Starting phenix.real_space_refine on Wed Sep 25 01:46:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/09_2024/8fel_29032.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/09_2024/8fel_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/09_2024/8fel_29032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/09_2024/8fel_29032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/09_2024/8fel_29032.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fel_29032/09_2024/8fel_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-5461/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: 5.95, per 1000 atoms: 0.65 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: 2.59 Conformation dependent library (CDL) restraints added in 1.2 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: 1.04 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: 2.55 Time building geometry restraints manager: 3.00 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.120 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.460 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.384 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: 0.1334 time to fit residues: 5.3153 Evaluate side-chains 13 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 11 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4187 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 : 8.95 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 A 253 PHE 0.013 0.002 PHE B 230 TYR 0.007 0.001 TYR C 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 fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.386 Fit side-chains REVERT: A 142 MET cc_start: 0.1509 (mmp) cc_final: 0.0960 (tpt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1492 time to fit residues: 3.1947 Evaluate side-chains 10 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.0170 chunk 32 optimal weight: 0.6980 chunk 88 optimal weight: 0.1980 chunk 72 optimal weight: 0.4980 chunk 29 optimal weight: 0.0040 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.2830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4280 moved from start: 0.2873 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= 0.114 Angle : 0.492 7.039 12654 Z= 0.252 Chirality : 0.042 0.143 1542 Planarity : 0.002 0.014 1617 Dihedral : 3.305 13.894 1269 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 0.20 (0.25), residues: 1173 helix: 1.84 (0.24), residues: 447 sheet: -0.93 (0.52), residues: 87 loop : -0.99 (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 C 253 PHE 0.011 0.001 PHE B 230 TYR 0.012 0.001 TYR B 468 ARG 0.001 0.000 ARG B 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 fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.382 Fit side-chains REVERT: A 421 LEU cc_start: 0.7145 (mp) cc_final: 0.6934 (tp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1394 time to fit residues: 3.2803 Evaluate side-chains 10 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 101 optimal weight: 0.0070 chunk 30 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4487 moved from start: 0.3526 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= 0.126 Angle : 0.495 6.051 12654 Z= 0.256 Chirality : 0.042 0.129 1542 Planarity : 0.002 0.014 1617 Dihedral : 3.444 13.151 1269 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: 0.36 (0.25), residues: 1173 helix: 2.08 (0.24), residues: 447 sheet: -0.98 (0.54), residues: 84 loop : -0.96 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 303 HIS 0.000 0.000 HIS B 253 PHE 0.009 0.001 PHE C 230 TYR 0.012 0.001 TYR C 468 ARG 0.001 0.000 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 4 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 12 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.383 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1627 time to fit residues: 2.8647 Evaluate side-chains 10 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 10.0000 chunk 1 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.0370 chunk 96 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 101 optimal weight: 0.0000 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4558 moved from start: 0.4055 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= 0.131 Angle : 0.508 6.106 12654 Z= 0.267 Chirality : 0.042 0.128 1542 Planarity : 0.002 0.017 1617 Dihedral : 3.359 13.722 1269 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: 0.37 (0.25), residues: 1173 helix: 2.12 (0.24), residues: 447 sheet: -0.94 (0.55), residues: 84 loop : -0.99 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.009 0.006 HIS B 253 PHE 0.009 0.001 PHE B 230 TYR 0.013 0.001 TYR A 468 ARG 0.001 0.000 ARG A 64 *********************** 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 16 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.340 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1246 time to fit residues: 2.9226 Evaluate side-chains 10 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.0050 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 113 optimal weight: 0.0270 chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 109 optimal weight: 0.1980 overall best weight: 0.3252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4504 moved from start: 0.4167 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= 0.114 Angle : 0.484 5.674 12654 Z= 0.250 Chirality : 0.042 0.128 1542 Planarity : 0.002 0.024 1617 Dihedral : 3.343 13.264 1269 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 0.10 (0.25), residues: 1173 helix: 1.77 (0.24), residues: 447 sheet: -1.03 (0.54), residues: 84 loop : -1.05 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 303 HIS 0.000 0.000 HIS B 253 PHE 0.009 0.001 PHE C 230 TYR 0.015 0.001 TYR A 468 ARG 0.001 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.352 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1350 time to fit residues: 2.6692 Evaluate side-chains 10 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 70 optimal weight: 0.0170 chunk 68 optimal weight: 0.0270 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4752 moved from start: 0.4971 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= 0.150 Angle : 0.531 7.330 12654 Z= 0.277 Chirality : 0.042 0.128 1542 Planarity : 0.002 0.019 1617 Dihedral : 3.681 16.054 1269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % 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: -0.27 (0.25), residues: 1173 helix: 1.51 (0.24), residues: 447 sheet: -1.56 (0.49), residues: 84 loop : -1.26 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 303 HIS 0.002 0.001 HIS A 253 PHE 0.018 0.001 PHE A 475 TYR 0.008 0.001 TYR A 270 ARG 0.004 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.369 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1990 time to fit residues: 3.5391 Evaluate side-chains 10 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.0970 chunk 76 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4727 moved from start: 0.5294 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= 0.124 Angle : 0.488 5.733 12654 Z= 0.251 Chirality : 0.042 0.145 1542 Planarity : 0.002 0.021 1617 Dihedral : 3.564 15.278 1269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.47 (0.24), residues: 1173 helix: 1.34 (0.24), residues: 447 sheet: -1.55 (0.50), residues: 84 loop : -1.40 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 303 HIS 0.001 0.001 HIS A 253 PHE 0.018 0.001 PHE A 475 TYR 0.007 0.001 TYR A 270 ARG 0.003 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 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 fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.353 Fit side-chains REVERT: A 390 MET cc_start: 0.7687 (tmm) cc_final: 0.6416 (pmm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1495 time to fit residues: 2.9133 Evaluate side-chains 11 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4841 moved from start: 0.6181 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= 0.134 Angle : 0.498 6.838 12654 Z= 0.258 Chirality : 0.043 0.131 1542 Planarity : 0.003 0.021 1617 Dihedral : 3.749 16.166 1269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.66 (0.24), residues: 1173 helix: 1.25 (0.24), residues: 447 sheet: -1.54 (0.52), residues: 84 loop : -1.59 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP C 303 HIS 0.002 0.001 HIS A 253 PHE 0.015 0.002 PHE C 475 TYR 0.012 0.001 TYR C 468 ARG 0.002 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 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 fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.349 Fit side-chains REVERT: A 479 ILE cc_start: 0.7869 (tp) cc_final: 0.7646 (tt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0888 time to fit residues: 2.2376 Evaluate side-chains 11 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.0570 chunk 67 optimal weight: 5.9990 chunk 52 optimal weight: 0.1980 chunk 77 optimal weight: 0.0970 chunk 116 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 92 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 overall best weight: 0.0852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4628 moved from start: 0.5991 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= 0.113 Angle : 0.492 7.606 12654 Z= 0.245 Chirality : 0.042 0.130 1542 Planarity : 0.003 0.030 1617 Dihedral : 3.498 16.656 1269 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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: -0.85 (0.24), residues: 1173 helix: 1.05 (0.24), residues: 447 sheet: -1.39 (0.54), residues: 84 loop : -1.71 (0.23), residues: 642 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 0.017 0.001 PHE C 475 TYR 0.012 0.001 TYR A 468 ARG 0.001 0.000 ARG C 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 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 fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.369 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1001 time to fit residues: 2.5855 Evaluate side-chains 12 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0970 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 0.0570 chunk 95 optimal weight: 8.9990 chunk 11 optimal weight: 0.0170 chunk 17 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.080602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.076700 restraints weight = 25640.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.076357 restraints weight = 26669.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.076490 restraints weight = 19340.864| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4778 moved from start: 0.6026 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= 0.108 Angle : 0.478 5.026 12654 Z= 0.239 Chirality : 0.042 0.129 1542 Planarity : 0.002 0.020 1617 Dihedral : 3.475 17.712 1269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % 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: -0.77 (0.24), residues: 1173 helix: 1.17 (0.24), residues: 447 sheet: -1.42 (0.52), residues: 84 loop : -1.69 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 303 HIS 0.000 0.000 HIS B 253 PHE 0.017 0.001 PHE B 475 TYR 0.009 0.001 TYR C 468 ARG 0.001 0.000 ARG C 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1574.42 seconds wall clock time: 29 minutes 9.71 seconds (1749.71 seconds total)