Starting phenix.real_space_refine on Fri Mar 14 05:34:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1r_15084/03_2025/8a1r_15084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1r_15084/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8a1r_15084/03_2025/8a1r_15084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1r_15084/03_2025/8a1r_15084.map" model { file = "/net/cci-nas-00/data/ceres_data/8a1r_15084/03_2025/8a1r_15084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1r_15084/03_2025/8a1r_15084.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.29, per 1000 atoms: 0.68 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: 2.32 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.74 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: 3.81 Time building geometry restraints manager: 2.78 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 598 or resid 601)) selection = (chain 'B' and (resid 6 through 598 or resid 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: 1.730 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.860 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.190 ------------------------------------------------------------------------------- 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 9486 Z= 0.767 Angle : 0.859 23.517 12898 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 : 11.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 194 HIS 0.005 0.001 HIS A 502 PHE 0.017 0.002 PHE B 578 TYR 0.017 0.001 TYR B 429 ARG 0.005 0.000 ARG B 78 *********************** 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 : 2.911 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: 0.4544 time to fit residues: 60.4104 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 : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 0.0570 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 overall best weight: 2.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS A 435 ASN B 225 ASN B 468 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.042607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.031140 restraints weight = 81961.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.032039 restraints weight = 57454.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.032549 restraints weight = 45041.613| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9486 Z= 0.334 Angle : 0.692 10.589 12898 Z= 0.352 Chirality : 0.046 0.153 1478 Planarity : 0.005 0.050 1606 Dihedral : 12.473 176.764 1564 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.91 % Allowed : 8.33 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1182 helix: 1.10 (0.25), residues: 404 sheet: -1.08 (0.34), residues: 236 loop : -0.61 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 183 HIS 0.006 0.001 HIS A 502 PHE 0.025 0.002 PHE A 304 TYR 0.021 0.002 TYR B 91 ARG 0.004 0.001 ARG B 78 *********************** 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: 9 poor density : 69 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.7783 (mtp) cc_final: 0.7449 (ttm) REVERT: B 336 MET cc_start: 0.9363 (mpp) cc_final: 0.8974 (mpp) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.2588 time to fit residues: 28.1157 Evaluate side-chains 60 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 47 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 24 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 435 ASN B 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.042287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.030908 restraints weight = 84984.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.031808 restraints weight = 59397.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.032335 restraints weight = 45211.279| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9486 Z= 0.260 Angle : 0.643 9.329 12898 Z= 0.324 Chirality : 0.044 0.146 1478 Planarity : 0.004 0.052 1606 Dihedral : 12.042 176.788 1564 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.63 % Allowed : 11.79 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.25), residues: 1182 helix: 0.91 (0.25), residues: 406 sheet: -1.09 (0.34), residues: 236 loop : -0.56 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 183 HIS 0.006 0.002 HIS B 166 PHE 0.028 0.002 PHE B 304 TYR 0.021 0.002 TYR B 91 ARG 0.005 0.001 ARG A 78 *********************** 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 77 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 MET cc_start: 0.9369 (mpp) cc_final: 0.9018 (mpp) REVERT: B 557 MET cc_start: 0.9507 (ppp) cc_final: 0.8933 (ppp) outliers start: 16 outliers final: 12 residues processed: 74 average time/residue: 0.2285 time to fit residues: 24.1957 Evaluate side-chains 68 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 62 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.041906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.030702 restraints weight = 83966.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.031584 restraints weight = 56775.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.032117 restraints weight = 44563.245| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 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 = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9486 Z= 0.244 Angle : 0.625 9.906 12898 Z= 0.315 Chirality : 0.044 0.134 1478 Planarity : 0.004 0.052 1606 Dihedral : 11.685 176.238 1564 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.83 % Allowed : 13.92 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1182 helix: 0.87 (0.25), residues: 406 sheet: -1.03 (0.33), residues: 234 loop : -0.63 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.010 0.002 HIS A 173 PHE 0.039 0.002 PHE B 304 TYR 0.013 0.001 TYR B 296 ARG 0.003 0.000 ARG A 78 *********************** 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 76 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 336 MET cc_start: 0.9382 (mpp) cc_final: 0.9020 (mpp) REVERT: B 486 GLU cc_start: 0.8376 (pt0) cc_final: 0.8155 (pt0) REVERT: B 522 MET cc_start: 0.7679 (mtp) cc_final: 0.7015 (ttm) REVERT: B 557 MET cc_start: 0.9522 (ppp) cc_final: 0.9071 (ppp) outliers start: 18 outliers final: 13 residues processed: 72 average time/residue: 0.2782 time to fit residues: 29.6843 Evaluate side-chains 67 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 1.583 ------------------------------------------------------------------------------- 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 255 LEU 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 42 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.042028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.030712 restraints weight = 82497.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.031527 restraints weight = 57527.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.032002 restraints weight = 44889.105| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- 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 = 0.24 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 = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9486 Z= 0.213 Angle : 0.614 8.906 12898 Z= 0.309 Chirality : 0.044 0.146 1478 Planarity : 0.004 0.053 1606 Dihedral : 11.404 175.644 1564 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.83 % Allowed : 14.33 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.25), residues: 1182 helix: 0.92 (0.25), residues: 406 sheet: -0.80 (0.33), residues: 240 loop : -0.69 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 183 HIS 0.005 0.001 HIS A 339 PHE 0.038 0.002 PHE B 304 TYR 0.038 0.001 TYR A 91 ARG 0.003 0.000 ARG A 414 *********************** 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 76 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.9614 (p0) cc_final: 0.9031 (m-30) REVERT: B 23 PHE cc_start: 0.9505 (m-80) cc_final: 0.9226 (t80) REVERT: B 103 GLU cc_start: 0.9525 (tp30) cc_final: 0.9251 (pt0) REVERT: B 336 MET cc_start: 0.9392 (mpp) cc_final: 0.9004 (mpp) REVERT: B 557 MET cc_start: 0.9474 (ppp) cc_final: 0.9160 (ppp) outliers start: 18 outliers final: 12 residues processed: 70 average time/residue: 0.2254 time to fit residues: 24.0036 Evaluate side-chains 68 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 255 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 555 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.041696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.030312 restraints weight = 86013.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.031209 restraints weight = 60604.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.031793 restraints weight = 46564.563| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 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 = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9486 Z= 0.230 Angle : 0.618 9.781 12898 Z= 0.312 Chirality : 0.045 0.172 1478 Planarity : 0.004 0.053 1606 Dihedral : 11.213 175.190 1564 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.13 % Allowed : 15.04 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1182 helix: 0.91 (0.26), residues: 406 sheet: -0.83 (0.33), residues: 240 loop : -0.68 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 183 HIS 0.005 0.001 HIS A 339 PHE 0.027 0.002 PHE B 304 TYR 0.037 0.002 TYR A 91 ARG 0.003 0.000 ARG A 414 *********************** 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 79 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 GLU cc_start: 0.9563 (tp30) cc_final: 0.9254 (pt0) REVERT: B 336 MET cc_start: 0.9368 (mpp) cc_final: 0.9027 (mpp) REVERT: B 557 MET cc_start: 0.9459 (ppp) cc_final: 0.9206 (ppp) outliers start: 21 outliers final: 16 residues processed: 74 average time/residue: 0.1900 time to fit residues: 21.1240 Evaluate side-chains 71 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 555 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 321 LEU 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 24 optimal weight: 10.0000 chunk 56 optimal weight: 0.0980 chunk 67 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.040245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.028853 restraints weight = 87616.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.029720 restraints weight = 60908.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.030318 restraints weight = 46814.464| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9486 Z= 0.346 Angle : 0.718 11.067 12898 Z= 0.366 Chirality : 0.046 0.202 1478 Planarity : 0.005 0.051 1606 Dihedral : 11.223 175.205 1564 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.44 % Allowed : 16.36 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1182 helix: 0.61 (0.25), residues: 410 sheet: -0.98 (0.32), residues: 242 loop : -0.80 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 194 HIS 0.006 0.002 HIS A 339 PHE 0.018 0.002 PHE B 304 TYR 0.037 0.002 TYR A 91 ARG 0.003 0.001 ARG B 322 *********************** 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 79 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.9449 (m-80) cc_final: 0.9220 (t80) REVERT: B 336 MET cc_start: 0.9359 (mpp) cc_final: 0.9049 (mpp) REVERT: B 486 GLU cc_start: 0.8364 (pt0) cc_final: 0.8046 (pt0) outliers start: 24 outliers final: 16 residues processed: 73 average time/residue: 0.2137 time to fit residues: 23.4219 Evaluate side-chains 70 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 370 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 45 optimal weight: 0.0170 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.041789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.030407 restraints weight = 80937.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.031193 restraints weight = 56985.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.031748 restraints weight = 45288.681| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 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 = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9486 Z= 0.180 Angle : 0.624 10.489 12898 Z= 0.315 Chirality : 0.045 0.164 1478 Planarity : 0.004 0.052 1606 Dihedral : 11.030 173.778 1564 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.52 % Allowed : 17.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1182 helix: 0.84 (0.25), residues: 404 sheet: -0.85 (0.33), residues: 240 loop : -0.68 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 10 HIS 0.005 0.001 HIS B 502 PHE 0.020 0.002 PHE A 304 TYR 0.037 0.002 TYR A 91 ARG 0.003 0.000 ARG A 414 *********************** 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 74 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 1.022 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: B 10 TRP cc_start: 0.8887 (m-10) cc_final: 0.8554 (m-10) REVERT: B 23 PHE cc_start: 0.9494 (m-80) cc_final: 0.9261 (t80) REVERT: B 336 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9107 (mpp) outliers start: 15 outliers final: 11 residues processed: 70 average time/residue: 0.2107 time to fit residues: 21.6510 Evaluate side-chains 70 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 555 ILE 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 336 MET 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 49 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 82 optimal weight: 0.0050 chunk 117 optimal weight: 0.0060 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 overall best weight: 0.8014 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.042077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.030989 restraints weight = 78976.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.031788 restraints weight = 55530.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.032269 restraints weight = 43433.416| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9486 Z= 0.176 Angle : 0.645 10.980 12898 Z= 0.320 Chirality : 0.046 0.301 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.896 173.588 1564 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.63 % Allowed : 17.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1182 helix: 0.87 (0.26), residues: 404 sheet: -0.83 (0.33), residues: 240 loop : -0.61 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.004 0.001 HIS B 502 PHE 0.025 0.002 PHE A 304 TYR 0.038 0.001 TYR A 91 ARG 0.002 0.000 ARG A 414 *********************** 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 74 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 1.110 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: B 10 TRP cc_start: 0.8846 (m-10) cc_final: 0.8514 (m-10) REVERT: B 23 PHE cc_start: 0.9494 (m-80) cc_final: 0.9275 (t80) REVERT: B 50 LEU cc_start: 0.9026 (mp) cc_final: 0.8760 (mp) REVERT: B 336 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.9049 (mpp) outliers start: 16 outliers final: 13 residues processed: 68 average time/residue: 0.2158 time to fit residues: 21.5474 Evaluate side-chains 71 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 370 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 555 ILE 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 336 MET 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 101 optimal weight: 5.9990 chunk 39 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.042638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.031480 restraints weight = 79480.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.032216 restraints weight = 55770.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.032717 restraints weight = 44403.619| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 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 = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9486 Z= 0.161 Angle : 0.625 11.047 12898 Z= 0.311 Chirality : 0.045 0.256 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.755 173.898 1564 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1182 helix: 0.94 (0.26), residues: 404 sheet: -0.75 (0.33), residues: 240 loop : -0.53 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 210 HIS 0.004 0.001 HIS B 502 PHE 0.026 0.002 PHE A 304 TYR 0.039 0.001 TYR A 91 ARG 0.002 0.000 ARG A 414 ********************** 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 71 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 1.112 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: A 84 ASP cc_start: 0.9334 (p0) cc_final: 0.8570 (m-30) REVERT: A 557 MET cc_start: 0.9608 (pmm) cc_final: 0.8991 (pmm) REVERT: B 10 TRP cc_start: 0.8771 (m-10) cc_final: 0.8433 (m-10) REVERT: B 23 PHE cc_start: 0.9491 (m-80) cc_final: 0.9260 (t80) REVERT: B 50 LEU cc_start: 0.9012 (mp) cc_final: 0.8735 (mp) REVERT: B 336 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.9042 (mpp) outliers start: 12 outliers final: 11 residues processed: 68 average time/residue: 0.2159 time to fit residues: 21.5494 Evaluate side-chains 71 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 370 VAL Chi-restraints excluded: chain A residue 555 ILE 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 336 MET 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 26 optimal weight: 0.9990 chunk 111 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.042230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.031106 restraints weight = 80364.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.031938 restraints weight = 57026.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.032563 restraints weight = 44354.448| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 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 = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9486 Z= 0.177 Angle : 0.640 11.092 12898 Z= 0.317 Chirality : 0.045 0.245 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.715 173.860 1564 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.42 % Allowed : 18.19 % Favored : 80.39 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1182 helix: 0.98 (0.26), residues: 404 sheet: -0.70 (0.33), residues: 240 loop : -0.50 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.004 0.001 HIS A 502 PHE 0.050 0.002 PHE B 304 TYR 0.039 0.001 TYR A 91 ARG 0.002 0.000 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4110.62 seconds wall clock time: 73 minutes 49.00 seconds (4429.00 seconds total)