Starting phenix.real_space_refine on Tue Mar 3 23:44:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cui_27000/03_2026/8cui_27000.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cui_27000/03_2026/8cui_27000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cui_27000/03_2026/8cui_27000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cui_27000/03_2026/8cui_27000.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cui_27000/03_2026/8cui_27000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cui_27000/03_2026/8cui_27000.map" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 6132 2.51 5 N 1491 2.21 5 O 1671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9357 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3119 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 11, 'TRANS': 398} Chain breaks: 2 Restraints were copied for chains: B, C Time building chain proxies: 2.21, per 1000 atoms: 0.24 Number of scatterers: 9357 At special positions: 0 Unit cell: (108.204, 103.944, 75.828, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1671 8.00 N 1491 7.00 C 6132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 441 " distance=2.95 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 441 " distance=2.95 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 441 " distance=2.95 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 351.1 milliseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 84.6% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.678A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.624A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 removed outlier: 3.553A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.598A pdb=" N ILE A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.546A pdb=" N MET A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.743A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.772A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.790A pdb=" N VAL A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 284 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.860A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 removed outlier: 4.126A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 405 removed outlier: 3.967A pdb=" N SER A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 429 through 436 removed outlier: 4.165A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.942A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.778A pdb=" N ASP A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.679A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.624A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 removed outlier: 3.553A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 117 removed outlier: 3.598A pdb=" N ILE B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.547A pdb=" N MET B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 230 removed outlier: 3.743A pdb=" N GLY B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 removed outlier: 3.772A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.790A pdb=" N VAL B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.860A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 366 Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 removed outlier: 4.125A pdb=" N ALA B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 405 removed outlier: 3.967A pdb=" N SER B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.165A pdb=" N ASP B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR B 434 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.942A pdb=" N ARG B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 474 removed outlier: 3.778A pdb=" N ASP B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 42 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.677A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 66 removed outlier: 3.624A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 81 removed outlier: 3.553A pdb=" N LEU C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 117 removed outlier: 3.598A pdb=" N ILE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.546A pdb=" N MET C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 230 removed outlier: 3.744A pdb=" N GLY C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 removed outlier: 3.772A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.790A pdb=" N VAL C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 284 through 299 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.860A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 366 Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 removed outlier: 4.126A pdb=" N ALA C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 removed outlier: 3.966A pdb=" N SER C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 426 Processing helix chain 'C' and resid 429 through 436 removed outlier: 4.164A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR C 434 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.942A pdb=" N ARG C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 474 removed outlier: 3.778A pdb=" N ASP C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 732 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2925 1.34 - 1.46: 1778 1.46 - 1.58: 4675 1.58 - 1.70: 0 1.70 - 1.81: 117 Bond restraints: 9495 Sorted by residual: bond pdb=" N CYS B 269 " pdb=" CA CYS B 269 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.38e+00 bond pdb=" N CYS B 441 " pdb=" CA CYS B 441 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.33e+00 bond pdb=" N CYS A 441 " pdb=" CA CYS A 441 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.32e+00 bond pdb=" N CYS A 269 " pdb=" CA CYS A 269 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.95e+00 bond pdb=" N CYS C 441 " pdb=" CA CYS C 441 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 4.90e+00 ... (remaining 9490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 12679 1.71 - 3.42: 173 3.42 - 5.13: 30 5.13 - 6.84: 3 6.84 - 8.55: 3 Bond angle restraints: 12888 Sorted by residual: angle pdb=" CA CYS A 441 " pdb=" C CYS A 441 " pdb=" O CYS A 441 " ideal model delta sigma weight residual 120.90 118.22 2.68 1.07e+00 8.73e-01 6.27e+00 angle pdb=" CA CYS B 441 " pdb=" C CYS B 441 " pdb=" O CYS B 441 " ideal model delta sigma weight residual 120.82 118.20 2.62 1.05e+00 9.07e-01 6.23e+00 angle pdb=" CA CYS C 441 " pdb=" C CYS C 441 " pdb=" O CYS C 441 " ideal model delta sigma weight residual 120.90 118.25 2.65 1.07e+00 8.73e-01 6.13e+00 angle pdb=" CA LEU B 416 " pdb=" CB LEU B 416 " pdb=" CG LEU B 416 " ideal model delta sigma weight residual 116.30 124.85 -8.55 3.50e+00 8.16e-02 5.96e+00 angle pdb=" CA LEU C 416 " pdb=" CB LEU C 416 " pdb=" CG LEU C 416 " ideal model delta sigma weight residual 116.30 124.82 -8.52 3.50e+00 8.16e-02 5.93e+00 ... (remaining 12883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5028 17.90 - 35.79: 480 35.79 - 53.69: 147 53.69 - 71.58: 21 71.58 - 89.48: 9 Dihedral angle restraints: 5685 sinusoidal: 2160 harmonic: 3525 Sorted by residual: dihedral pdb=" CB CYS B 269 " pdb=" SG CYS B 269 " pdb=" SG CYS B 441 " pdb=" CB CYS B 441 " ideal model delta sinusoidal sigma weight residual -86.00 -17.09 -68.91 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS C 269 " pdb=" SG CYS C 269 " pdb=" SG CYS C 441 " pdb=" CB CYS C 441 " ideal model delta sinusoidal sigma weight residual -86.00 -17.11 -68.89 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CB CYS A 269 " pdb=" SG CYS A 269 " pdb=" SG CYS A 441 " pdb=" CB CYS A 441 " ideal model delta sinusoidal sigma weight residual -86.00 -17.12 -68.88 1 1.00e+01 1.00e-02 6.14e+01 ... (remaining 5682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1164 0.034 - 0.069: 355 0.069 - 0.103: 90 0.103 - 0.137: 22 0.137 - 0.172: 4 Chirality restraints: 1635 Sorted by residual: chirality pdb=" CA CYS B 441 " pdb=" N CYS B 441 " pdb=" C CYS B 441 " pdb=" CB CYS B 441 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA CYS A 441 " pdb=" N CYS A 441 " pdb=" C CYS A 441 " pdb=" CB CYS A 441 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA CYS C 441 " pdb=" N CYS C 441 " pdb=" C CYS C 441 " pdb=" CB CYS C 441 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1632 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 295 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C ILE C 295 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE C 295 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS C 296 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 295 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C ILE A 295 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 295 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS A 296 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 295 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C ILE B 295 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE B 295 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS B 296 " 0.010 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2140 2.79 - 3.32: 9133 3.32 - 3.85: 15322 3.85 - 4.37: 17103 4.37 - 4.90: 31050 Nonbonded interactions: 74748 Sorted by model distance: nonbonded pdb=" O GLY B 392 " pdb=" OG1 THR B 396 " model vdw 2.264 3.040 nonbonded pdb=" O GLY A 392 " pdb=" OG1 THR A 396 " model vdw 2.265 3.040 nonbonded pdb=" O GLY C 392 " pdb=" OG1 THR C 396 " model vdw 2.265 3.040 nonbonded pdb=" O VAL C 20 " pdb=" OG1 THR C 24 " model vdw 2.316 3.040 nonbonded pdb=" O VAL B 20 " pdb=" OG1 THR B 24 " model vdw 2.316 3.040 ... (remaining 74743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.630 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.017 0.923 9498 Z= 0.834 Angle : 0.895 43.044 12894 Z= 0.455 Chirality : 0.037 0.172 1635 Planarity : 0.004 0.030 1572 Dihedral : 15.717 89.480 3402 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 22.87 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.24), residues: 1212 helix: 1.71 (0.16), residues: 978 sheet: 0.95 (0.68), residues: 54 loop : -1.99 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.009 0.001 TYR A 98 PHE 0.009 0.001 PHE A 240 TRP 0.005 0.001 TRP C 19 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9495) covalent geometry : angle 0.53377 (12888) SS BOND : bond 0.92318 ( 3) SS BOND : angle 33.31220 ( 6) hydrogen bonds : bond 0.11764 ( 732) hydrogen bonds : angle 5.19579 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.343 Fit side-chains REVERT: A 252 GLN cc_start: 0.7831 (tt0) cc_final: 0.7048 (tp-100) REVERT: B 37 LEU cc_start: 0.7938 (tp) cc_final: 0.7658 (mp) REVERT: B 165 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7669 (ptpt) REVERT: B 200 TYR cc_start: 0.7839 (m-80) cc_final: 0.7567 (m-80) REVERT: B 205 MET cc_start: 0.8755 (ptm) cc_final: 0.8494 (ptp) REVERT: B 252 GLN cc_start: 0.7788 (tt0) cc_final: 0.7023 (tp-100) REVERT: C 252 GLN cc_start: 0.7726 (tt0) cc_final: 0.6925 (tp-100) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.6128 time to fit residues: 89.5041 Evaluate side-chains 130 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.155517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109514 restraints weight = 9808.054| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.89 r_work: 0.3089 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9498 Z= 0.137 Angle : 0.518 7.699 12894 Z= 0.277 Chirality : 0.038 0.134 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.636 13.782 1290 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.13 % Allowed : 20.53 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.24), residues: 1212 helix: 1.91 (0.16), residues: 975 sheet: 0.59 (0.64), residues: 54 loop : -2.03 (0.39), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 315 TYR 0.008 0.001 TYR A 98 PHE 0.012 0.001 PHE C 240 TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9495) covalent geometry : angle 0.51685 (12888) SS BOND : bond 0.00713 ( 3) SS BOND : angle 1.94048 ( 6) hydrogen bonds : bond 0.05744 ( 732) hydrogen bonds : angle 4.31622 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.8055 (tt0) cc_final: 0.7113 (tp-100) REVERT: A 437 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7585 (tt) REVERT: B 37 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7351 (mp) REVERT: B 205 MET cc_start: 0.9031 (ptm) cc_final: 0.8777 (ptp) REVERT: B 248 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7468 (mpp) REVERT: B 252 GLN cc_start: 0.8096 (tt0) cc_final: 0.7087 (tp-100) REVERT: B 419 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6820 (ttt) REVERT: C 473 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8252 (mtp) outliers start: 32 outliers final: 8 residues processed: 146 average time/residue: 0.5614 time to fit residues: 87.7126 Evaluate side-chains 143 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 473 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 30 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 0.0770 chunk 31 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.154923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108662 restraints weight = 9797.872| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.92 r_work: 0.3080 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9498 Z= 0.138 Angle : 0.514 8.521 12894 Z= 0.275 Chirality : 0.038 0.168 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.671 14.635 1290 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.74 % Allowed : 20.14 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.24), residues: 1212 helix: 1.88 (0.16), residues: 975 sheet: 0.16 (0.61), residues: 54 loop : -2.05 (0.38), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 315 TYR 0.008 0.001 TYR A 98 PHE 0.013 0.002 PHE C 240 TRP 0.006 0.001 TRP A 19 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9495) covalent geometry : angle 0.51412 (12888) SS BOND : bond 0.00970 ( 3) SS BOND : angle 0.55950 ( 6) hydrogen bonds : bond 0.05783 ( 732) hydrogen bonds : angle 4.26148 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 437 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7680 (tt) REVERT: B 37 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7315 (mp) REVERT: B 205 MET cc_start: 0.9024 (ptm) cc_final: 0.8762 (ptp) REVERT: B 248 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7501 (mpp) REVERT: B 252 GLN cc_start: 0.8076 (tt0) cc_final: 0.7061 (tp-100) REVERT: B 419 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6808 (ttt) REVERT: C 241 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8443 (m110) REVERT: C 473 MET cc_start: 0.8410 (mtt) cc_final: 0.8165 (mtp) outliers start: 28 outliers final: 11 residues processed: 149 average time/residue: 0.5685 time to fit residues: 90.6561 Evaluate side-chains 150 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 351 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.0000 chunk 116 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104619 restraints weight = 9775.580| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.90 r_work: 0.3019 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9498 Z= 0.184 Angle : 0.593 8.030 12894 Z= 0.314 Chirality : 0.041 0.179 1635 Planarity : 0.004 0.036 1572 Dihedral : 3.867 14.583 1290 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.93 % Allowed : 20.14 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.23), residues: 1212 helix: 1.59 (0.16), residues: 978 sheet: 0.93 (0.49), residues: 48 loop : -2.41 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 315 TYR 0.011 0.002 TYR A 98 PHE 0.017 0.002 PHE A 240 TRP 0.008 0.001 TRP A 19 HIS 0.002 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 9495) covalent geometry : angle 0.59288 (12888) SS BOND : bond 0.01052 ( 3) SS BOND : angle 0.59063 ( 6) hydrogen bonds : bond 0.07161 ( 732) hydrogen bonds : angle 4.44396 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 322 GLN cc_start: 0.7876 (tt0) cc_final: 0.7017 (mp10) REVERT: A 437 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7749 (tt) REVERT: B 205 MET cc_start: 0.9035 (ptm) cc_final: 0.8778 (ptp) REVERT: B 248 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7579 (mpp) REVERT: B 252 GLN cc_start: 0.8228 (tt0) cc_final: 0.7193 (tp-100) REVERT: B 322 GLN cc_start: 0.7753 (tt0) cc_final: 0.6767 (mt0) REVERT: B 419 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6948 (ttt) REVERT: C 318 MET cc_start: 0.7598 (mtt) cc_final: 0.7305 (ttm) REVERT: C 322 GLN cc_start: 0.7815 (tt0) cc_final: 0.6759 (mp10) REVERT: C 419 MET cc_start: 0.6874 (ttt) cc_final: 0.6513 (ttt) REVERT: C 473 MET cc_start: 0.8530 (mtt) cc_final: 0.8291 (mtp) outliers start: 30 outliers final: 14 residues processed: 143 average time/residue: 0.5458 time to fit residues: 83.6201 Evaluate side-chains 149 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 57 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.154861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108700 restraints weight = 9814.062| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.89 r_work: 0.3077 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9498 Z= 0.135 Angle : 0.513 7.740 12894 Z= 0.273 Chirality : 0.038 0.175 1635 Planarity : 0.004 0.034 1572 Dihedral : 3.726 14.777 1290 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.64 % Allowed : 21.21 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.24), residues: 1212 helix: 1.75 (0.16), residues: 978 sheet: -0.11 (0.60), residues: 54 loop : -2.22 (0.38), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 315 TYR 0.008 0.001 TYR C 98 PHE 0.011 0.001 PHE A 240 TRP 0.008 0.001 TRP C 19 HIS 0.001 0.000 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9495) covalent geometry : angle 0.51342 (12888) SS BOND : bond 0.00894 ( 3) SS BOND : angle 0.49144 ( 6) hydrogen bonds : bond 0.05667 ( 732) hydrogen bonds : angle 4.25226 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.8056 (tt0) cc_final: 0.7107 (tp-100) REVERT: A 322 GLN cc_start: 0.7893 (tt0) cc_final: 0.7014 (mp10) REVERT: A 437 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7777 (tt) REVERT: B 205 MET cc_start: 0.9028 (ptm) cc_final: 0.8765 (ptp) REVERT: B 248 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.7528 (mpp) REVERT: B 252 GLN cc_start: 0.8085 (tt0) cc_final: 0.7055 (tp-100) REVERT: B 318 MET cc_start: 0.7743 (mtm) cc_final: 0.7414 (ttm) REVERT: B 322 GLN cc_start: 0.7711 (tt0) cc_final: 0.6700 (mt0) REVERT: B 406 ILE cc_start: 0.8384 (tt) cc_final: 0.8024 (tp) REVERT: B 419 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6944 (ttt) REVERT: C 252 GLN cc_start: 0.8005 (tt0) cc_final: 0.7026 (tp-100) REVERT: C 322 GLN cc_start: 0.7703 (tt0) cc_final: 0.6672 (mp10) REVERT: C 473 MET cc_start: 0.8408 (mtt) cc_final: 0.8201 (mtp) outliers start: 27 outliers final: 15 residues processed: 147 average time/residue: 0.5619 time to fit residues: 88.2015 Evaluate side-chains 153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.154059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107705 restraints weight = 9785.804| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.88 r_work: 0.3060 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9498 Z= 0.144 Angle : 0.529 8.374 12894 Z= 0.282 Chirality : 0.039 0.183 1635 Planarity : 0.004 0.035 1572 Dihedral : 3.729 14.367 1290 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.74 % Allowed : 21.11 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.24), residues: 1212 helix: 1.72 (0.16), residues: 978 sheet: -0.15 (0.59), residues: 54 loop : -2.23 (0.38), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.009 0.001 TYR C 98 PHE 0.013 0.002 PHE A 240 TRP 0.008 0.001 TRP C 19 HIS 0.001 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9495) covalent geometry : angle 0.52887 (12888) SS BOND : bond 0.00900 ( 3) SS BOND : angle 0.57956 ( 6) hydrogen bonds : bond 0.06001 ( 732) hydrogen bonds : angle 4.27994 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 322 GLN cc_start: 0.7871 (tt0) cc_final: 0.7000 (mp10) REVERT: A 437 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7777 (tt) REVERT: B 205 MET cc_start: 0.9035 (ptm) cc_final: 0.8778 (ptp) REVERT: B 248 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7534 (mpp) REVERT: B 252 GLN cc_start: 0.8137 (tt0) cc_final: 0.7125 (tp-100) REVERT: B 318 MET cc_start: 0.7713 (mtm) cc_final: 0.7386 (ttm) REVERT: B 322 GLN cc_start: 0.7705 (tt0) cc_final: 0.6695 (mt0) REVERT: B 329 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.6845 (mpp) REVERT: B 406 ILE cc_start: 0.8404 (tt) cc_final: 0.8058 (tp) REVERT: B 419 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.7004 (ttt) REVERT: C 241 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8508 (m110) REVERT: C 322 GLN cc_start: 0.7690 (tt0) cc_final: 0.6677 (mp10) REVERT: C 419 MET cc_start: 0.6839 (ttt) cc_final: 0.6498 (ttt) outliers start: 28 outliers final: 18 residues processed: 146 average time/residue: 0.5513 time to fit residues: 86.1806 Evaluate side-chains 156 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 chunk 24 optimal weight: 0.0170 chunk 14 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.157397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111522 restraints weight = 9835.408| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.89 r_work: 0.3116 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9498 Z= 0.123 Angle : 0.491 8.388 12894 Z= 0.261 Chirality : 0.037 0.186 1635 Planarity : 0.004 0.034 1572 Dihedral : 3.601 14.241 1290 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.74 % Allowed : 20.72 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.24), residues: 1212 helix: 1.85 (0.16), residues: 981 sheet: -0.07 (0.61), residues: 54 loop : -2.65 (0.34), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.007 0.001 TYR C 98 PHE 0.009 0.001 PHE C 239 TRP 0.008 0.001 TRP C 19 HIS 0.001 0.000 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9495) covalent geometry : angle 0.49051 (12888) SS BOND : bond 0.00890 ( 3) SS BOND : angle 0.56468 ( 6) hydrogen bonds : bond 0.05022 ( 732) hydrogen bonds : angle 4.14003 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7974 (tt0) cc_final: 0.7030 (tp-100) REVERT: A 322 GLN cc_start: 0.7801 (tt0) cc_final: 0.6935 (mp10) REVERT: A 437 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7721 (tt) REVERT: B 205 MET cc_start: 0.9024 (ptm) cc_final: 0.8763 (ptp) REVERT: B 248 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7474 (mpp) REVERT: B 252 GLN cc_start: 0.8052 (tt0) cc_final: 0.7083 (tp-100) REVERT: B 318 MET cc_start: 0.7632 (mtm) cc_final: 0.7340 (ttm) REVERT: B 322 GLN cc_start: 0.7600 (tt0) cc_final: 0.6575 (mt0) REVERT: B 329 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.6696 (mpp) REVERT: B 406 ILE cc_start: 0.8360 (tt) cc_final: 0.8022 (tp) REVERT: C 252 GLN cc_start: 0.7912 (tt0) cc_final: 0.6955 (tp-100) REVERT: C 322 GLN cc_start: 0.7642 (tt0) cc_final: 0.6629 (mp10) REVERT: C 406 ILE cc_start: 0.8279 (tt) cc_final: 0.7858 (tp) outliers start: 28 outliers final: 14 residues processed: 153 average time/residue: 0.5272 time to fit residues: 86.5659 Evaluate side-chains 154 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.155056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108446 restraints weight = 9826.919| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.89 r_work: 0.3068 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9498 Z= 0.141 Angle : 0.526 8.652 12894 Z= 0.280 Chirality : 0.038 0.188 1635 Planarity : 0.004 0.035 1572 Dihedral : 3.657 14.277 1290 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.35 % Allowed : 21.31 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1212 helix: 1.76 (0.16), residues: 978 sheet: -0.16 (0.60), residues: 54 loop : -2.19 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 315 TYR 0.009 0.001 TYR C 98 PHE 0.013 0.002 PHE A 240 TRP 0.007 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9495) covalent geometry : angle 0.52540 (12888) SS BOND : bond 0.00839 ( 3) SS BOND : angle 0.91342 ( 6) hydrogen bonds : bond 0.05826 ( 732) hydrogen bonds : angle 4.23898 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 272 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7226 (mt-10) REVERT: A 322 GLN cc_start: 0.7890 (tt0) cc_final: 0.7027 (mp10) REVERT: A 437 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7741 (tt) REVERT: A 473 MET cc_start: 0.8309 (mtt) cc_final: 0.7929 (mtp) REVERT: B 205 MET cc_start: 0.9022 (ptm) cc_final: 0.8761 (ptp) REVERT: B 248 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7519 (mpp) REVERT: B 252 GLN cc_start: 0.8123 (tt0) cc_final: 0.7127 (tp-100) REVERT: B 318 MET cc_start: 0.7660 (mtm) cc_final: 0.7343 (ttm) REVERT: B 322 GLN cc_start: 0.7686 (tt0) cc_final: 0.6662 (mt0) REVERT: B 329 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.6755 (mpp) REVERT: B 406 ILE cc_start: 0.8397 (tt) cc_final: 0.8060 (tp) REVERT: C 322 GLN cc_start: 0.7738 (tt0) cc_final: 0.6690 (mp10) REVERT: C 406 ILE cc_start: 0.8305 (tt) cc_final: 0.7866 (tp) REVERT: C 419 MET cc_start: 0.6823 (ttt) cc_final: 0.6500 (ttt) outliers start: 24 outliers final: 15 residues processed: 152 average time/residue: 0.5415 time to fit residues: 88.1610 Evaluate side-chains 155 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.0030 chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.0670 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 overall best weight: 0.4528 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.159392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113762 restraints weight = 9828.811| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.89 r_work: 0.3147 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9498 Z= 0.118 Angle : 0.488 8.645 12894 Z= 0.257 Chirality : 0.037 0.188 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.508 13.769 1290 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.76 % Allowed : 22.09 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.24), residues: 1212 helix: 2.09 (0.16), residues: 957 sheet: 0.01 (0.62), residues: 54 loop : -1.88 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 315 TYR 0.008 0.001 TYR C 98 PHE 0.008 0.001 PHE C 239 TRP 0.007 0.001 TRP C 19 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9495) covalent geometry : angle 0.48729 (12888) SS BOND : bond 0.00847 ( 3) SS BOND : angle 0.92010 ( 6) hydrogen bonds : bond 0.04624 ( 732) hydrogen bonds : angle 4.08225 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7959 (tt0) cc_final: 0.7043 (tp-100) REVERT: A 312 ASN cc_start: 0.8177 (t0) cc_final: 0.7780 (t0) REVERT: A 322 GLN cc_start: 0.7793 (tt0) cc_final: 0.6913 (mt0) REVERT: A 406 ILE cc_start: 0.8289 (tt) cc_final: 0.8020 (tp) REVERT: A 437 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7630 (tt) REVERT: A 473 MET cc_start: 0.8185 (mtt) cc_final: 0.7784 (mtp) REVERT: B 37 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7378 (mp) REVERT: B 205 MET cc_start: 0.9005 (ptm) cc_final: 0.8748 (ptp) REVERT: B 248 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7441 (mpp) REVERT: B 252 GLN cc_start: 0.8045 (tt0) cc_final: 0.7086 (tp-100) REVERT: B 318 MET cc_start: 0.7626 (mtm) cc_final: 0.7340 (ttm) REVERT: B 322 GLN cc_start: 0.7602 (tt0) cc_final: 0.6602 (mt0) REVERT: B 406 ILE cc_start: 0.8365 (tt) cc_final: 0.8054 (tp) REVERT: C 252 GLN cc_start: 0.7884 (tt0) cc_final: 0.6947 (tp-100) REVERT: C 322 GLN cc_start: 0.7651 (tt0) cc_final: 0.6652 (mp10) REVERT: C 406 ILE cc_start: 0.8272 (tt) cc_final: 0.7850 (tp) outliers start: 18 outliers final: 11 residues processed: 150 average time/residue: 0.5610 time to fit residues: 90.1329 Evaluate side-chains 154 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.157373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111065 restraints weight = 9853.814| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.89 r_work: 0.3106 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9498 Z= 0.128 Angle : 0.514 8.589 12894 Z= 0.268 Chirality : 0.037 0.187 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.528 13.345 1290 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.66 % Allowed : 21.80 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.24), residues: 1212 helix: 2.05 (0.16), residues: 957 sheet: -0.09 (0.61), residues: 54 loop : -1.90 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 315 TYR 0.007 0.001 TYR C 98 PHE 0.011 0.001 PHE C 240 TRP 0.007 0.001 TRP C 19 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9495) covalent geometry : angle 0.51371 (12888) SS BOND : bond 0.00823 ( 3) SS BOND : angle 1.14548 ( 6) hydrogen bonds : bond 0.05238 ( 732) hydrogen bonds : angle 4.12911 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 322 GLN cc_start: 0.7843 (tt0) cc_final: 0.6962 (mt0) REVERT: A 406 ILE cc_start: 0.8301 (tt) cc_final: 0.8038 (tp) REVERT: A 437 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7760 (tt) REVERT: A 473 MET cc_start: 0.8212 (mtt) cc_final: 0.7857 (mtp) REVERT: B 37 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7409 (mp) REVERT: B 205 MET cc_start: 0.9023 (ptm) cc_final: 0.8767 (ptp) REVERT: B 248 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7472 (mpp) REVERT: B 252 GLN cc_start: 0.8077 (tt0) cc_final: 0.7100 (tp-100) REVERT: B 318 MET cc_start: 0.7645 (mtm) cc_final: 0.7347 (ttm) REVERT: B 322 GLN cc_start: 0.7670 (tt0) cc_final: 0.6686 (mt0) REVERT: B 406 ILE cc_start: 0.8352 (tt) cc_final: 0.8043 (tp) REVERT: C 322 GLN cc_start: 0.7640 (tt0) cc_final: 0.6631 (mp10) REVERT: C 406 ILE cc_start: 0.8282 (tt) cc_final: 0.7861 (tp) REVERT: C 419 MET cc_start: 0.6889 (ttt) cc_final: 0.6549 (ttt) outliers start: 17 outliers final: 12 residues processed: 146 average time/residue: 0.5273 time to fit residues: 82.4472 Evaluate side-chains 153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 0.0010 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.158633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112696 restraints weight = 9795.447| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.89 r_work: 0.3133 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9498 Z= 0.122 Angle : 0.504 8.567 12894 Z= 0.263 Chirality : 0.037 0.191 1635 Planarity : 0.004 0.034 1572 Dihedral : 3.497 13.278 1290 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.56 % Allowed : 22.09 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.24), residues: 1212 helix: 2.09 (0.16), residues: 957 sheet: -0.09 (0.62), residues: 54 loop : -1.89 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 315 TYR 0.008 0.001 TYR A 285 PHE 0.009 0.001 PHE C 240 TRP 0.007 0.001 TRP C 19 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9495) covalent geometry : angle 0.50389 (12888) SS BOND : bond 0.00830 ( 3) SS BOND : angle 1.16491 ( 6) hydrogen bonds : bond 0.04905 ( 732) hydrogen bonds : angle 4.08782 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3785.72 seconds wall clock time: 64 minutes 55.17 seconds (3895.17 seconds total)