Starting phenix.real_space_refine on Wed Mar 4 22:02:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uqf_20846/03_2026/6uqf_20846.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uqf_20846/03_2026/6uqf_20846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uqf_20846/03_2026/6uqf_20846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uqf_20846/03_2026/6uqf_20846.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uqf_20846/03_2026/6uqf_20846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uqf_20846/03_2026/6uqf_20846.map" } resolution = 3.04 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= 0.088 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 Hg 4 10.96 5 P 4 5.49 5 S 136 5.16 5 C 10704 2.51 5 N 2828 2.21 5 O 2852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16528 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4109 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 16, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 2, 'PHE:plan': 3, 'GLU:plan': 12, 'ASN:plan1': 4, 'ASP:plan': 9, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 160 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' HG': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 711 SG CYS A 186 56.848 98.681 88.722 1.00148.82 S ATOM 1195 SG CYS A 264 54.921 95.626 91.187 1.00147.30 S Restraints were copied for chains: B, C, D Time building chain proxies: 3.50, per 1000 atoms: 0.21 Number of scatterers: 16528 At special positions: 0 Unit cell: (122.57, 122.57, 128.75, 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) Hg 4 79.96 S 136 16.00 P 4 15.00 O 2852 8.00 N 2828 7.00 C 10704 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: 1.48 Conformation dependent library (CDL) restraints added in 740.1 milliseconds 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 12 sheets defined 75.8% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 139 through 167 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 193 Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.550A pdb=" N ASP A 225 " --> pdb=" O TRP A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.690A pdb=" N PHE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.975A pdb=" N LEU A 263 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 271 removed outlier: 3.874A pdb=" N LEU A 268 " --> pdb=" O CYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 Processing helix chain 'A' and resid 290 through 322 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'A' and resid 401 through 421 Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 473 through 479 Processing helix chain 'A' and resid 480 through 491 Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'A' and resid 566 through 576 Processing helix chain 'A' and resid 576 through 595 removed outlier: 3.842A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 611 Processing helix chain 'A' and resid 615 through 635 Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 139 through 167 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 193 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 221 through 230 removed outlier: 3.550A pdb=" N ASP B 225 " --> pdb=" O TRP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 240 removed outlier: 3.689A pdb=" N PHE B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.975A pdb=" N LEU B 263 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 removed outlier: 3.873A pdb=" N LEU B 268 " --> pdb=" O CYS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 289 Processing helix chain 'B' and resid 290 through 322 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 Processing helix chain 'B' and resid 401 through 421 Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 473 through 479 Processing helix chain 'B' and resid 480 through 491 Processing helix chain 'B' and resid 540 through 546 Processing helix chain 'B' and resid 566 through 576 Processing helix chain 'B' and resid 576 through 595 removed outlier: 3.843A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 611 Processing helix chain 'B' and resid 615 through 635 Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 139 through 167 Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 193 Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 221 through 230 removed outlier: 3.550A pdb=" N ASP C 225 " --> pdb=" O TRP C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 240 removed outlier: 3.689A pdb=" N PHE C 236 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE C 238 " --> pdb=" O TYR C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.975A pdb=" N LEU C 263 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 271 removed outlier: 3.873A pdb=" N LEU C 268 " --> pdb=" O CYS C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 289 Processing helix chain 'C' and resid 290 through 322 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 Processing helix chain 'C' and resid 401 through 421 Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 473 through 479 Processing helix chain 'C' and resid 480 through 491 Processing helix chain 'C' and resid 540 through 546 Processing helix chain 'C' and resid 566 through 576 Processing helix chain 'C' and resid 576 through 595 removed outlier: 3.842A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 611 Processing helix chain 'C' and resid 615 through 635 Processing helix chain 'D' and resid 95 through 103 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 139 through 167 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 193 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 221 through 230 removed outlier: 3.549A pdb=" N ASP D 225 " --> pdb=" O TRP D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 240 removed outlier: 3.689A pdb=" N PHE D 236 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE D 238 " --> pdb=" O TYR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.975A pdb=" N LEU D 263 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 271 removed outlier: 3.874A pdb=" N LEU D 268 " --> pdb=" O CYS D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 289 Processing helix chain 'D' and resid 290 through 322 Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 335 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 Processing helix chain 'D' and resid 401 through 421 Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 Processing helix chain 'D' and resid 473 through 479 Processing helix chain 'D' and resid 480 through 491 Processing helix chain 'D' and resid 540 through 546 Processing helix chain 'D' and resid 566 through 576 Processing helix chain 'D' and resid 576 through 595 removed outlier: 3.842A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 615 through 635 Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 200 removed outlier: 3.993A pdb=" N THR A 198 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 206 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.231A pdb=" N TYR A 562 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE A 515 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 564 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR A 513 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.210A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 198 through 200 removed outlier: 3.992A pdb=" N THR B 198 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 206 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.231A pdb=" N TYR B 562 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE B 515 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 564 " --> pdb=" O TYR B 513 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR B 513 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.210A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 198 through 200 removed outlier: 3.992A pdb=" N THR C 198 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 206 " --> pdb=" O THR C 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.231A pdb=" N TYR C 562 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE C 515 " --> pdb=" O TYR C 562 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU C 564 " --> pdb=" O TYR C 513 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR C 513 " --> pdb=" O LEU C 564 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.210A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 198 through 200 removed outlier: 3.992A pdb=" N THR D 198 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE D 206 " --> pdb=" O THR D 198 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.231A pdb=" N TYR D 562 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE D 515 " --> pdb=" O TYR D 562 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU D 564 " --> pdb=" O TYR D 513 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR D 513 " --> pdb=" O LEU D 564 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.210A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) 1205 hydrogen bonds defined for protein. 3531 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: 2.74 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5250 1.34 - 1.46: 3586 1.46 - 1.58: 7828 1.58 - 1.69: 8 1.69 - 1.81: 232 Bond restraints: 16904 Sorted by residual: bond pdb=" C3' CMP C 901 " pdb=" C4' CMP C 901 " ideal model delta sigma weight residual 1.521 1.497 0.024 1.50e-02 4.44e+03 2.53e+00 bond pdb=" C3' CMP B 901 " pdb=" C4' CMP B 901 " ideal model delta sigma weight residual 1.521 1.498 0.023 1.50e-02 4.44e+03 2.43e+00 bond pdb=" C3' CMP D 901 " pdb=" C4' CMP D 901 " ideal model delta sigma weight residual 1.521 1.498 0.023 1.50e-02 4.44e+03 2.40e+00 bond pdb=" C3' CMP A 901 " pdb=" C4' CMP A 901 " ideal model delta sigma weight residual 1.521 1.498 0.023 1.50e-02 4.44e+03 2.29e+00 bond pdb=" C4 CMP D 901 " pdb=" C5 CMP D 901 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 16899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 22545 1.73 - 3.47: 327 3.47 - 5.20: 40 5.20 - 6.93: 12 6.93 - 8.67: 8 Bond angle restraints: 22932 Sorted by residual: angle pdb=" O1P CMP A 901 " pdb=" P CMP A 901 " pdb=" O2P CMP A 901 " ideal model delta sigma weight residual 109.50 118.17 -8.67 3.00e+00 1.11e-01 8.34e+00 angle pdb=" O1P CMP B 901 " pdb=" P CMP B 901 " pdb=" O2P CMP B 901 " ideal model delta sigma weight residual 109.50 118.16 -8.66 3.00e+00 1.11e-01 8.32e+00 angle pdb=" O1P CMP D 901 " pdb=" P CMP D 901 " pdb=" O2P CMP D 901 " ideal model delta sigma weight residual 109.50 118.15 -8.65 3.00e+00 1.11e-01 8.32e+00 angle pdb=" O1P CMP C 901 " pdb=" P CMP C 901 " pdb=" O2P CMP C 901 " ideal model delta sigma weight residual 109.50 118.14 -8.64 3.00e+00 1.11e-01 8.29e+00 angle pdb=" C3' CMP C 901 " pdb=" O3' CMP C 901 " pdb=" P CMP C 901 " ideal model delta sigma weight residual 120.50 112.35 8.15 3.00e+00 1.11e-01 7.37e+00 ... (remaining 22927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.69: 9708 25.69 - 51.38: 304 51.38 - 77.07: 28 77.07 - 102.76: 8 102.76 - 128.46: 4 Dihedral angle restraints: 10052 sinusoidal: 3796 harmonic: 6256 Sorted by residual: dihedral pdb=" CA ASP D 189 " pdb=" CB ASP D 189 " pdb=" CG ASP D 189 " pdb=" OD1 ASP D 189 " ideal model delta sinusoidal sigma weight residual -30.00 -86.72 56.72 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP B 189 " pdb=" CB ASP B 189 " pdb=" CG ASP B 189 " pdb=" OD1 ASP B 189 " ideal model delta sinusoidal sigma weight residual -30.00 -86.71 56.71 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " pdb=" CG ASP A 189 " pdb=" OD1 ASP A 189 " ideal model delta sinusoidal sigma weight residual -30.00 -86.70 56.70 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 10049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1677 0.029 - 0.058: 556 0.058 - 0.088: 256 0.088 - 0.117: 100 0.117 - 0.146: 15 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CA ILE B 523 " pdb=" N ILE B 523 " pdb=" C ILE B 523 " pdb=" CB ILE B 523 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ILE D 523 " pdb=" N ILE D 523 " pdb=" C ILE D 523 " pdb=" CB ILE D 523 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE C 523 " pdb=" N ILE C 523 " pdb=" C ILE C 523 " pdb=" CB ILE C 523 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 2601 not shown) Planarity restraints: 2864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 576 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 577 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 577 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 577 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 576 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO D 577 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 577 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 577 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 576 " 0.019 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO B 577 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 577 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 577 " 0.017 5.00e-02 4.00e+02 ... (remaining 2861 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 272 2.69 - 3.24: 16847 3.24 - 3.79: 26051 3.79 - 4.35: 32085 4.35 - 4.90: 55027 Nonbonded interactions: 130282 Sorted by model distance: nonbonded pdb=" O ASN A 216 " pdb=" OG SER A 220 " model vdw 2.135 3.040 nonbonded pdb=" O ASN B 216 " pdb=" OG SER B 220 " model vdw 2.136 3.040 nonbonded pdb=" O ASN D 216 " pdb=" OG SER D 220 " model vdw 2.136 3.040 nonbonded pdb=" O ASN C 216 " pdb=" OG SER C 220 " model vdw 2.136 3.040 nonbonded pdb=" SG CYS C 264 " pdb="HG HG C 902 " model vdw 2.181 2.880 ... (remaining 130277 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.290 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.003 0.029 16904 Z= 0.163 Angle : 0.576 8.666 22932 Z= 0.325 Chirality : 0.039 0.146 2604 Planarity : 0.003 0.030 2864 Dihedral : 13.015 128.456 5996 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.16), residues: 2108 helix: 0.17 (0.12), residues: 1516 sheet: -0.20 (0.47), residues: 108 loop : -2.97 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 554 TYR 0.011 0.001 TYR A 411 PHE 0.009 0.001 PHE C 493 TRP 0.010 0.001 TRP B 373 HIS 0.003 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00340 (16904) covalent geometry : angle 0.57602 (22932) hydrogen bonds : bond 0.08605 ( 1205) hydrogen bonds : angle 4.99854 ( 3531) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.516 Fit side-chains REVERT: A 101 MET cc_start: 0.7372 (mmt) cc_final: 0.7120 (mmt) REVERT: A 108 LYS cc_start: 0.6840 (mmmt) cc_final: 0.6520 (tttt) REVERT: A 336 MET cc_start: 0.8465 (ptp) cc_final: 0.8036 (ptp) REVERT: A 492 ARG cc_start: 0.7298 (ttt-90) cc_final: 0.7091 (ttp80) REVERT: B 101 MET cc_start: 0.7628 (mmt) cc_final: 0.7250 (mmt) REVERT: B 108 LYS cc_start: 0.6970 (mmmt) cc_final: 0.6710 (tttt) REVERT: B 113 MET cc_start: 0.7792 (tpp) cc_final: 0.7550 (tpt) REVERT: B 336 MET cc_start: 0.8569 (ptp) cc_final: 0.8300 (ptp) REVERT: B 460 GLU cc_start: 0.7065 (tt0) cc_final: 0.6768 (mt-10) REVERT: C 101 MET cc_start: 0.7595 (mmt) cc_final: 0.7165 (mmt) REVERT: C 108 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6666 (tttt) REVERT: C 113 MET cc_start: 0.7879 (tpp) cc_final: 0.7653 (tpt) REVERT: C 336 MET cc_start: 0.8577 (ptp) cc_final: 0.8222 (ptp) REVERT: C 460 GLU cc_start: 0.7064 (tt0) cc_final: 0.6782 (mt-10) REVERT: C 492 ARG cc_start: 0.7168 (ttt-90) cc_final: 0.6944 (ttp80) REVERT: D 101 MET cc_start: 0.7648 (mmt) cc_final: 0.7257 (mmt) REVERT: D 108 LYS cc_start: 0.7065 (mmmt) cc_final: 0.6775 (tttt) REVERT: D 113 MET cc_start: 0.7813 (tpp) cc_final: 0.7580 (tpt) REVERT: D 336 MET cc_start: 0.8579 (ptp) cc_final: 0.8248 (ptp) REVERT: D 460 GLU cc_start: 0.7066 (tt0) cc_final: 0.6758 (mt-10) REVERT: D 492 ARG cc_start: 0.7252 (ttt-90) cc_final: 0.7004 (ttp80) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1317 time to fit residues: 54.9673 Evaluate side-chains 212 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 451 ASN A 463 ASN A 497 GLN B 408 GLN B 451 ASN B 463 ASN C 398 GLN C 408 GLN C 451 ASN C 463 ASN D 398 GLN D 408 GLN D 451 ASN D 463 ASN D 517 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.175131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125561 restraints weight = 8818.363| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.36 r_work: 0.3443 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16904 Z= 0.152 Angle : 0.552 7.988 22932 Z= 0.286 Chirality : 0.041 0.166 2604 Planarity : 0.004 0.032 2864 Dihedral : 6.937 131.425 2356 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.64 % Allowed : 4.74 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2108 helix: 1.42 (0.12), residues: 1528 sheet: 0.16 (0.47), residues: 108 loop : -2.25 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 580 TYR 0.012 0.001 TYR B 277 PHE 0.010 0.001 PHE B 493 TRP 0.014 0.001 TRP A 330 HIS 0.003 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00336 (16904) covalent geometry : angle 0.55234 (22932) hydrogen bonds : bond 0.04809 ( 1205) hydrogen bonds : angle 4.45202 ( 3531) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 0.627 Fit side-chains REVERT: A 101 MET cc_start: 0.7558 (mmt) cc_final: 0.7170 (mmt) REVERT: A 336 MET cc_start: 0.8855 (ptp) cc_final: 0.8341 (ptp) REVERT: A 356 MET cc_start: 0.8358 (ttm) cc_final: 0.8131 (ttm) REVERT: B 101 MET cc_start: 0.7827 (mmt) cc_final: 0.7354 (mmt) REVERT: B 108 LYS cc_start: 0.7338 (mmmt) cc_final: 0.6924 (tttt) REVERT: B 336 MET cc_start: 0.8763 (ptp) cc_final: 0.8349 (ptp) REVERT: B 460 GLU cc_start: 0.8006 (tt0) cc_final: 0.7666 (mt-10) REVERT: C 108 LYS cc_start: 0.7256 (mmmt) cc_final: 0.7045 (tttt) REVERT: C 336 MET cc_start: 0.8859 (ptp) cc_final: 0.8296 (ptp) REVERT: C 356 MET cc_start: 0.8345 (ttm) cc_final: 0.8097 (ttm) REVERT: C 460 GLU cc_start: 0.7990 (tt0) cc_final: 0.7653 (mt-10) REVERT: D 101 MET cc_start: 0.7859 (mmt) cc_final: 0.7416 (mmt) REVERT: D 108 LYS cc_start: 0.7402 (mmmt) cc_final: 0.6999 (tttt) REVERT: D 353 MET cc_start: 0.8711 (ttp) cc_final: 0.8447 (mtp) REVERT: D 356 MET cc_start: 0.8354 (ttm) cc_final: 0.8151 (ttm) REVERT: D 460 GLU cc_start: 0.8030 (tt0) cc_final: 0.7674 (mt-10) outliers start: 27 outliers final: 6 residues processed: 246 average time/residue: 0.1153 time to fit residues: 45.4867 Evaluate side-chains 212 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 206 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 235 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 178 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 169 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.173443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125851 restraints weight = 6575.179| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.15 r_work: 0.3450 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16904 Z= 0.191 Angle : 0.578 8.626 22932 Z= 0.299 Chirality : 0.042 0.169 2604 Planarity : 0.004 0.037 2864 Dihedral : 6.913 130.083 2356 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.01 % Allowed : 7.18 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.18), residues: 2108 helix: 1.73 (0.13), residues: 1528 sheet: 0.22 (0.46), residues: 108 loop : -1.86 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 580 TYR 0.017 0.002 TYR D 347 PHE 0.014 0.001 PHE B 109 TRP 0.013 0.002 TRP D 330 HIS 0.004 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00450 (16904) covalent geometry : angle 0.57768 (22932) hydrogen bonds : bond 0.05166 ( 1205) hydrogen bonds : angle 4.45570 ( 3531) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.725 Fit side-chains REVERT: A 336 MET cc_start: 0.8836 (ptp) cc_final: 0.8248 (ptp) REVERT: A 356 MET cc_start: 0.8390 (ttm) cc_final: 0.8132 (ttm) REVERT: B 101 MET cc_start: 0.7842 (mmt) cc_final: 0.7395 (mmt) REVERT: B 108 LYS cc_start: 0.7349 (mmmt) cc_final: 0.7102 (tttt) REVERT: B 460 GLU cc_start: 0.8014 (tt0) cc_final: 0.7750 (mt-10) REVERT: C 101 MET cc_start: 0.7729 (mmm) cc_final: 0.7402 (mmt) REVERT: C 356 MET cc_start: 0.8379 (ttm) cc_final: 0.8148 (ttm) REVERT: D 101 MET cc_start: 0.7864 (mmt) cc_final: 0.7399 (mmt) REVERT: D 108 LYS cc_start: 0.7349 (mmmt) cc_final: 0.7084 (tttt) REVERT: D 353 MET cc_start: 0.8700 (ttp) cc_final: 0.8486 (mtp) REVERT: D 356 MET cc_start: 0.8359 (ttm) cc_final: 0.8121 (ttm) outliers start: 33 outliers final: 13 residues processed: 252 average time/residue: 0.1283 time to fit residues: 49.7163 Evaluate side-chains 223 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 235 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.175555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128676 restraints weight = 6703.612| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.15 r_work: 0.3459 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16904 Z= 0.158 Angle : 0.540 8.053 22932 Z= 0.280 Chirality : 0.041 0.163 2604 Planarity : 0.004 0.035 2864 Dihedral : 6.940 131.415 2356 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.76 % Allowed : 8.70 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.18), residues: 2108 helix: 1.93 (0.13), residues: 1528 sheet: -0.02 (0.44), residues: 108 loop : -1.71 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 580 TYR 0.014 0.001 TYR D 347 PHE 0.012 0.001 PHE A 222 TRP 0.010 0.001 TRP D 330 HIS 0.004 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00360 (16904) covalent geometry : angle 0.54007 (22932) hydrogen bonds : bond 0.04720 ( 1205) hydrogen bonds : angle 4.32952 ( 3531) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 0.641 Fit side-chains REVERT: A 336 MET cc_start: 0.8756 (ptp) cc_final: 0.8155 (ptp) REVERT: B 101 MET cc_start: 0.7742 (mmt) cc_final: 0.7303 (mmt) REVERT: B 108 LYS cc_start: 0.7219 (mmmt) cc_final: 0.6989 (tttt) REVERT: B 336 MET cc_start: 0.8670 (ptp) cc_final: 0.8336 (ptp) REVERT: C 101 MET cc_start: 0.7679 (mmm) cc_final: 0.7374 (mmt) REVERT: C 336 MET cc_start: 0.8772 (ptp) cc_final: 0.8315 (ptp) REVERT: D 101 MET cc_start: 0.7784 (mmt) cc_final: 0.7295 (mmt) REVERT: D 108 LYS cc_start: 0.7173 (mmmt) cc_final: 0.6946 (tttt) REVERT: D 336 MET cc_start: 0.8642 (ptp) cc_final: 0.8309 (ptp) REVERT: D 356 MET cc_start: 0.8312 (ttm) cc_final: 0.8091 (ttm) outliers start: 29 outliers final: 16 residues processed: 235 average time/residue: 0.1085 time to fit residues: 40.7677 Evaluate side-chains 220 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 127 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.174042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125620 restraints weight = 7487.490| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.24 r_work: 0.3438 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16904 Z= 0.172 Angle : 0.550 8.247 22932 Z= 0.286 Chirality : 0.041 0.167 2604 Planarity : 0.004 0.036 2864 Dihedral : 6.919 130.981 2356 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.13 % Allowed : 9.06 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.18), residues: 2108 helix: 1.98 (0.13), residues: 1528 sheet: -0.10 (0.43), residues: 108 loop : -1.58 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 593 TYR 0.015 0.001 TYR B 347 PHE 0.012 0.001 PHE A 222 TRP 0.011 0.001 TRP B 330 HIS 0.004 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00403 (16904) covalent geometry : angle 0.55047 (22932) hydrogen bonds : bond 0.04857 ( 1205) hydrogen bonds : angle 4.33896 ( 3531) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.706 Fit side-chains REVERT: A 270 ARG cc_start: 0.5361 (OUTLIER) cc_final: 0.4912 (ptp-170) REVERT: A 336 MET cc_start: 0.8796 (ptp) cc_final: 0.8182 (ptp) REVERT: B 101 MET cc_start: 0.7763 (mmt) cc_final: 0.7335 (mmt) REVERT: B 108 LYS cc_start: 0.7186 (mmmt) cc_final: 0.6974 (tttt) REVERT: B 336 MET cc_start: 0.8698 (ptp) cc_final: 0.8256 (ptp) REVERT: C 101 MET cc_start: 0.7714 (mmm) cc_final: 0.7402 (mmt) REVERT: C 270 ARG cc_start: 0.5289 (OUTLIER) cc_final: 0.4926 (ptp-170) REVERT: C 336 MET cc_start: 0.8794 (ptp) cc_final: 0.8369 (ptp) REVERT: D 101 MET cc_start: 0.7810 (mmt) cc_final: 0.7335 (mmt) REVERT: D 108 LYS cc_start: 0.7217 (mmmt) cc_final: 0.6991 (tttt) REVERT: D 270 ARG cc_start: 0.5279 (OUTLIER) cc_final: 0.4768 (ptp-170) REVERT: D 336 MET cc_start: 0.8644 (ptp) cc_final: 0.8204 (ptp) outliers start: 35 outliers final: 18 residues processed: 236 average time/residue: 0.1342 time to fit residues: 48.1755 Evaluate side-chains 231 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 270 ARG Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 178 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 131 optimal weight: 0.1980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.172958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123269 restraints weight = 8946.922| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.37 r_work: 0.3410 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16904 Z= 0.179 Angle : 0.557 8.182 22932 Z= 0.289 Chirality : 0.042 0.167 2604 Planarity : 0.004 0.036 2864 Dihedral : 6.917 130.916 2356 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.01 % Allowed : 9.55 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.18), residues: 2108 helix: 2.00 (0.13), residues: 1528 sheet: -0.15 (0.43), residues: 108 loop : -1.50 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 428 TYR 0.016 0.001 TYR D 347 PHE 0.011 0.001 PHE A 222 TRP 0.012 0.001 TRP B 330 HIS 0.004 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00420 (16904) covalent geometry : angle 0.55654 (22932) hydrogen bonds : bond 0.04931 ( 1205) hydrogen bonds : angle 4.34013 ( 3531) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 0.480 Fit side-chains REVERT: A 270 ARG cc_start: 0.5340 (OUTLIER) cc_final: 0.4916 (ptp-170) REVERT: A 336 MET cc_start: 0.8820 (ptp) cc_final: 0.8249 (ptp) REVERT: B 101 MET cc_start: 0.7783 (mmt) cc_final: 0.7333 (mmt) REVERT: B 108 LYS cc_start: 0.7242 (mmmt) cc_final: 0.7001 (tttt) REVERT: B 170 GLN cc_start: 0.5983 (pm20) cc_final: 0.5759 (pm20) REVERT: B 336 MET cc_start: 0.8701 (ptp) cc_final: 0.8255 (ptp) REVERT: C 101 MET cc_start: 0.7729 (mmm) cc_final: 0.7408 (mmt) REVERT: C 270 ARG cc_start: 0.5325 (OUTLIER) cc_final: 0.4960 (ptp-170) REVERT: C 336 MET cc_start: 0.8804 (ptp) cc_final: 0.8374 (ptp) REVERT: D 101 MET cc_start: 0.7814 (mmt) cc_final: 0.7347 (mmt) REVERT: D 108 LYS cc_start: 0.7226 (mmmt) cc_final: 0.6990 (tttt) REVERT: D 170 GLN cc_start: 0.6011 (pm20) cc_final: 0.5670 (pm20) REVERT: D 270 ARG cc_start: 0.5338 (OUTLIER) cc_final: 0.4814 (ptp-170) REVERT: D 336 MET cc_start: 0.8661 (ptp) cc_final: 0.8222 (ptp) outliers start: 33 outliers final: 26 residues processed: 243 average time/residue: 0.1252 time to fit residues: 46.9131 Evaluate side-chains 236 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 270 ARG Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 4 optimal weight: 0.5980 chunk 163 optimal weight: 0.3980 chunk 204 optimal weight: 0.5980 chunk 188 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.176684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127801 restraints weight = 9214.740| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.39 r_work: 0.3453 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16904 Z= 0.125 Angle : 0.519 7.829 22932 Z= 0.266 Chirality : 0.039 0.155 2604 Planarity : 0.004 0.035 2864 Dihedral : 6.957 132.760 2356 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.76 % Allowed : 10.58 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.18), residues: 2108 helix: 2.22 (0.13), residues: 1524 sheet: -0.09 (0.45), residues: 108 loop : -1.39 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 258 TYR 0.013 0.001 TYR C 277 PHE 0.010 0.001 PHE A 222 TRP 0.009 0.001 TRP B 175 HIS 0.002 0.001 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.00262 (16904) covalent geometry : angle 0.51908 (22932) hydrogen bonds : bond 0.04162 ( 1205) hydrogen bonds : angle 4.19774 ( 3531) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.672 Fit side-chains REVERT: A 270 ARG cc_start: 0.5496 (OUTLIER) cc_final: 0.5033 (ptp-170) REVERT: A 336 MET cc_start: 0.8773 (ptp) cc_final: 0.8205 (ptp) REVERT: B 101 MET cc_start: 0.7782 (mmt) cc_final: 0.7348 (mmt) REVERT: B 336 MET cc_start: 0.8587 (ptp) cc_final: 0.8147 (ptp) REVERT: C 101 MET cc_start: 0.7725 (mmm) cc_final: 0.7458 (mmt) REVERT: C 270 ARG cc_start: 0.5400 (OUTLIER) cc_final: 0.5053 (ptp-170) REVERT: C 336 MET cc_start: 0.8658 (ptp) cc_final: 0.8258 (ptp) REVERT: D 101 MET cc_start: 0.7837 (mmt) cc_final: 0.7382 (mmt) REVERT: D 270 ARG cc_start: 0.5467 (OUTLIER) cc_final: 0.4974 (ptp-170) REVERT: D 336 MET cc_start: 0.8567 (ptp) cc_final: 0.8165 (ptp) outliers start: 29 outliers final: 22 residues processed: 237 average time/residue: 0.1270 time to fit residues: 46.1948 Evaluate side-chains 240 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 270 ARG Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 110 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.175397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125531 restraints weight = 8621.399| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.41 r_work: 0.3437 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16904 Z= 0.137 Angle : 0.548 9.308 22932 Z= 0.275 Chirality : 0.040 0.159 2604 Planarity : 0.004 0.035 2864 Dihedral : 6.906 131.949 2356 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.07 % Allowed : 11.07 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.18), residues: 2108 helix: 2.23 (0.13), residues: 1532 sheet: -0.10 (0.44), residues: 108 loop : -1.30 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 267 TYR 0.014 0.001 TYR D 277 PHE 0.010 0.001 PHE A 222 TRP 0.011 0.001 TRP B 175 HIS 0.003 0.001 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00302 (16904) covalent geometry : angle 0.54797 (22932) hydrogen bonds : bond 0.04298 ( 1205) hydrogen bonds : angle 4.19788 ( 3531) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.657 Fit side-chains REVERT: A 270 ARG cc_start: 0.5397 (OUTLIER) cc_final: 0.4937 (ptp-170) REVERT: A 336 MET cc_start: 0.8728 (ptp) cc_final: 0.8161 (ptp) REVERT: B 101 MET cc_start: 0.7767 (mmt) cc_final: 0.7334 (mmt) REVERT: B 336 MET cc_start: 0.8559 (ptp) cc_final: 0.8118 (ptp) REVERT: C 101 MET cc_start: 0.7722 (mmm) cc_final: 0.7429 (mmt) REVERT: C 270 ARG cc_start: 0.5355 (OUTLIER) cc_final: 0.4997 (ptp-170) REVERT: C 336 MET cc_start: 0.8642 (ptp) cc_final: 0.8236 (ptp) REVERT: D 101 MET cc_start: 0.7816 (mmt) cc_final: 0.7363 (mmt) REVERT: D 270 ARG cc_start: 0.5424 (OUTLIER) cc_final: 0.4936 (ptp-170) REVERT: D 336 MET cc_start: 0.8549 (ptp) cc_final: 0.8147 (ptp) outliers start: 34 outliers final: 23 residues processed: 240 average time/residue: 0.1295 time to fit residues: 47.8516 Evaluate side-chains 241 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 270 ARG Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 100 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.176012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128415 restraints weight = 7815.845| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.26 r_work: 0.3458 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16904 Z= 0.144 Angle : 0.554 8.993 22932 Z= 0.279 Chirality : 0.040 0.162 2604 Planarity : 0.004 0.035 2864 Dihedral : 6.902 131.805 2356 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.76 % Allowed : 11.98 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.18), residues: 2108 helix: 2.24 (0.13), residues: 1532 sheet: -0.06 (0.45), residues: 108 loop : -1.25 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 593 TYR 0.014 0.001 TYR B 347 PHE 0.010 0.001 PHE A 222 TRP 0.011 0.001 TRP B 175 HIS 0.003 0.001 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00324 (16904) covalent geometry : angle 0.55448 (22932) hydrogen bonds : bond 0.04399 ( 1205) hydrogen bonds : angle 4.21424 ( 3531) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.485 Fit side-chains REVERT: A 270 ARG cc_start: 0.5525 (OUTLIER) cc_final: 0.5065 (ptp-170) REVERT: A 336 MET cc_start: 0.8761 (ptp) cc_final: 0.8207 (ptp) REVERT: B 101 MET cc_start: 0.7791 (mmt) cc_final: 0.7344 (mmt) REVERT: B 113 MET cc_start: 0.8258 (mmm) cc_final: 0.7833 (ttt) REVERT: B 336 MET cc_start: 0.8616 (ptp) cc_final: 0.8179 (ptp) REVERT: C 101 MET cc_start: 0.7747 (mmm) cc_final: 0.7444 (mmt) REVERT: C 270 ARG cc_start: 0.5484 (OUTLIER) cc_final: 0.5128 (ptp-170) REVERT: C 336 MET cc_start: 0.8702 (ptp) cc_final: 0.8288 (ptp) REVERT: D 101 MET cc_start: 0.7840 (mmt) cc_final: 0.7379 (mmt) REVERT: D 270 ARG cc_start: 0.5570 (OUTLIER) cc_final: 0.5069 (ptp-170) REVERT: D 336 MET cc_start: 0.8597 (ptp) cc_final: 0.8167 (ptp) outliers start: 29 outliers final: 24 residues processed: 237 average time/residue: 0.1202 time to fit residues: 43.6787 Evaluate side-chains 236 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 270 ARG Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 10 optimal weight: 0.3980 chunk 206 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.177236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.129219 restraints weight = 7740.408| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.31 r_work: 0.3467 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16904 Z= 0.128 Angle : 0.544 9.056 22932 Z= 0.272 Chirality : 0.039 0.157 2604 Planarity : 0.003 0.034 2864 Dihedral : 6.920 132.418 2356 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.76 % Allowed : 11.92 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.18), residues: 2108 helix: 2.30 (0.13), residues: 1532 sheet: -0.04 (0.45), residues: 108 loop : -1.19 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 258 TYR 0.012 0.001 TYR D 277 PHE 0.010 0.001 PHE A 222 TRP 0.011 0.001 TRP B 175 HIS 0.003 0.001 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00277 (16904) covalent geometry : angle 0.54425 (22932) hydrogen bonds : bond 0.04146 ( 1205) hydrogen bonds : angle 4.16378 ( 3531) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.579 Fit side-chains REVERT: A 270 ARG cc_start: 0.5435 (OUTLIER) cc_final: 0.4970 (ptp-170) REVERT: A 336 MET cc_start: 0.8708 (ptp) cc_final: 0.8149 (ptp) REVERT: B 101 MET cc_start: 0.7774 (mmt) cc_final: 0.7330 (mmt) REVERT: B 336 MET cc_start: 0.8553 (ptp) cc_final: 0.8148 (ptp) REVERT: C 101 MET cc_start: 0.7737 (mmm) cc_final: 0.7436 (mmt) REVERT: C 270 ARG cc_start: 0.5404 (OUTLIER) cc_final: 0.5033 (ptp-170) REVERT: C 336 MET cc_start: 0.8634 (ptp) cc_final: 0.8231 (ptp) REVERT: D 101 MET cc_start: 0.7826 (mmt) cc_final: 0.7371 (mmt) REVERT: D 270 ARG cc_start: 0.5487 (OUTLIER) cc_final: 0.4987 (ptp-170) REVERT: D 336 MET cc_start: 0.8542 (ptp) cc_final: 0.8141 (ptp) outliers start: 29 outliers final: 23 residues processed: 237 average time/residue: 0.1190 time to fit residues: 43.6120 Evaluate side-chains 236 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 270 ARG Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 626 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 165 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 135 optimal weight: 0.1980 chunk 177 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.176949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128204 restraints weight = 7683.821| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.32 r_work: 0.3473 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16904 Z= 0.123 Angle : 0.537 8.927 22932 Z= 0.269 Chirality : 0.039 0.155 2604 Planarity : 0.003 0.034 2864 Dihedral : 6.917 132.660 2356 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.82 % Allowed : 12.04 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.18), residues: 2108 helix: 2.35 (0.13), residues: 1532 sheet: 0.04 (0.46), residues: 108 loop : -1.17 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 258 TYR 0.012 0.001 TYR D 277 PHE 0.019 0.001 PHE D 109 TRP 0.013 0.001 TRP D 175 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00259 (16904) covalent geometry : angle 0.53723 (22932) hydrogen bonds : bond 0.04033 ( 1205) hydrogen bonds : angle 4.14369 ( 3531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4604.54 seconds wall clock time: 79 minutes 21.43 seconds (4761.43 seconds total)