Starting phenix.real_space_refine on Sat Sep 12 03:47:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ld5_23282/09_2026/7ld5_23282.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ld5_23282/09_2026/7ld5_23282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ld5_23282/09_2026/7ld5_23282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ld5_23282/09_2026/7ld5_23282.map" model { file = "/net/cci-nas-00/data/ceres_data/7ld5_23282/09_2026/7ld5_23282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ld5_23282/09_2026/7ld5_23282.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ld5_23282/09_2026/7ld5_23282.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ld5_23282/09_2026/7ld5_23282.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.110 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 6 5.21 5 S 54 5.16 5 C 8451 2.51 5 N 2358 2.21 5 O 2664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13542 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4416 Classifications: {'peptide': 587} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 555} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Classifications: {'DNA': 1, 'RNAv2': 4} Modifications used: {'5*END': 1, 'rna3p_pur': 4} Link IDs: {'rna3p': 4} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, E, F Residues with excluded nonbonded symmetry interactions: 15 residue: pdb=" O5' A D 1 " occ=0.30 ... (17 atoms not shown) pdb=" C4 A D 1 " occ=0.30 residue: pdb=" P A D 2 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A D 2 " occ=0.30 residue: pdb=" P A D 3 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A D 3 " occ=0.30 residue: pdb=" P A D 4 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A D 4 " occ=0.30 residue: pdb=" C1' A D 9 " occ=0.30 ... (9 atoms not shown) pdb=" C4 A D 9 " occ=0.30 residue: pdb=" O5' A E 1 " occ=0.30 ... (17 atoms not shown) pdb=" C4 A E 1 " occ=0.30 residue: pdb=" P A E 2 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A E 2 " occ=0.30 residue: pdb=" P A E 3 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A E 3 " occ=0.30 residue: pdb=" P A E 4 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A E 4 " occ=0.30 residue: pdb=" C1' A E 9 " occ=0.30 ... (9 atoms not shown) pdb=" C4 A E 9 " occ=0.30 residue: pdb=" O5' A F 1 " occ=0.30 ... (17 atoms not shown) pdb=" C4 A F 1 " occ=0.30 residue: pdb=" P A F 2 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A F 2 " occ=0.30 ... (remaining 3 not shown) Time building chain proxies: 4.49, per 1000 atoms: 0.33 Number of scatterers: 13542 At special positions: 0 Unit cell: (114.912, 122.36, 89.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 9 15.00 Mg 6 11.99 O 2664 8.00 N 2358 7.00 C 8451 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.07 Conformation dependent library (CDL) restraints added in 591.6 milliseconds 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 12 sheets defined 37.8% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 97 through 112 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 138 through 153 removed outlier: 4.043A pdb=" N ASN A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 229 through 240 Processing helix chain 'A' and resid 240 through 258 removed outlier: 3.520A pdb=" N ILE A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 292 removed outlier: 3.657A pdb=" N TYR A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 314 Processing helix chain 'A' and resid 321 through 345 Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.629A pdb=" N THR A 419 " --> pdb=" O PRO A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.587A pdb=" N ILE A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 470 through 485 Processing helix chain 'A' and resid 523 through 527 removed outlier: 3.594A pdb=" N ASP A 526 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 581 removed outlier: 4.005A pdb=" N GLU A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 97 through 112 Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 138 through 153 removed outlier: 4.044A pdb=" N ASN B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 229 through 240 Processing helix chain 'B' and resid 240 through 258 removed outlier: 3.520A pdb=" N ILE B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 292 removed outlier: 3.657A pdb=" N TYR B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 314 Processing helix chain 'B' and resid 321 through 345 Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.629A pdb=" N THR B 419 " --> pdb=" O PRO B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 441 removed outlier: 3.588A pdb=" N ILE B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'B' and resid 470 through 485 Processing helix chain 'B' and resid 523 through 527 removed outlier: 3.595A pdb=" N ASP B 526 " --> pdb=" O GLY B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 581 removed outlier: 4.005A pdb=" N GLU B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 97 through 112 Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 138 through 153 removed outlier: 4.043A pdb=" N ASN C 144 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 229 through 240 Processing helix chain 'C' and resid 240 through 258 removed outlier: 3.520A pdb=" N ILE C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 292 removed outlier: 3.657A pdb=" N TYR C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 314 Processing helix chain 'C' and resid 321 through 345 Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.629A pdb=" N THR C 419 " --> pdb=" O PRO C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 441 removed outlier: 3.588A pdb=" N ILE C 433 " --> pdb=" O LYS C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 470 through 485 Processing helix chain 'C' and resid 523 through 527 removed outlier: 3.594A pdb=" N ASP C 526 " --> pdb=" O GLY C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 581 removed outlier: 4.004A pdb=" N GLU C 579 " --> pdb=" O ASP C 575 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA C 580 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 581 " --> pdb=" O MET C 577 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 18 removed outlier: 6.206A pdb=" N MET A 51 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.424A pdb=" N PHE A 187 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL A 186 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA A 213 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP A 188 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA A 211 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 190 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 209 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 192 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N MET A 207 " --> pdb=" O THR A 549 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR A 543 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 363 removed outlier: 6.303A pdb=" N GLN A 381 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET A 409 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N SER A 461 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS A 411 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA A 463 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ASN A 413 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLY A 465 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 18 removed outlier: 6.206A pdb=" N MET B 51 " --> pdb=" O MET B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175 removed outlier: 4.425A pdb=" N PHE B 187 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL B 186 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA B 213 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP B 188 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA B 211 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 190 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL B 209 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 192 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N MET B 207 " --> pdb=" O THR B 549 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 543 " --> pdb=" O ALA B 213 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 363 removed outlier: 6.303A pdb=" N GLN B 381 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET B 409 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N SER B 461 " --> pdb=" O MET B 409 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS B 411 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA B 463 " --> pdb=" O HIS B 411 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ASN B 413 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLY B 465 " --> pdb=" O ASN B 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 395 through 396 Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 18 removed outlier: 6.206A pdb=" N MET C 51 " --> pdb=" O MET C 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 172 through 175 removed outlier: 4.425A pdb=" N PHE C 187 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 186 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA C 213 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP C 188 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA C 211 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 190 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL C 209 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 192 " --> pdb=" O MET C 207 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N MET C 207 " --> pdb=" O THR C 549 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR C 543 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 359 through 363 removed outlier: 6.304A pdb=" N GLN C 381 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET C 409 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N SER C 461 " --> pdb=" O MET C 409 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS C 411 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA C 463 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ASN C 413 " --> pdb=" O ALA C 463 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY C 465 " --> pdb=" O ASN C 413 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 395 through 396 720 hydrogen bonds defined for protein. 1980 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: 2.16 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4601 1.34 - 1.45: 1539 1.45 - 1.57: 7531 1.57 - 1.69: 18 1.69 - 1.80: 99 Bond restraints: 13788 Sorted by residual: bond pdb=" CB GLU A 298 " pdb=" CG GLU A 298 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" CB GLU C 298 " pdb=" CG GLU C 298 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CB GLU B 298 " pdb=" CG GLU B 298 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.10e+00 bond pdb=" CA ILE C 366 " pdb=" CB ILE C 366 " ideal model delta sigma weight residual 1.537 1.523 0.014 1.29e-02 6.01e+03 1.25e+00 bond pdb=" CA ILE B 366 " pdb=" CB ILE B 366 " ideal model delta sigma weight residual 1.537 1.523 0.014 1.29e-02 6.01e+03 1.20e+00 ... (remaining 13783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 18399 1.88 - 3.77: 333 3.77 - 5.65: 30 5.65 - 7.53: 6 7.53 - 9.42: 6 Bond angle restraints: 18774 Sorted by residual: angle pdb=" CA GLU A 298 " pdb=" CB GLU A 298 " pdb=" CG GLU A 298 " ideal model delta sigma weight residual 114.10 123.52 -9.42 2.00e+00 2.50e-01 2.22e+01 angle pdb=" CA GLU B 298 " pdb=" CB GLU B 298 " pdb=" CG GLU B 298 " ideal model delta sigma weight residual 114.10 123.49 -9.39 2.00e+00 2.50e-01 2.21e+01 angle pdb=" CA GLU C 298 " pdb=" CB GLU C 298 " pdb=" CG GLU C 298 " ideal model delta sigma weight residual 114.10 123.48 -9.38 2.00e+00 2.50e-01 2.20e+01 angle pdb=" CG1 ILE B 293 " pdb=" CB ILE B 293 " pdb=" CG2 ILE B 293 " ideal model delta sigma weight residual 110.70 101.52 9.18 3.00e+00 1.11e-01 9.36e+00 angle pdb=" CG1 ILE C 293 " pdb=" CB ILE C 293 " pdb=" CG2 ILE C 293 " ideal model delta sigma weight residual 110.70 101.54 9.16 3.00e+00 1.11e-01 9.31e+00 ... (remaining 18769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 7253 16.59 - 33.19: 771 33.19 - 49.78: 256 49.78 - 66.38: 57 66.38 - 82.97: 15 Dihedral angle restraints: 8352 sinusoidal: 3312 harmonic: 5040 Sorted by residual: dihedral pdb=" CA VAL C 507 " pdb=" C VAL C 507 " pdb=" N ASP C 508 " pdb=" CA ASP C 508 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA VAL B 507 " pdb=" C VAL B 507 " pdb=" N ASP B 508 " pdb=" CA ASP B 508 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL A 507 " pdb=" C VAL A 507 " pdb=" N ASP A 508 " pdb=" CA ASP A 508 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 8349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1558 0.046 - 0.093: 471 0.093 - 0.139: 134 0.139 - 0.185: 9 0.185 - 0.232: 12 Chirality restraints: 2184 Sorted by residual: chirality pdb=" P A D 3 " pdb=" OP1 A D 3 " pdb=" OP2 A D 3 " pdb=" O5' A D 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" P A E 3 " pdb=" OP1 A E 3 " pdb=" OP2 A E 3 " pdb=" O5' A E 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE B 293 " pdb=" CA ILE B 293 " pdb=" CG1 ILE B 293 " pdb=" CG2 ILE B 293 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2181 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 444 " -0.033 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO C 445 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 445 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 445 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 444 " -0.033 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO B 445 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 445 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 445 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 444 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO A 445 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " 0.027 5.00e-02 4.00e+02 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 273 2.66 - 3.22: 12389 3.22 - 3.78: 19572 3.78 - 4.34: 28398 4.34 - 4.90: 48333 Nonbonded interactions: 108965 Sorted by model distance: nonbonded pdb=" OG SER B 418 " pdb=" O ALA B 463 " model vdw 2.102 3.040 nonbonded pdb=" OG SER A 418 " pdb=" O ALA A 463 " model vdw 2.102 3.040 nonbonded pdb=" OG SER C 418 " pdb=" O ALA C 463 " model vdw 2.103 3.040 nonbonded pdb=" OE2 GLU C 77 " pdb=" OH TYR C 138 " model vdw 2.153 3.040 nonbonded pdb=" OE2 GLU B 77 " pdb=" OH TYR B 138 " model vdw 2.153 3.040 ... (remaining 108960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.040 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.006 0.047 13788 Z= 0.264 Angle : 0.677 9.415 18774 Z= 0.375 Chirality : 0.050 0.232 2184 Planarity : 0.004 0.049 2439 Dihedral : 16.070 82.970 5112 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.51 % Allowed : 15.84 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.18), residues: 1755 helix: -0.76 (0.20), residues: 549 sheet: -0.72 (0.23), residues: 444 loop : -2.17 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 313 TYR 0.011 0.002 TYR A 45 PHE 0.016 0.001 PHE A 157 TRP 0.003 0.001 TRP B 173 HIS 0.001 0.000 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.26 (13788) covalent geometry : angle 0.67683 / 0.38 (18774) hydrogen bonds : bond 0.14108 / 9.44 ( 720) hydrogen bonds : angle 6.74148 / 4.64 ( 1980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 193 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.7657 (ptpp) cc_final: 0.7378 (ptpt) REVERT: A 79 MET cc_start: 0.8695 (tpp) cc_final: 0.8370 (tpp) REVERT: A 130 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7981 (mtt) REVERT: A 356 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7221 (mt) REVERT: B 74 ASP cc_start: 0.7829 (m-30) cc_final: 0.7628 (m-30) REVERT: B 329 PHE cc_start: 0.8412 (t80) cc_final: 0.8060 (t80) REVERT: B 348 ILE cc_start: 0.8425 (pt) cc_final: 0.8210 (pt) REVERT: B 356 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7441 (mt) REVERT: B 397 ILE cc_start: 0.8574 (mm) cc_final: 0.8334 (mm) REVERT: C 63 LYS cc_start: 0.7607 (ptpp) cc_final: 0.7272 (ptpp) REVERT: C 95 ARG cc_start: 0.7801 (ptt180) cc_final: 0.7391 (ptm-80) REVERT: C 122 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: C 130 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8291 (mtt) REVERT: C 383 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8176 (tp) outliers start: 90 outliers final: 49 residues processed: 272 average time/residue: 0.1078 time to fit residues: 43.6743 Evaluate side-chains 223 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 61 ASN A 339 GLN A 381 GLN A 546 GLN B 61 ASN B 339 GLN B 381 GLN B 546 GLN C 36 GLN C 61 ASN C 381 GLN C 396 GLN C 546 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.165270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124679 restraints weight = 14416.134| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.96 r_work: 0.3334 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13788 Z= 0.138 Angle : 0.567 6.433 18774 Z= 0.298 Chirality : 0.045 0.150 2184 Planarity : 0.004 0.054 2439 Dihedral : 7.318 51.509 2123 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.47 % Allowed : 17.64 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 1755 helix: 0.83 (0.21), residues: 555 sheet: -0.24 (0.24), residues: 444 loop : -1.50 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 330 TYR 0.013 0.001 TYR B 80 PHE 0.014 0.001 PHE A 157 TRP 0.008 0.002 TRP B 173 HIS 0.001 0.000 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (13788) covalent geometry : angle 0.56728 / 0.30 (18774) hydrogen bonds : bond 0.04160 / 2.76 ( 720) hydrogen bonds : angle 5.20826 / 3.57 ( 1980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7665 (ttp-170) REVERT: A 63 LYS cc_start: 0.7632 (ptpp) cc_final: 0.7073 (ptpt) REVERT: A 122 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: A 397 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8217 (mm) REVERT: B 74 ASP cc_start: 0.8634 (m-30) cc_final: 0.8383 (m-30) REVERT: B 330 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7378 (mtm-85) REVERT: B 397 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8295 (mm) REVERT: C 63 LYS cc_start: 0.7734 (ptpp) cc_final: 0.7488 (ptpt) REVERT: C 330 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7472 (mtm110) REVERT: C 397 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8188 (mm) outliers start: 48 outliers final: 31 residues processed: 214 average time/residue: 0.1110 time to fit residues: 35.4072 Evaluate side-chains 206 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 152 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 67 optimal weight: 0.0870 chunk 23 optimal weight: 0.0170 chunk 86 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 339 GLN B 396 GLN C 396 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.166389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125765 restraints weight = 14448.446| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.98 r_work: 0.3357 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13788 Z= 0.107 Angle : 0.507 4.866 18774 Z= 0.264 Chirality : 0.043 0.133 2184 Planarity : 0.004 0.029 2439 Dihedral : 6.079 49.305 2075 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.60 % Allowed : 19.52 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.20), residues: 1755 helix: 1.47 (0.22), residues: 558 sheet: 0.10 (0.24), residues: 444 loop : -1.13 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 330 TYR 0.012 0.001 TYR C 80 PHE 0.012 0.001 PHE B 157 TRP 0.008 0.002 TRP B 173 HIS 0.002 0.000 HIS C 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (13788) covalent geometry : angle 0.50726 / 0.26 (18774) hydrogen bonds : bond 0.03456 / 2.29 ( 720) hydrogen bonds : angle 4.81949 / 3.30 ( 1980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7053 (m-30) REVERT: A 122 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: B 47 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: B 66 PHE cc_start: 0.7959 (m-80) cc_final: 0.7675 (m-80) REVERT: B 330 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7347 (mtm110) REVERT: B 397 ILE cc_start: 0.8553 (mm) cc_final: 0.8271 (mm) REVERT: C 47 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6463 (m-30) REVERT: C 330 ARG cc_start: 0.7694 (mtm110) cc_final: 0.7350 (mtm110) REVERT: C 332 LEU cc_start: 0.8441 (tp) cc_final: 0.8148 (mp) REVERT: C 397 ILE cc_start: 0.8439 (mm) cc_final: 0.8198 (mm) REVERT: C 470 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7922 (p) outliers start: 36 outliers final: 22 residues processed: 204 average time/residue: 0.1072 time to fit residues: 33.1475 Evaluate side-chains 195 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 522 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 135 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 173 optimal weight: 0.0030 chunk 97 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 339 GLN C 339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.165291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124775 restraints weight = 14513.292| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.98 r_work: 0.3340 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13788 Z= 0.132 Angle : 0.519 5.037 18774 Z= 0.270 Chirality : 0.044 0.135 2184 Planarity : 0.004 0.037 2439 Dihedral : 5.400 44.121 2060 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.40 % Allowed : 19.09 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1755 helix: 1.67 (0.22), residues: 558 sheet: 0.33 (0.24), residues: 444 loop : -1.00 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 313 TYR 0.018 0.001 TYR C 318 PHE 0.014 0.001 PHE A 157 TRP 0.007 0.002 TRP B 173 HIS 0.002 0.000 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (13788) covalent geometry : angle 0.51874 / 0.27 (18774) hydrogen bonds : bond 0.03510 / 2.32 ( 720) hydrogen bonds : angle 4.68811 / 3.22 ( 1980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: A 130 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8252 (mtt) REVERT: B 66 PHE cc_start: 0.8017 (m-80) cc_final: 0.7733 (m-80) REVERT: B 330 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7335 (mtm-85) REVERT: B 397 ILE cc_start: 0.8552 (mm) cc_final: 0.8285 (mm) REVERT: C 130 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8585 (mtt) REVERT: C 330 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7410 (mtm110) REVERT: C 383 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8033 (tp) REVERT: C 470 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7940 (p) outliers start: 47 outliers final: 31 residues processed: 206 average time/residue: 0.1098 time to fit residues: 34.2026 Evaluate side-chains 203 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 130 optimal weight: 0.1980 chunk 173 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.166846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126564 restraints weight = 14518.636| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.97 r_work: 0.3365 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 13788 Z= 0.105 Angle : 0.488 4.949 18774 Z= 0.254 Chirality : 0.043 0.132 2184 Planarity : 0.004 0.033 2439 Dihedral : 5.020 42.483 2055 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.25 % Allowed : 19.67 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.20), residues: 1755 helix: 1.81 (0.22), residues: 561 sheet: 0.53 (0.24), residues: 444 loop : -0.81 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 330 TYR 0.011 0.001 TYR C 80 PHE 0.012 0.001 PHE A 157 TRP 0.007 0.002 TRP B 173 HIS 0.001 0.000 HIS C 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13788) covalent geometry : angle 0.48825 / 0.25 (18774) hydrogen bonds : bond 0.03219 / 2.13 ( 720) hydrogen bonds : angle 4.55407 / 3.11 ( 1980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: A 130 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8060 (mtt) REVERT: B 63 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6798 (ptpt) REVERT: B 74 ASP cc_start: 0.8586 (m-30) cc_final: 0.8357 (m-30) REVERT: B 314 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7776 (tp) REVERT: B 330 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7375 (mtm-85) REVERT: B 356 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7142 (mt) REVERT: B 397 ILE cc_start: 0.8535 (mm) cc_final: 0.8277 (mm) REVERT: C 330 ARG cc_start: 0.7713 (mtm110) cc_final: 0.7413 (mtm110) REVERT: C 332 LEU cc_start: 0.8370 (tp) cc_final: 0.8113 (mp) REVERT: C 383 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8011 (tp) REVERT: C 470 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7860 (p) outliers start: 45 outliers final: 28 residues processed: 213 average time/residue: 0.1052 time to fit residues: 33.7327 Evaluate side-chains 203 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 538 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 144 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 1 optimal weight: 0.0030 chunk 162 optimal weight: 3.9990 chunk 21 optimal weight: 0.0470 chunk 155 optimal weight: 0.0070 chunk 136 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 overall best weight: 0.6108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.166727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.126497 restraints weight = 14413.938| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.95 r_work: 0.3375 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13788 Z= 0.113 Angle : 0.493 5.989 18774 Z= 0.255 Chirality : 0.043 0.133 2184 Planarity : 0.004 0.036 2439 Dihedral : 4.943 41.274 2055 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.40 % Allowed : 19.88 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.20), residues: 1755 helix: 1.90 (0.22), residues: 561 sheet: 0.66 (0.24), residues: 444 loop : -0.70 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 330 TYR 0.010 0.001 TYR C 80 PHE 0.012 0.001 PHE A 157 TRP 0.006 0.002 TRP B 173 HIS 0.001 0.000 HIS B 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (13788) covalent geometry : angle 0.49253 / 0.26 (18774) hydrogen bonds : bond 0.03254 / 2.15 ( 720) hydrogen bonds : angle 4.48158 / 3.07 ( 1980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: A 130 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8051 (mtt) REVERT: A 314 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7585 (tp) REVERT: B 74 ASP cc_start: 0.8620 (m-30) cc_final: 0.8390 (m-30) REVERT: B 314 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7540 (tp) REVERT: B 356 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7137 (mt) REVERT: B 397 ILE cc_start: 0.8516 (mm) cc_final: 0.8255 (mm) REVERT: C 130 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8499 (mtt) REVERT: C 314 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7903 (tt) REVERT: C 330 ARG cc_start: 0.7715 (mtm110) cc_final: 0.7396 (mtm110) REVERT: C 332 LEU cc_start: 0.8394 (tp) cc_final: 0.8123 (mp) REVERT: C 383 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8030 (tp) REVERT: C 397 ILE cc_start: 0.8391 (mm) cc_final: 0.8138 (mm) REVERT: C 470 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7913 (p) outliers start: 47 outliers final: 33 residues processed: 209 average time/residue: 0.1050 time to fit residues: 32.7334 Evaluate side-chains 211 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 538 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 77 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 57 optimal weight: 0.0770 chunk 145 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.166678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126495 restraints weight = 14420.578| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.96 r_work: 0.3374 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13788 Z= 0.118 Angle : 0.493 5.193 18774 Z= 0.255 Chirality : 0.043 0.136 2184 Planarity : 0.004 0.034 2439 Dihedral : 4.879 40.085 2055 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.05 % Allowed : 19.31 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1755 helix: 1.96 (0.22), residues: 561 sheet: 0.71 (0.24), residues: 444 loop : -0.61 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 330 TYR 0.014 0.001 TYR C 515 PHE 0.013 0.001 PHE A 157 TRP 0.007 0.002 TRP B 173 HIS 0.001 0.000 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (13788) covalent geometry : angle 0.49346 / 0.26 (18774) hydrogen bonds : bond 0.03283 / 2.17 ( 720) hydrogen bonds : angle 4.46476 / 3.05 ( 1980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: A 130 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8062 (mtt) REVERT: A 314 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7630 (tp) REVERT: A 330 ARG cc_start: 0.7577 (mtm180) cc_final: 0.7132 (mtm-85) REVERT: A 389 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8019 (t70) REVERT: B 63 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6706 (ptpt) REVERT: B 74 ASP cc_start: 0.8629 (m-30) cc_final: 0.8401 (m-30) REVERT: B 122 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: B 314 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7555 (tp) REVERT: B 356 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7132 (mt) REVERT: B 397 ILE cc_start: 0.8499 (mm) cc_final: 0.8255 (mm) REVERT: C 130 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8511 (mtt) REVERT: C 314 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8013 (tp) REVERT: C 330 ARG cc_start: 0.7691 (mtm110) cc_final: 0.7340 (mtm110) REVERT: C 332 LEU cc_start: 0.8409 (tp) cc_final: 0.8143 (mp) REVERT: C 383 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7997 (tp) REVERT: C 397 ILE cc_start: 0.8394 (mm) cc_final: 0.8139 (mm) REVERT: C 470 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7917 (p) outliers start: 56 outliers final: 41 residues processed: 218 average time/residue: 0.1007 time to fit residues: 32.8993 Evaluate side-chains 228 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 46 optimal weight: 0.0980 chunk 118 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 155 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128850 restraints weight = 14227.810| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.79 r_work: 0.3382 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13788 Z= 0.102 Angle : 0.476 4.962 18774 Z= 0.246 Chirality : 0.043 0.136 2184 Planarity : 0.003 0.033 2439 Dihedral : 4.767 38.979 2055 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.69 % Allowed : 19.60 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1755 helix: 2.06 (0.22), residues: 561 sheet: 0.76 (0.24), residues: 444 loop : -0.49 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 330 TYR 0.011 0.001 TYR C 80 PHE 0.012 0.001 PHE B 157 TRP 0.007 0.002 TRP B 173 HIS 0.001 0.000 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (13788) covalent geometry : angle 0.47646 / 0.25 (18774) hydrogen bonds : bond 0.03089 / 2.04 ( 720) hydrogen bonds : angle 4.39362 / 3.00 ( 1980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 174 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: A 130 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8008 (mtt) REVERT: A 330 ARG cc_start: 0.7541 (mtm180) cc_final: 0.7103 (mtm-85) REVERT: A 389 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7973 (t70) REVERT: A 397 ILE cc_start: 0.8417 (mm) cc_final: 0.8210 (mm) REVERT: A 528 PHE cc_start: 0.7501 (m-10) cc_final: 0.7221 (m-10) REVERT: B 63 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6721 (ptpt) REVERT: B 74 ASP cc_start: 0.8590 (m-30) cc_final: 0.8361 (m-30) REVERT: B 122 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: B 207 MET cc_start: 0.8197 (mtm) cc_final: 0.7796 (ptp) REVERT: B 314 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7603 (tp) REVERT: B 330 ARG cc_start: 0.7589 (mtm180) cc_final: 0.6981 (mtm-85) REVERT: B 356 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7162 (mt) REVERT: B 397 ILE cc_start: 0.8500 (mm) cc_final: 0.8263 (mm) REVERT: C 111 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7729 (mp) REVERT: C 130 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8451 (mtt) REVERT: C 314 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8037 (tp) REVERT: C 330 ARG cc_start: 0.7662 (mtm110) cc_final: 0.7331 (mtm110) REVERT: C 332 LEU cc_start: 0.8458 (tp) cc_final: 0.8200 (mp) REVERT: C 383 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8002 (tp) REVERT: C 397 ILE cc_start: 0.8361 (mm) cc_final: 0.8094 (mm) outliers start: 51 outliers final: 35 residues processed: 211 average time/residue: 0.1134 time to fit residues: 35.8681 Evaluate side-chains 216 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 10 optimal weight: 0.0470 chunk 51 optimal weight: 0.3980 chunk 151 optimal weight: 0.7980 overall best weight: 1.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.164823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125786 restraints weight = 14455.761| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.78 r_work: 0.3346 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13788 Z= 0.175 Angle : 0.547 15.619 18774 Z= 0.278 Chirality : 0.045 0.172 2184 Planarity : 0.004 0.031 2439 Dihedral : 4.854 39.060 2055 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.62 % Allowed : 20.46 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1755 helix: 1.92 (0.22), residues: 561 sheet: 0.67 (0.24), residues: 444 loop : -0.57 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 313 TYR 0.011 0.002 TYR C 80 PHE 0.016 0.001 PHE A 533 TRP 0.006 0.002 TRP B 173 HIS 0.002 0.000 HIS B 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (13788) covalent geometry : angle 0.54693 / 0.28 (18774) hydrogen bonds : bond 0.03727 / 2.45 ( 720) hydrogen bonds : angle 4.54037 / 3.10 ( 1980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: A 130 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8360 (mtt) REVERT: B 122 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: B 314 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7754 (tp) REVERT: B 356 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7268 (mt) REVERT: B 397 ILE cc_start: 0.8565 (mm) cc_final: 0.8311 (mm) REVERT: C 111 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7823 (mp) REVERT: C 130 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8539 (mtt) REVERT: C 314 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8000 (tp) REVERT: C 330 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7341 (mtm110) REVERT: C 332 LEU cc_start: 0.8474 (tp) cc_final: 0.8236 (mp) REVERT: C 383 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8057 (tp) outliers start: 50 outliers final: 38 residues processed: 212 average time/residue: 0.1108 time to fit residues: 35.4895 Evaluate side-chains 223 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 133 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.165522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126284 restraints weight = 14325.603| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.78 r_work: 0.3358 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13788 Z= 0.145 Angle : 0.522 13.239 18774 Z= 0.267 Chirality : 0.044 0.148 2184 Planarity : 0.004 0.032 2439 Dihedral : 4.838 39.993 2055 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.47 % Allowed : 20.46 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1755 helix: 1.95 (0.22), residues: 561 sheet: 0.69 (0.24), residues: 444 loop : -0.51 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 330 TYR 0.011 0.001 TYR C 80 PHE 0.013 0.001 PHE A 157 TRP 0.007 0.002 TRP B 173 HIS 0.002 0.000 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.14 (13788) covalent geometry : angle 0.52190 / 0.27 (18774) hydrogen bonds : bond 0.03518 / 2.32 ( 720) hydrogen bonds : angle 4.52859 / 3.09 ( 1980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: A 130 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8241 (mtt) REVERT: A 330 ARG cc_start: 0.7569 (mtm180) cc_final: 0.7229 (mtm-85) REVERT: A 393 MET cc_start: 0.9204 (mmm) cc_final: 0.8975 (mmp) REVERT: A 397 ILE cc_start: 0.8498 (mm) cc_final: 0.8252 (mm) REVERT: A 528 PHE cc_start: 0.7567 (m-10) cc_final: 0.7329 (m-10) REVERT: B 122 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: B 314 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7769 (tp) REVERT: B 330 ARG cc_start: 0.7557 (mtm180) cc_final: 0.7024 (mtm-85) REVERT: B 356 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7233 (mt) REVERT: B 386 THR cc_start: 0.8454 (t) cc_final: 0.7958 (t) REVERT: B 397 ILE cc_start: 0.8566 (mm) cc_final: 0.8312 (mm) REVERT: C 111 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7774 (mp) REVERT: C 130 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8554 (mtt) REVERT: C 330 ARG cc_start: 0.7672 (mtm110) cc_final: 0.7337 (mtm110) REVERT: C 332 LEU cc_start: 0.8466 (tp) cc_final: 0.8224 (mp) REVERT: C 383 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8051 (tp) REVERT: C 462 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7891 (mm-30) outliers start: 48 outliers final: 36 residues processed: 211 average time/residue: 0.1045 time to fit residues: 33.2563 Evaluate side-chains 218 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 37 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 113 optimal weight: 4.9990 chunk 167 optimal weight: 0.0020 chunk 109 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.166063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126811 restraints weight = 14469.826| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.80 r_work: 0.3359 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13788 Z= 0.128 Angle : 0.521 13.597 18774 Z= 0.264 Chirality : 0.044 0.142 2184 Planarity : 0.004 0.032 2439 Dihedral : 4.793 39.743 2055 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.47 % Allowed : 20.54 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1755 helix: 2.01 (0.22), residues: 561 sheet: 0.71 (0.24), residues: 444 loop : -0.47 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 313 TYR 0.011 0.001 TYR C 80 PHE 0.013 0.001 PHE A 157 TRP 0.007 0.002 TRP B 173 HIS 0.001 0.000 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (13788) covalent geometry : angle 0.52137 / 0.26 (18774) hydrogen bonds : bond 0.03392 / 2.24 ( 720) hydrogen bonds : angle 4.48744 / 3.06 ( 1980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3604.31 seconds wall clock time: 62 minutes 12.96 seconds (3732.96 seconds total)