Starting phenix.real_space_refine on Thu Feb 13 18:20:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fel_29032/02_2025/8fel_29032.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fel_29032/02_2025/8fel_29032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fel_29032/02_2025/8fel_29032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fel_29032/02_2025/8fel_29032.map" model { file = "/net/cci-nas-00/data/ceres_data/8fel_29032/02_2025/8fel_29032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fel_29032/02_2025/8fel_29032.cif" } resolution = 4.64 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= 0.002 sd= 0.078 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 51 5.16 5 C 5820 2.51 5 N 1509 2.21 5 O 1821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9201 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3067 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain breaks: 2 Restraints were copied for chains: C, B Time building chain proxies: 6.22, per 1000 atoms: 0.68 Number of scatterers: 9201 At special positions: 0 Unit cell: (93.96, 91.8, 172.8, 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 51 16.00 O 1821 8.00 N 1509 7.00 C 5820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " 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: 2.73 Conformation dependent library (CDL) restraints added in 1.1 seconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 15 sheets defined 41.8% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 142 through 177 removed outlier: 3.854A pdb=" N GLN A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 210 removed outlier: 3.554A pdb=" N PHE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.613A pdb=" N GLN A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 233 through 241 removed outlier: 4.046A pdb=" N MET A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 255 removed outlier: 3.633A pdb=" N LEU A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 removed outlier: 3.787A pdb=" N ILE A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 477 removed outlier: 3.603A pdb=" N GLU A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 142 through 177 removed outlier: 3.855A pdb=" N GLN B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 171 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 210 removed outlier: 3.554A pdb=" N PHE B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.613A pdb=" N GLN B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 233 through 241 removed outlier: 4.045A pdb=" N MET B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.635A pdb=" N LEU B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.789A pdb=" N ILE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 477 removed outlier: 3.601A pdb=" N GLU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 471 " --> pdb=" O ASP B 467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 472 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 142 through 177 removed outlier: 3.855A pdb=" N GLN C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 210 removed outlier: 3.553A pdb=" N PHE C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.613A pdb=" N GLN C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 233 through 241 removed outlier: 4.046A pdb=" N MET C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 255 removed outlier: 3.634A pdb=" N LEU C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 353 removed outlier: 3.789A pdb=" N ILE C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 477 removed outlier: 3.602A pdb=" N GLU C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS C 471 " --> pdb=" O ASP C 467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 472 " --> pdb=" O TYR C 468 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 281 through 282 removed outlier: 5.940A pdb=" N ASN A 40 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N CYS A 335 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS A 42 " --> pdb=" O CYS A 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 264 removed outlier: 7.107A pdb=" N ALA A 272 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 290 removed outlier: 3.852A pdb=" N GLN A 289 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 311 " --> pdb=" O GLN A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.693A pdb=" N ALA A 372 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 281 through 282 removed outlier: 5.940A pdb=" N ASN B 40 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N CYS B 335 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS B 42 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 261 through 264 removed outlier: 7.107A pdb=" N ALA B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 288 through 290 removed outlier: 3.852A pdb=" N GLN B 289 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 311 " --> pdb=" O GLN B 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 296 through 298 Processing sheet with id=AB1, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.692A pdb=" N ALA B 372 " --> pdb=" O TYR B 379 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 281 through 282 removed outlier: 5.940A pdb=" N ASN C 40 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N CYS C 335 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS C 42 " --> pdb=" O CYS C 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 261 through 264 removed outlier: 7.107A pdb=" N ALA C 272 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 288 through 290 removed outlier: 3.853A pdb=" N GLN C 289 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 311 " --> pdb=" O GLN C 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 296 through 298 Processing sheet with id=AB6, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.693A pdb=" N ALA C 372 " --> pdb=" O TYR C 379 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1071 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: 2.35 Time building geometry restraints manager: 2.82 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: 3033 1.34 - 1.46: 1803 1.46 - 1.58: 4410 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9318 Sorted by residual: bond pdb=" C ILE A 179 " pdb=" N PRO A 180 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.76e-01 bond pdb=" C ILE C 179 " pdb=" N PRO C 180 " ideal model delta sigma weight residual 1.334 1.354 -0.021 2.34e-02 1.83e+03 7.68e-01 bond pdb=" C ILE B 179 " pdb=" N PRO B 180 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.67e-01 bond pdb=" N GLY B 36 " pdb=" CA GLY B 36 " ideal model delta sigma weight residual 1.445 1.451 -0.007 8.30e-03 1.45e+04 6.90e-01 bond pdb=" N GLY C 36 " pdb=" CA GLY C 36 " ideal model delta sigma weight residual 1.445 1.451 -0.007 8.30e-03 1.45e+04 6.54e-01 ... (remaining 9313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 12435 0.97 - 1.94: 159 1.94 - 2.91: 45 2.91 - 3.88: 6 3.88 - 4.85: 9 Bond angle restraints: 12654 Sorted by residual: angle pdb=" CA TYR B 468 " pdb=" CB TYR B 468 " pdb=" CG TYR B 468 " ideal model delta sigma weight residual 113.90 118.53 -4.63 1.80e+00 3.09e-01 6.63e+00 angle pdb=" CA TYR C 468 " pdb=" CB TYR C 468 " pdb=" CG TYR C 468 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.59e+00 angle pdb=" CA TYR A 468 " pdb=" CB TYR A 468 " pdb=" CG TYR A 468 " ideal model delta sigma weight residual 113.90 118.48 -4.58 1.80e+00 3.09e-01 6.48e+00 angle pdb=" C PRO C 84 " pdb=" N VAL C 85 " pdb=" CA VAL C 85 " ideal model delta sigma weight residual 121.97 126.32 -4.35 1.80e+00 3.09e-01 5.84e+00 angle pdb=" C PRO A 84 " pdb=" N VAL A 85 " pdb=" CA VAL A 85 " ideal model delta sigma weight residual 121.97 126.30 -4.33 1.80e+00 3.09e-01 5.79e+00 ... (remaining 12649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5116 17.77 - 35.54: 413 35.54 - 53.31: 159 53.31 - 71.08: 15 71.08 - 88.85: 6 Dihedral angle restraints: 5709 sinusoidal: 2241 harmonic: 3468 Sorted by residual: dihedral pdb=" CB CYS A 326 " pdb=" SG CYS A 326 " pdb=" SG CYS A 335 " pdb=" CB CYS A 335 " ideal model delta sinusoidal sigma weight residual 93.00 123.67 -30.67 1 1.00e+01 1.00e-02 1.34e+01 dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 412 " pdb=" CB CYS A 412 " ideal model delta sinusoidal sigma weight residual 93.00 64.79 28.21 1 1.00e+01 1.00e-02 1.14e+01 dihedral pdb=" CB GLU A 432 " pdb=" CG GLU A 432 " pdb=" CD GLU A 432 " pdb=" OE1 GLU A 432 " ideal model delta sinusoidal sigma weight residual 0.00 88.85 -88.85 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 5706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 968 0.024 - 0.048: 307 0.048 - 0.072: 123 0.072 - 0.096: 66 0.096 - 0.120: 78 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA ILE C 57 " pdb=" N ILE C 57 " pdb=" C ILE C 57 " pdb=" CB ILE C 57 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE B 57 " pdb=" N ILE B 57 " pdb=" C ILE B 57 " pdb=" CB ILE B 57 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE C 321 " pdb=" N ILE C 321 " pdb=" C ILE C 321 " pdb=" CB ILE C 321 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 1539 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 468 " -0.007 2.00e-02 2.50e+03 6.63e-03 8.78e-01 pdb=" CG TYR C 468 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 468 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 468 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 468 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 468 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 468 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 468 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 468 " -0.007 2.00e-02 2.50e+03 6.61e-03 8.73e-01 pdb=" CG TYR A 468 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 468 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 468 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 468 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 468 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 468 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 468 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 468 " -0.007 2.00e-02 2.50e+03 6.50e-03 8.46e-01 pdb=" CG TYR B 468 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 468 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 468 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 468 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 468 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 468 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 468 " -0.000 2.00e-02 2.50e+03 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 114 2.60 - 3.18: 7961 3.18 - 3.75: 13674 3.75 - 4.33: 18081 4.33 - 4.90: 28198 Nonbonded interactions: 68028 Sorted by model distance: nonbonded pdb=" SG CYS C 326 " pdb=" SG CYS C 335 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 66 " pdb=" SG CYS C 187 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 389 " pdb=" SG CYS B 412 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 389 " pdb=" SG CYS C 412 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 350 " pdb=" SG CYS C 358 " model vdw 2.031 3.760 ... (remaining 68023 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.310 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.010 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3825 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 : 0.001 0.021 9318 Z= 0.082 Angle : 0.349 4.845 12654 Z= 0.194 Chirality : 0.039 0.120 1542 Planarity : 0.002 0.020 1617 Dihedral : 14.882 88.852 3462 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.98 % Allowed : 17.28 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.24), residues: 1173 helix: 1.32 (0.24), residues: 414 sheet: -0.98 (0.54), residues: 87 loop : -1.02 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 303 HIS 0.000 0.000 HIS B 253 PHE 0.002 0.000 PHE A 230 TYR 0.016 0.001 TYR C 468 ARG 0.001 0.000 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.382 Fit side-chains REVERT: A 168 ASP cc_start: 0.8283 (t0) cc_final: 0.8005 (m-30) REVERT: A 273 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.4942 (pt) outliers start: 7 outliers final: 1 residues processed: 30 average time/residue: 0.1353 time to fit residues: 5.3665 Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.088104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.082958 restraints weight = 24788.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.083516 restraints weight = 20217.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.084020 restraints weight = 15659.687| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4262 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9318 Z= 0.143 Angle : 0.563 6.856 12654 Z= 0.291 Chirality : 0.043 0.176 1542 Planarity : 0.003 0.018 1617 Dihedral : 3.521 14.746 1269 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.25), residues: 1173 helix: 2.06 (0.25), residues: 429 sheet: -0.97 (0.52), residues: 87 loop : -0.98 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.002 0.001 HIS C 253 PHE 0.013 0.002 PHE B 230 TYR 0.007 0.001 TYR A 270 ARG 0.003 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.373 Fit side-chains REVERT: A 142 MET cc_start: 0.1637 (mmp) cc_final: 0.0963 (tpt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1429 time to fit residues: 3.0842 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 31 optimal weight: 0.3980 chunk 41 optimal weight: 0.0040 chunk 83 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 88 optimal weight: 0.0970 chunk 36 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 76 optimal weight: 0.0870 overall best weight: 0.1968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.088349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.082936 restraints weight = 24737.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.083610 restraints weight = 19718.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.083994 restraints weight = 15190.840| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4438 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9318 Z= 0.113 Angle : 0.492 6.927 12654 Z= 0.252 Chirality : 0.041 0.146 1542 Planarity : 0.002 0.014 1617 Dihedral : 3.300 13.510 1269 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.25), residues: 1173 helix: 1.84 (0.24), residues: 447 sheet: -0.91 (0.52), residues: 87 loop : -0.98 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 303 HIS 0.002 0.001 HIS B 253 PHE 0.011 0.001 PHE A 230 TYR 0.012 0.001 TYR B 468 ARG 0.001 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.371 Fit side-chains REVERT: A 142 MET cc_start: 0.1735 (mmp) cc_final: 0.1233 (tpt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1379 time to fit residues: 3.1757 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 19 optimal weight: 0.9980 chunk 110 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.083968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.081016 restraints weight = 25819.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.080949 restraints weight = 23247.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.081192 restraints weight = 15588.874| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4517 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9318 Z= 0.138 Angle : 0.528 8.432 12654 Z= 0.273 Chirality : 0.042 0.133 1542 Planarity : 0.002 0.018 1617 Dihedral : 3.619 16.368 1269 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.25), residues: 1173 helix: 2.11 (0.24), residues: 447 sheet: -1.13 (0.49), residues: 99 loop : -0.98 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.001 0.000 HIS A 253 PHE 0.010 0.001 PHE B 230 TYR 0.010 0.001 TYR A 468 ARG 0.002 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.354 Fit side-chains REVERT: C 92 MET cc_start: 0.6369 (mpp) cc_final: 0.6141 (mpp) REVERT: C 142 MET cc_start: 0.0666 (mmp) cc_final: -0.0429 (tpt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1332 time to fit residues: 2.9308 Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 0.0980 chunk 66 optimal weight: 0.0470 chunk 95 optimal weight: 8.9990 chunk 81 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.0770 chunk 102 optimal weight: 0.0050 chunk 31 optimal weight: 0.0270 overall best weight: 0.0508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.086884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.081422 restraints weight = 24952.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.081621 restraints weight = 21367.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.081977 restraints weight = 18295.687| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4533 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9318 Z= 0.110 Angle : 0.494 6.990 12654 Z= 0.250 Chirality : 0.041 0.132 1542 Planarity : 0.002 0.016 1617 Dihedral : 3.315 12.356 1269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.25), residues: 1173 helix: 1.77 (0.24), residues: 447 sheet: -1.12 (0.50), residues: 99 loop : -1.02 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 303 HIS 0.005 0.003 HIS C 253 PHE 0.009 0.001 PHE B 230 TYR 0.015 0.001 TYR C 468 ARG 0.001 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.357 Fit side-chains REVERT: C 92 MET cc_start: 0.6464 (mpp) cc_final: 0.6229 (mpp) REVERT: C 142 MET cc_start: 0.1231 (mmp) cc_final: 0.0875 (tpt) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1461 time to fit residues: 2.8567 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 54 optimal weight: 0.0970 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.084520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.079424 restraints weight = 25806.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.079941 restraints weight = 28743.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.080569 restraints weight = 22825.152| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4564 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9318 Z= 0.112 Angle : 0.483 6.489 12654 Z= 0.246 Chirality : 0.042 0.126 1542 Planarity : 0.002 0.017 1617 Dihedral : 3.348 13.505 1269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.25), residues: 1173 helix: 1.68 (0.24), residues: 447 sheet: -0.92 (0.55), residues: 84 loop : -1.08 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 303 HIS 0.001 0.001 HIS C 253 PHE 0.009 0.001 PHE A 230 TYR 0.015 0.001 TYR A 468 ARG 0.002 0.000 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.374 Fit side-chains REVERT: C 92 MET cc_start: 0.6451 (mpp) cc_final: 0.6154 (mpp) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1622 time to fit residues: 2.8742 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 10 optimal weight: 0.9990 chunk 71 optimal weight: 0.0000 chunk 82 optimal weight: 0.0060 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.086889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.081373 restraints weight = 24848.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.082110 restraints weight = 19770.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.082511 restraints weight = 15955.448| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4577 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9318 Z= 0.108 Angle : 0.476 5.663 12654 Z= 0.243 Chirality : 0.041 0.125 1542 Planarity : 0.002 0.018 1617 Dihedral : 3.219 13.402 1269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.25), residues: 1173 helix: 1.70 (0.24), residues: 444 sheet: -0.97 (0.54), residues: 84 loop : -1.06 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 303 HIS 0.000 0.000 HIS A 253 PHE 0.009 0.001 PHE B 230 TYR 0.007 0.001 TYR A 270 ARG 0.003 0.000 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.287 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0927 time to fit residues: 1.7616 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 0.0170 chunk 94 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 60 optimal weight: 0.4980 chunk 85 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 71 optimal weight: 0.0770 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.083630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.080192 restraints weight = 25526.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.080757 restraints weight = 23427.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.080877 restraints weight = 13406.609| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4505 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9318 Z= 0.110 Angle : 0.487 5.372 12654 Z= 0.250 Chirality : 0.042 0.124 1542 Planarity : 0.002 0.020 1617 Dihedral : 3.172 13.610 1269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.25), residues: 1173 helix: 1.82 (0.24), residues: 444 sheet: -1.03 (0.53), residues: 84 loop : -1.11 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 303 HIS 0.000 0.000 HIS A 253 PHE 0.009 0.001 PHE C 230 TYR 0.008 0.001 TYR C 468 ARG 0.001 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1558 time to fit residues: 2.7469 Evaluate side-chains 9 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 0.0070 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.083452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.078765 restraints weight = 25541.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.080104 restraints weight = 30307.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.080586 restraints weight = 16027.626| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4627 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9318 Z= 0.134 Angle : 0.516 8.581 12654 Z= 0.267 Chirality : 0.042 0.148 1542 Planarity : 0.002 0.022 1617 Dihedral : 3.533 13.943 1269 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.25), residues: 1173 helix: 1.88 (0.24), residues: 444 sheet: -1.06 (0.52), residues: 84 loop : -1.12 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.001 0.001 HIS A 253 PHE 0.010 0.001 PHE C 230 TYR 0.007 0.001 TYR B 270 ARG 0.005 0.000 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.384 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1020 time to fit residues: 2.0670 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 0.0770 chunk 3 optimal weight: 0.0060 chunk 63 optimal weight: 0.0050 chunk 34 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 overall best weight: 0.2368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.084596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.079830 restraints weight = 24980.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.079727 restraints weight = 21036.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.079727 restraints weight = 17826.701| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4796 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9318 Z= 0.106 Angle : 0.473 4.773 12654 Z= 0.240 Chirality : 0.041 0.125 1542 Planarity : 0.002 0.024 1617 Dihedral : 3.297 14.995 1269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1173 helix: 1.86 (0.24), residues: 444 sheet: -0.89 (0.53), residues: 84 loop : -1.11 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 303 HIS 0.000 0.000 HIS A 253 PHE 0.009 0.001 PHE B 230 TYR 0.009 0.001 TYR A 468 ARG 0.001 0.000 ARG A 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1594 time to fit residues: 3.1849 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 0.5980 chunk 81 optimal weight: 0.0770 chunk 79 optimal weight: 0.0050 chunk 86 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 overall best weight: 0.3552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.082103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.078450 restraints weight = 25174.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.078488 restraints weight = 24809.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.078597 restraints weight = 16474.907| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4637 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9318 Z= 0.104 Angle : 0.470 4.773 12654 Z= 0.237 Chirality : 0.041 0.125 1542 Planarity : 0.002 0.025 1617 Dihedral : 3.258 13.574 1269 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1173 helix: 1.92 (0.24), residues: 444 sheet: -0.83 (0.53), residues: 84 loop : -1.11 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.000 0.000 HIS A 253 PHE 0.009 0.001 PHE B 230 TYR 0.010 0.001 TYR C 468 ARG 0.001 0.000 ARG B 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2046.69 seconds wall clock time: 38 minutes 7.51 seconds (2287.51 seconds total)