Starting phenix.real_space_refine on Sun Jun 8 13:20:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1r_15084/06_2025/8a1r_15084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1r_15084/06_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_15084/06_2025/8a1r_15084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1r_15084/06_2025/8a1r_15084.map" model { file = "/net/cci-nas-00/data/ceres_data/8a1r_15084/06_2025/8a1r_15084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1r_15084/06_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-5710/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: 6.46, per 1000 atoms: 0.70 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: 2.51 Conformation dependent library (CDL) restraints added in 1.1 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: 1.85 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: 3.47 Time building geometry restraints manager: 2.86 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: 1.580 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.130 Find NCS groups from input model: 0.460 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: 0.000 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- 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 : 11.72 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 Details of bonding type rmsd hydrogen bonds : bond 0.15107 ( 412) hydrogen bonds : angle 7.12871 ( 1176) SS BOND : bond 0.00225 ( 4) SS BOND : angle 0.69178 ( 8) covalent geometry : bond 0.01087 ( 9486) covalent geometry : angle 0.85938 (12898) *********************** 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 : 1.242 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: 0.2942 time to fit residues: 38.5472 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 : 1.139 ------------------------------------------------------------------------------- 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 9490 Z= 0.251 Angle : 0.692 10.589 12906 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 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 412) hydrogen bonds : angle 5.89217 ( 1176) SS BOND : bond 0.00444 ( 4) SS BOND : angle 0.60039 ( 8) covalent geometry : bond 0.00513 ( 9486) covalent geometry : angle 0.69186 (12898) *********************** 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 : 1.054 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: 0.2508 time to fit residues: 27.3045 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 : 1.279 ------------------------------------------------------------------------------- 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: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.042514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.031106 restraints weight = 84342.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.031999 restraints weight = 59524.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.032487 restraints weight = 46055.975| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 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 = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9490 Z= 0.180 Angle : 0.638 9.060 12906 Z= 0.320 Chirality : 0.044 0.139 1478 Planarity : 0.004 0.052 1606 Dihedral : 12.045 176.845 1564 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.63 % Allowed : 11.69 % Favored : 86.69 % 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: -0.30 (0.25), residues: 1182 helix: 0.93 (0.25), residues: 406 sheet: -1.08 (0.34), residues: 236 loop : -0.55 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 183 HIS 0.005 0.001 HIS A 502 PHE 0.032 0.002 PHE B 304 TYR 0.021 0.001 TYR B 91 ARG 0.004 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 412) hydrogen bonds : angle 5.61757 ( 1176) SS BOND : bond 0.00208 ( 4) SS BOND : angle 0.82596 ( 8) covalent geometry : bond 0.00378 ( 9486) covalent geometry : angle 0.63751 (12898) *********************** 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 : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 MET cc_start: 0.9370 (mpp) cc_final: 0.8983 (mpp) REVERT: B 557 MET cc_start: 0.9490 (ppp) cc_final: 0.8866 (ppp) outliers start: 16 outliers final: 12 residues processed: 74 average time/residue: 0.2847 time to fit residues: 30.5844 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 : 1.369 ------------------------------------------------------------------------------- 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: 0.8980 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 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 = 0.3412 r_free = 0.3412 target = 0.042130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.030825 restraints weight = 83584.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.031754 restraints weight = 59439.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.032263 restraints weight = 45523.170| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- 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 = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9490 Z= 0.170 Angle : 0.623 9.457 12906 Z= 0.315 Chirality : 0.044 0.136 1478 Planarity : 0.004 0.052 1606 Dihedral : 11.685 176.358 1564 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.52 % Allowed : 13.92 % Favored : 84.55 % 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: 0.90 (0.26), residues: 406 sheet: -1.01 (0.34), residues: 234 loop : -0.57 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.012 0.001 HIS A 173 PHE 0.041 0.002 PHE B 304 TYR 0.013 0.001 TYR B 296 ARG 0.003 0.000 ARG A 414 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 412) hydrogen bonds : angle 5.52417 ( 1176) SS BOND : bond 0.00356 ( 4) SS BOND : angle 0.79907 ( 8) covalent geometry : bond 0.00358 ( 9486) covalent geometry : angle 0.62272 (12898) *********************** 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 72 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 MET cc_start: 0.9393 (mpp) cc_final: 0.8998 (mpp) REVERT: B 486 GLU cc_start: 0.8381 (pt0) cc_final: 0.8175 (pt0) REVERT: B 522 MET cc_start: 0.7602 (mtp) cc_final: 0.7052 (ttm) REVERT: B 557 MET cc_start: 0.9503 (ppp) cc_final: 0.9163 (ppp) outliers start: 15 outliers final: 11 residues processed: 69 average time/residue: 0.1997 time to fit residues: 20.6306 Evaluate side-chains 66 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 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 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: 10.0000 chunk 72 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 25 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 overall best weight: 1.0560 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.042586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.031177 restraints weight = 82580.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.032053 restraints weight = 57153.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.032660 restraints weight = 44469.810| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 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 = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9490 Z= 0.131 Angle : 0.598 9.639 12906 Z= 0.300 Chirality : 0.044 0.144 1478 Planarity : 0.004 0.053 1606 Dihedral : 11.377 175.650 1564 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.73 % Allowed : 14.23 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.23 (0.25), residues: 1182 helix: 0.96 (0.26), residues: 406 sheet: -0.77 (0.33), residues: 240 loop : -0.63 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.004 0.001 HIS A 339 PHE 0.041 0.002 PHE B 304 TYR 0.039 0.001 TYR A 91 ARG 0.004 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 412) hydrogen bonds : angle 5.35387 ( 1176) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.80505 ( 8) covalent geometry : bond 0.00285 ( 9486) covalent geometry : angle 0.59810 (12898) *********************** 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 77 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.9589 (p0) cc_final: 0.9002 (m-30) REVERT: B 23 PHE cc_start: 0.9529 (m-80) cc_final: 0.9280 (t80) REVERT: B 103 GLU cc_start: 0.9524 (tp30) cc_final: 0.9255 (pt0) REVERT: B 336 MET cc_start: 0.9392 (mpp) cc_final: 0.9015 (mpp) REVERT: B 557 MET cc_start: 0.9469 (ppp) cc_final: 0.8959 (ppp) outliers start: 17 outliers final: 11 residues processed: 72 average time/residue: 0.2025 time to fit residues: 22.0159 Evaluate side-chains 69 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 255 LEU 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 321 LEU Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.042905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.031396 restraints weight = 80516.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.032355 restraints weight = 56223.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.032978 restraints weight = 43630.005| |-----------------------------------------------------------------------------| 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 = 0.24 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 = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2788 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= 0.123 Angle : 0.596 9.522 12906 Z= 0.299 Chirality : 0.044 0.167 1478 Planarity : 0.004 0.053 1606 Dihedral : 11.191 175.568 1564 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.03 % Allowed : 14.84 % Favored : 83.13 % 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: 1.01 (0.26), residues: 406 sheet: -0.76 (0.33), residues: 240 loop : -0.58 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.004 0.001 HIS A 339 PHE 0.041 0.002 PHE B 304 TYR 0.036 0.001 TYR A 91 ARG 0.003 0.000 ARG A 414 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 412) hydrogen bonds : angle 5.28580 ( 1176) SS BOND : bond 0.00249 ( 4) SS BOND : angle 1.60903 ( 8) covalent geometry : bond 0.00270 ( 9486) covalent geometry : angle 0.59510 (12898) *********************** 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: 20 poor density : 59 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.9544 (p0) cc_final: 0.8921 (m-30) REVERT: B 103 GLU cc_start: 0.9553 (tp30) cc_final: 0.9264 (pt0) REVERT: B 336 MET cc_start: 0.9354 (mpp) cc_final: 0.8994 (mpp) REVERT: B 486 GLU cc_start: 0.8418 (pt0) cc_final: 0.8168 (pt0) REVERT: B 557 MET cc_start: 0.9427 (ppp) cc_final: 0.8822 (ppp) outliers start: 20 outliers final: 13 residues processed: 75 average time/residue: 0.1977 time to fit residues: 22.3447 Evaluate side-chains 70 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 555 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.042679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.031192 restraints weight = 81459.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.032144 restraints weight = 56530.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.032765 restraints weight = 43948.823| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 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 = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9490 Z= 0.131 Angle : 0.615 10.565 12906 Z= 0.306 Chirality : 0.044 0.175 1478 Planarity : 0.004 0.053 1606 Dihedral : 11.045 175.539 1564 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.52 % Allowed : 15.96 % Favored : 82.52 % 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: 0.99 (0.25), residues: 408 sheet: -0.76 (0.33), residues: 240 loop : -0.57 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 210 HIS 0.004 0.001 HIS A 339 PHE 0.039 0.002 PHE B 304 TYR 0.036 0.001 TYR A 91 ARG 0.003 0.000 ARG A 414 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 412) hydrogen bonds : angle 5.29678 ( 1176) SS BOND : bond 0.00258 ( 4) SS BOND : angle 1.48123 ( 8) covalent geometry : bond 0.00284 ( 9486) covalent geometry : angle 0.61402 (12898) *********************** 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 72 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.9466 (m-80) cc_final: 0.9232 (t80) REVERT: B 103 GLU cc_start: 0.9567 (tp30) cc_final: 0.9263 (pt0) REVERT: B 336 MET cc_start: 0.9354 (OUTLIER) cc_final: 0.9019 (mpp) REVERT: B 557 MET cc_start: 0.9420 (ppp) cc_final: 0.9016 (ppp) outliers start: 15 outliers final: 12 residues processed: 68 average time/residue: 0.1951 time to fit residues: 19.8838 Evaluate side-chains 70 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 159 CYS 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 47 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 336 MET 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: 1.9990 chunk 50 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.042065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.030734 restraints weight = 80690.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.031604 restraints weight = 57866.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.032215 restraints weight = 44794.079| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 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 = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9490 Z= 0.154 Angle : 0.617 10.340 12906 Z= 0.310 Chirality : 0.044 0.254 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.966 175.571 1564 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.52 % Allowed : 16.67 % Favored : 81.81 % 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: 0.98 (0.26), residues: 408 sheet: -0.79 (0.33), residues: 240 loop : -0.53 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 10 HIS 0.006 0.001 HIS B 166 PHE 0.043 0.002 PHE B 304 TYR 0.036 0.001 TYR A 91 ARG 0.003 0.000 ARG A 414 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 412) hydrogen bonds : angle 5.35278 ( 1176) SS BOND : bond 0.00300 ( 4) SS BOND : angle 1.11680 ( 8) covalent geometry : bond 0.00326 ( 9486) covalent geometry : angle 0.61684 (12898) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 1.174 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 23 PHE cc_start: 0.9488 (m-80) cc_final: 0.9266 (t80) REVERT: B 336 MET cc_start: 0.9355 (mpp) cc_final: 0.9018 (mpp) REVERT: B 557 MET cc_start: 0.9426 (ppp) cc_final: 0.9140 (ppp) outliers start: 15 outliers final: 13 residues processed: 72 average time/residue: 0.2229 time to fit residues: 23.6028 Evaluate side-chains 69 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 159 CYS Chi-restraints excluded: chain A residue 255 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 321 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 0.0270 chunk 50 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.5844 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.041859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.030593 restraints weight = 80859.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.031382 restraints weight = 58217.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.032006 restraints weight = 45660.292| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 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 = 0.3124 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: 0.8700 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9490 Z= 0.157 Angle : 0.640 10.284 12906 Z= 0.320 Chirality : 0.045 0.229 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.951 175.211 1564 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.52 % Allowed : 17.38 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.25), residues: 1182 helix: 0.96 (0.26), residues: 404 sheet: -0.75 (0.33), residues: 240 loop : -0.54 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 10 HIS 0.004 0.001 HIS A 502 PHE 0.029 0.002 PHE B 304 TYR 0.037 0.001 TYR A 91 ARG 0.005 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 412) hydrogen bonds : angle 5.35680 ( 1176) SS BOND : bond 0.00423 ( 4) SS BOND : angle 1.32619 ( 8) covalent geometry : bond 0.00334 ( 9486) covalent geometry : angle 0.63932 (12898) *********************** 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 73 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9456 (mm) REVERT: B 10 TRP cc_start: 0.8914 (m-10) cc_final: 0.8582 (m-10) REVERT: B 23 PHE cc_start: 0.9506 (m-80) cc_final: 0.9283 (t80) REVERT: B 336 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.9058 (mpp) REVERT: B 557 MET cc_start: 0.9430 (ppp) cc_final: 0.9158 (ppp) outliers start: 15 outliers final: 12 residues processed: 69 average time/residue: 0.2061 time to fit residues: 21.1345 Evaluate side-chains 71 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 159 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 305 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 321 LEU Chi-restraints excluded: chain B residue 336 MET 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 101 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 chunk 56 optimal weight: 0.0870 chunk 99 optimal weight: 0.0370 chunk 81 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.043053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.031485 restraints weight = 80219.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.032410 restraints weight = 56776.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.033020 restraints weight = 44361.953| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3268 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= 0.115 Angle : 0.643 10.845 12906 Z= 0.318 Chirality : 0.045 0.248 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.851 175.073 1564 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.52 % Allowed : 17.58 % Favored : 80.89 % 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: -0.12 (0.25), residues: 1182 helix: 0.93 (0.25), residues: 404 sheet: -0.63 (0.33), residues: 236 loop : -0.49 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 10 HIS 0.004 0.001 HIS A 502 PHE 0.075 0.002 PHE B 304 TYR 0.037 0.001 TYR A 91 ARG 0.002 0.000 ARG A 414 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 412) hydrogen bonds : angle 5.34678 ( 1176) SS BOND : bond 0.00216 ( 4) SS BOND : angle 0.99185 ( 8) covalent geometry : bond 0.00251 ( 9486) covalent geometry : angle 0.64313 (12898) ********************** 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 76 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.9444 (p0) cc_final: 0.8711 (m-30) REVERT: A 305 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9462 (mm) REVERT: A 336 MET cc_start: 0.9113 (mmm) cc_final: 0.8474 (mpp) REVERT: B 10 TRP cc_start: 0.8818 (m-10) cc_final: 0.8485 (m-10) REVERT: B 23 PHE cc_start: 0.9499 (m-80) cc_final: 0.9287 (t80) REVERT: B 50 LEU cc_start: 0.9006 (mp) cc_final: 0.8690 (mp) REVERT: B 336 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.8999 (mpp) REVERT: B 557 MET cc_start: 0.9369 (ppp) cc_final: 0.8976 (ppp) outliers start: 15 outliers final: 12 residues processed: 72 average time/residue: 0.2134 time to fit residues: 22.4792 Evaluate side-chains 72 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 255 LEU Chi-restraints excluded: chain A residue 305 LEU 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 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.042020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.030795 restraints weight = 81422.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.031657 restraints weight = 57601.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.032234 restraints weight = 44959.154| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 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 = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9490 Z= 0.156 Angle : 0.652 10.597 12906 Z= 0.326 Chirality : 0.045 0.319 1478 Planarity : 0.004 0.053 1606 Dihedral : 10.826 174.775 1564 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.63 % Allowed : 17.89 % Favored : 80.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.25), residues: 1182 helix: 0.88 (0.26), residues: 404 sheet: -0.58 (0.33), residues: 236 loop : -0.51 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 183 HIS 0.004 0.001 HIS A 339 PHE 0.057 0.002 PHE B 304 TYR 0.040 0.001 TYR A 91 ARG 0.004 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 412) hydrogen bonds : angle 5.43418 ( 1176) SS BOND : bond 0.00369 ( 4) SS BOND : angle 1.01359 ( 8) covalent geometry : bond 0.00333 ( 9486) covalent geometry : angle 0.65125 (12898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3747.89 seconds wall clock time: 66 minutes 13.13 seconds (3973.13 seconds total)