a simple way. whole: -0.20 (0.25), residues: 1182 helix: 0.86 (0.25), residues: 408 sheet: -0.67 (0.33), residues: 240 loop : -0.55 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.042 0.001 TYR A 91 PHE 0.023 0.002 PHE A 304 TRP 0.009 0.001 TRP A 10 HIS 0.004 0.001 HIS B 502 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9486) covalent geometry : angle 0.63326 (12898) SS BOND : bond 0.00184 ( 4) SS BOND : angle 1.15339 ( 8) hydrogen bonds : bond 0.03390 ( 412) hydrogen bonds : angle 5.41807 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.34 seconds wall clock time: 33 minutes 53.88 seconds (2033.88 seconds total)