Starting phenix.real_space_refine on Sat Sep 12 15:39:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uqf_20846/09_2026/6uqf_20846.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uqf_20846/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6uqf_20846/09_2026/6uqf_20846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uqf_20846/09_2026/6uqf_20846.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6uqf_20846/09_2026/6uqf_20846.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uqf_20846/09_2026/6uqf_20846.cif" model { file = "/net/cci-nas-00/data/ceres_data/6uqf_20846/09_2026/6uqf_20846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uqf_20846/09_2026/6uqf_20846.cif" } 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): 0.02s 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: 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: {'RNAv2': 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: 3.88, per 1000 atoms: 0.23 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: 1.21 Conformation dependent library (CDL) restraints added in 669.7 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: 0.46 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: 3.10 Time building geometry restraints manager: 1.65 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=" C4' CMP C 901 " pdb=" C5' CMP C 901 " ideal model delta sigma weight residual 1.524 1.495 0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C4' CMP A 901 " pdb=" C5' CMP A 901 " ideal model delta sigma weight residual 1.524 1.496 0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" C4' CMP B 901 " pdb=" C5' CMP B 901 " ideal model delta sigma weight residual 1.524 1.496 0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C4' CMP D 901 " pdb=" C5' CMP D 901 " ideal model delta sigma weight residual 1.524 1.496 0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" C3' CMP C 901 " pdb=" C4' CMP C 901 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.80e+00 ... (remaining 16899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 22638 2.05 - 4.09: 234 4.09 - 6.14: 32 6.14 - 8.19: 16 8.19 - 10.23: 12 Bond angle restraints: 22932 Sorted by residual: angle pdb=" C1' CMP C 901 " pdb=" C2' CMP C 901 " pdb=" C3' CMP C 901 " ideal model delta sigma weight residual 111.00 100.77 10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C1' CMP D 901 " pdb=" C2' CMP D 901 " pdb=" C3' CMP D 901 " ideal model delta sigma weight residual 111.00 100.77 10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C1' CMP A 901 " pdb=" C2' CMP A 901 " pdb=" C3' CMP A 901 " ideal model delta sigma weight residual 111.00 100.78 10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C1' CMP B 901 " pdb=" C2' CMP B 901 " pdb=" C3' CMP B 901 " ideal model delta sigma weight residual 111.00 100.78 10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C2' CMP D 901 " pdb=" C3' CMP D 901 " pdb=" C4' CMP D 901 " ideal model delta sigma weight residual 111.00 101.62 9.38 3.00e+00 1.11e-01 9.78e+00 ... (remaining 22927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 9117 16.42 - 32.84: 786 32.84 - 49.26: 109 49.26 - 65.68: 32 65.68 - 82.11: 8 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 - 0.053: 2127 0.053 - 0.106: 424 0.106 - 0.158: 49 0.158 - 0.211: 0 0.211 - 0.264: 4 Chirality restraints: 2604 Sorted by residual: chirality pdb=" C2' CMP A 901 " pdb=" C1' CMP A 901 " pdb=" C3' CMP A 901 " pdb=" O2' CMP A 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C2' CMP D 901 " pdb=" C1' CMP D 901 " pdb=" C3' CMP D 901 " pdb=" O2' CMP D 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C2' CMP C 901 " pdb=" C1' CMP C 901 " pdb=" C3' CMP C 901 " pdb=" O2' CMP C 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.73e+00 ... (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: 0.05 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: 2.790 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.460 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 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= 0.164 Angle : 0.619 10.235 22932 Z= 0.328 Chirality : 0.041 0.264 2604 Planarity : 0.003 0.030 2864 Dihedral : 12.598 82.106 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/Z covalent geometry : bond 0.00346 / 0.16 (16904) covalent geometry : angle 0.61872 / 0.33 (22932) hydrogen bonds : bond 0.08605 / 5.41 ( 1205) hydrogen bonds : angle 4.99854 / 3.56 ( 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 : 0.659 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: 0.1389 time to fit residues: 58.2923 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 : 0.755 ------------------------------------------------------------------------------- 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... 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 437 HIS D 451 ASN D 463 ASN D 517 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.174739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125275 restraints weight = 8888.636| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.36 r_work: 0.3451 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1044 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= 0.150 Angle : 0.586 9.358 22932 Z= 0.286 Chirality : 0.041 0.165 2604 Planarity : 0.004 0.031 2864 Dihedral : 4.109 29.366 2356 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.82 % Allowed : 4.68 % Favored : 93.49 % 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: 0.86 (0.17), residues: 2108 helix: 1.42 (0.12), residues: 1524 sheet: 0.15 (0.47), residues: 108 loop : -2.15 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 580 TYR 0.011 0.001 TYR B 411 PHE 0.009 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/Z covalent geometry : bond 0.00334 / 0.15 (16904) covalent geometry : angle 0.58568 / 0.29 (22932) hydrogen bonds : bond 0.04833 / 3.23 ( 1205) hydrogen bonds : angle 4.46944 / 3.20 ( 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 260 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.709 Fit side-chains REVERT: A 101 MET cc_start: 0.7624 (mmt) cc_final: 0.7233 (mmt) REVERT: A 336 MET cc_start: 0.8879 (ptp) cc_final: 0.8373 (ptp) REVERT: A 356 MET cc_start: 0.8409 (ttm) cc_final: 0.8187 (ttm) REVERT: B 101 MET cc_start: 0.7875 (mmt) cc_final: 0.7407 (mmt) REVERT: B 108 LYS cc_start: 0.7402 (mmmt) cc_final: 0.6993 (tttt) REVERT: B 336 MET cc_start: 0.8790 (ptp) cc_final: 0.8382 (ptp) REVERT: B 460 GLU cc_start: 0.8086 (tt0) cc_final: 0.7772 (mt-10) REVERT: C 108 LYS cc_start: 0.7315 (mmmt) cc_final: 0.7106 (tttt) REVERT: C 336 MET cc_start: 0.8886 (ptp) cc_final: 0.8332 (ptp) REVERT: C 460 GLU cc_start: 0.8069 (tt0) cc_final: 0.7757 (mt-10) REVERT: D 101 MET cc_start: 0.7903 (mmt) cc_final: 0.7463 (mmt) REVERT: D 108 LYS cc_start: 0.7468 (mmmt) cc_final: 0.7070 (tttt) REVERT: D 353 MET cc_start: 0.8781 (ttp) cc_final: 0.8492 (mtp) REVERT: D 460 GLU cc_start: 0.8111 (tt0) cc_final: 0.7780 (mt-10) outliers start: 30 outliers final: 9 residues processed: 249 average time/residue: 0.1119 time to fit residues: 44.6980 Evaluate side-chains 216 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 207 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 196 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 196 THR 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: 0.1980 chunk 169 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.174477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126780 restraints weight = 6742.646| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.17 r_work: 0.3453 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16904 Z= 0.168 Angle : 0.592 9.171 22932 Z= 0.288 Chirality : 0.041 0.162 2604 Planarity : 0.004 0.037 2864 Dihedral : 4.114 30.684 2356 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.89 % Allowed : 6.87 % Favored : 91.24 % 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: 1.40 (0.18), residues: 2108 helix: 1.79 (0.13), residues: 1528 sheet: 0.25 (0.47), residues: 108 loop : -1.84 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 580 TYR 0.014 0.001 TYR D 347 PHE 0.013 0.001 PHE B 109 TRP 0.013 0.001 TRP D 330 HIS 0.004 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (16904) covalent geometry : angle 0.59180 / 0.29 (22932) hydrogen bonds : bond 0.04861 / 3.26 ( 1205) hydrogen bonds : angle 4.39761 / 3.17 ( 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: 31 poor density : 231 time to evaluate : 0.654 Fit side-chains REVERT: A 336 MET cc_start: 0.8886 (ptp) cc_final: 0.8357 (ptp) REVERT: A 356 MET cc_start: 0.8353 (ttm) cc_final: 0.8111 (ttm) REVERT: B 101 MET cc_start: 0.7788 (mmt) cc_final: 0.7334 (mmt) REVERT: B 108 LYS cc_start: 0.7377 (mmmt) cc_final: 0.7073 (tttt) REVERT: C 101 MET cc_start: 0.7716 (mmm) cc_final: 0.7390 (mmt) REVERT: C 108 LYS cc_start: 0.7234 (mmmt) cc_final: 0.6994 (tttt) REVERT: C 336 MET cc_start: 0.8834 (ptp) cc_final: 0.8312 (ptp) REVERT: D 108 LYS cc_start: 0.7374 (mmmt) cc_final: 0.7056 (tttt) REVERT: D 336 MET cc_start: 0.8760 (ptp) cc_final: 0.8451 (ptp) REVERT: D 353 MET cc_start: 0.8693 (ttp) cc_final: 0.8455 (mtp) outliers start: 31 outliers final: 10 residues processed: 252 average time/residue: 0.1237 time to fit residues: 48.5302 Evaluate side-chains 222 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 235 ILE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 194 PHE 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: 2.9990 chunk 198 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.172185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124305 restraints weight = 6799.518| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.17 r_work: 0.3423 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16904 Z= 0.217 Angle : 0.632 9.608 22932 Z= 0.311 Chirality : 0.043 0.182 2604 Planarity : 0.004 0.037 2864 Dihedral : 4.203 31.434 2356 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.19 % Allowed : 8.82 % Favored : 88.99 % 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: 1.41 (0.18), residues: 2108 helix: 1.80 (0.13), residues: 1528 sheet: -0.15 (0.43), residues: 108 loop : -1.70 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 593 TYR 0.020 0.002 TYR D 347 PHE 0.014 0.001 PHE D 569 TRP 0.013 0.002 TRP D 330 HIS 0.005 0.001 HIS D 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (16904) covalent geometry : angle 0.63157 / 0.31 (22932) hydrogen bonds : bond 0.05408 / 3.63 ( 1205) hydrogen bonds : angle 4.49157 / 3.24 ( 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 252 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.630 Fit side-chains REVERT: A 170 GLN cc_start: 0.6163 (pm20) cc_final: 0.5802 (pm20) REVERT: A 270 ARG cc_start: 0.5374 (OUTLIER) cc_final: 0.4976 (ptp-170) REVERT: A 336 MET cc_start: 0.8864 (ptp) cc_final: 0.8478 (ptp) REVERT: B 101 MET cc_start: 0.7825 (mmt) cc_final: 0.7368 (mmt) REVERT: B 108 LYS cc_start: 0.7292 (mmmt) cc_final: 0.7056 (tttt) REVERT: C 101 MET cc_start: 0.7746 (mmm) cc_final: 0.7407 (mmt) REVERT: C 108 LYS cc_start: 0.7207 (mmmt) cc_final: 0.6986 (tttt) REVERT: D 108 LYS cc_start: 0.7285 (mmmt) cc_final: 0.7030 (tttt) outliers start: 36 outliers final: 19 residues processed: 240 average time/residue: 0.1256 time to fit residues: 46.4913 Evaluate side-chains 230 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 270 ARG 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 196 THR 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 196 THR 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 196 THR 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: 0.5980 chunk 23 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 205 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.175933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127815 restraints weight = 7384.322| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.23 r_work: 0.3464 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1809 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= 0.127 Angle : 0.551 8.686 22932 Z= 0.267 Chirality : 0.040 0.158 2604 Planarity : 0.004 0.037 2864 Dihedral : 4.071 31.077 2356 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.70 % Allowed : 9.25 % Favored : 89.05 % 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: 1.78 (0.18), residues: 2108 helix: 2.09 (0.13), residues: 1524 sheet: -0.21 (0.43), residues: 108 loop : -1.56 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 258 TYR 0.012 0.001 TYR D 277 PHE 0.011 0.001 PHE A 222 TRP 0.009 0.001 TRP A 145 HIS 0.003 0.001 HIS D 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (16904) covalent geometry : angle 0.55115 / 0.27 (22932) hydrogen bonds : bond 0.04340 / 2.90 ( 1205) hydrogen bonds : angle 4.25769 / 3.06 ( 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 260 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.765 Fit side-chains REVERT: A 336 MET cc_start: 0.8743 (ptp) cc_final: 0.8146 (ptp) REVERT: B 101 MET cc_start: 0.7751 (mmt) cc_final: 0.7313 (mmt) REVERT: B 108 LYS cc_start: 0.7281 (mmmt) cc_final: 0.7055 (tttt) REVERT: B 270 ARG cc_start: 0.5263 (OUTLIER) cc_final: 0.4758 (ptp-170) REVERT: B 336 MET cc_start: 0.8587 (ptp) cc_final: 0.8263 (ptp) REVERT: C 101 MET cc_start: 0.7668 (mmm) cc_final: 0.7400 (mmt) REVERT: C 270 ARG cc_start: 0.5278 (OUTLIER) cc_final: 0.4918 (ptp-170) REVERT: C 336 MET cc_start: 0.8727 (ptp) cc_final: 0.8333 (ptp) REVERT: D 101 MET cc_start: 0.7733 (mmm) cc_final: 0.7405 (mmt) REVERT: D 108 LYS cc_start: 0.7261 (mmmt) cc_final: 0.7038 (tttt) REVERT: D 270 ARG cc_start: 0.5278 (OUTLIER) cc_final: 0.4756 (ptp-170) REVERT: D 336 MET cc_start: 0.8577 (ptp) cc_final: 0.8251 (ptp) outliers start: 28 outliers final: 15 residues processed: 245 average time/residue: 0.1295 time to fit residues: 49.4271 Evaluate side-chains 228 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 419 SER 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 626 VAL 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 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 235 ILE Chi-restraints excluded: chain D residue 270 ARG 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: 3.9990 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.174627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125302 restraints weight = 8378.527| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.33 r_work: 0.3435 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16904 Z= 0.146 Angle : 0.577 9.012 22932 Z= 0.278 Chirality : 0.040 0.165 2604 Planarity : 0.004 0.036 2864 Dihedral : 4.058 31.430 2356 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.95 % Allowed : 9.73 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.18), residues: 2108 helix: 2.11 (0.13), residues: 1528 sheet: -0.12 (0.44), residues: 108 loop : -1.46 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 593 TYR 0.013 0.001 TYR D 347 PHE 0.013 0.001 PHE A 222 TRP 0.010 0.001 TRP D 330 HIS 0.003 0.001 HIS A 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (16904) covalent geometry : angle 0.57653 / 0.28 (22932) hydrogen bonds : bond 0.04513 / 3.02 ( 1205) hydrogen bonds : angle 4.26025 / 3.07 ( 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 255 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.673 Fit side-chains REVERT: A 170 GLN cc_start: 0.5862 (pm20) cc_final: 0.5552 (pm20) REVERT: A 336 MET cc_start: 0.8757 (ptp) cc_final: 0.8172 (ptp) REVERT: B 101 MET cc_start: 0.7762 (mmt) cc_final: 0.7317 (mmt) REVERT: B 108 LYS cc_start: 0.7307 (mmmt) cc_final: 0.7045 (tttt) REVERT: B 270 ARG cc_start: 0.5292 (OUTLIER) cc_final: 0.4794 (ptp-170) REVERT: B 336 MET cc_start: 0.8567 (ptp) cc_final: 0.8157 (ptp) REVERT: C 101 MET cc_start: 0.7699 (mmm) cc_final: 0.7417 (mmt) REVERT: C 170 GLN cc_start: 0.5822 (pm20) cc_final: 0.5517 (pm20) REVERT: C 270 ARG cc_start: 0.5294 (OUTLIER) cc_final: 0.4953 (ptp-170) REVERT: C 336 MET cc_start: 0.8703 (ptp) cc_final: 0.8304 (ptp) REVERT: D 101 MET cc_start: 0.7768 (mmm) cc_final: 0.7450 (mmt) REVERT: D 108 LYS cc_start: 0.7248 (mmmt) cc_final: 0.7029 (tttt) REVERT: D 270 ARG cc_start: 0.5296 (OUTLIER) cc_final: 0.4799 (ptp-170) REVERT: D 336 MET cc_start: 0.8564 (ptp) cc_final: 0.8152 (ptp) outliers start: 32 outliers final: 24 residues processed: 239 average time/residue: 0.1225 time to fit residues: 45.6698 Evaluate side-chains 241 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 235 ILE 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 196 THR 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 473 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 4 optimal weight: 0.0470 chunk 163 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.176790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127899 restraints weight = 9061.137| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.38 r_work: 0.3450 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16904 Z= 0.125 Angle : 0.557 8.852 22932 Z= 0.267 Chirality : 0.040 0.167 2604 Planarity : 0.003 0.033 2864 Dihedral : 3.977 31.150 2356 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.01 % Allowed : 9.67 % Favored : 88.32 % 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: 2.25 (0.13), residues: 1528 sheet: -0.11 (0.45), residues: 108 loop : -1.33 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 593 TYR 0.013 0.001 TYR C 277 PHE 0.010 0.001 PHE A 222 TRP 0.009 0.001 TRP A 145 HIS 0.003 0.001 HIS D 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (16904) covalent geometry : angle 0.55658 / 0.27 (22932) hydrogen bonds : bond 0.04165 / 2.77 ( 1205) hydrogen bonds : angle 4.16884 / 3.01 ( 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 255 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 0.680 Fit side-chains REVERT: A 336 MET cc_start: 0.8728 (ptp) cc_final: 0.8195 (ptp) REVERT: B 101 MET cc_start: 0.7786 (mmt) cc_final: 0.7344 (mmt) REVERT: B 270 ARG cc_start: 0.5379 (OUTLIER) cc_final: 0.4859 (ptp-170) REVERT: B 336 MET cc_start: 0.8501 (ptp) cc_final: 0.8118 (ptp) REVERT: C 101 MET cc_start: 0.7718 (mmm) cc_final: 0.7440 (mmt) REVERT: C 270 ARG cc_start: 0.5366 (OUTLIER) cc_final: 0.5019 (ptp-170) REVERT: C 336 MET cc_start: 0.8633 (ptp) cc_final: 0.8254 (ptp) REVERT: D 101 MET cc_start: 0.7741 (mmm) cc_final: 0.7434 (mmt) REVERT: D 270 ARG cc_start: 0.5380 (OUTLIER) cc_final: 0.4870 (ptp-170) REVERT: D 336 MET cc_start: 0.8494 (ptp) cc_final: 0.8109 (ptp) outliers start: 33 outliers final: 26 residues processed: 236 average time/residue: 0.1212 time to fit residues: 44.6577 Evaluate side-chains 241 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 473 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 134 ILE 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 473 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 602 LEU 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: 3.9990 chunk 62 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.175793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125481 restraints weight = 9080.579| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.45 r_work: 0.3440 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16904 Z= 0.134 Angle : 0.571 8.920 22932 Z= 0.272 Chirality : 0.040 0.160 2604 Planarity : 0.003 0.034 2864 Dihedral : 3.996 31.112 2356 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.25 % Allowed : 10.58 % Favored : 87.17 % 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: 2.08 (0.18), residues: 2108 helix: 2.25 (0.13), residues: 1532 sheet: -0.08 (0.44), residues: 108 loop : -1.27 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 593 TYR 0.013 0.001 TYR B 277 PHE 0.011 0.001 PHE A 222 TRP 0.009 0.001 TRP D 330 HIS 0.003 0.001 HIS D 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (16904) covalent geometry : angle 0.57065 / 0.27 (22932) hydrogen bonds : bond 0.04261 / 2.84 ( 1205) hydrogen bonds : angle 4.18440 / 3.02 ( 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 255 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.661 Fit side-chains REVERT: A 336 MET cc_start: 0.8723 (ptp) cc_final: 0.8155 (ptp) REVERT: B 101 MET cc_start: 0.7788 (mmt) cc_final: 0.7343 (mmt) REVERT: B 270 ARG cc_start: 0.5358 (OUTLIER) cc_final: 0.4853 (ptp-170) REVERT: B 336 MET cc_start: 0.8499 (ptp) cc_final: 0.8090 (ptp) REVERT: C 101 MET cc_start: 0.7720 (mmm) cc_final: 0.7453 (mmt) REVERT: C 270 ARG cc_start: 0.5294 (OUTLIER) cc_final: 0.4938 (ptp-170) REVERT: C 336 MET cc_start: 0.8605 (ptp) cc_final: 0.8226 (ptp) REVERT: D 101 MET cc_start: 0.7767 (mmm) cc_final: 0.7455 (mmt) REVERT: D 270 ARG cc_start: 0.5465 (OUTLIER) cc_final: 0.4976 (ptp-170) REVERT: D 336 MET cc_start: 0.8489 (ptp) cc_final: 0.8107 (ptp) outliers start: 37 outliers final: 28 residues processed: 235 average time/residue: 0.1200 time to fit residues: 44.0819 Evaluate side-chains 245 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 172 THR 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 172 THR 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 473 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 172 THR 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 473 MET 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: 1.9990 chunk 138 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.178164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129128 restraints weight = 8723.041| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.40 r_work: 0.3467 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16904 Z= 0.117 Angle : 0.562 9.000 22932 Z= 0.265 Chirality : 0.039 0.154 2604 Planarity : 0.003 0.033 2864 Dihedral : 3.959 30.745 2356 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.07 % Allowed : 10.95 % Favored : 86.98 % 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: 2.22 (0.18), residues: 2108 helix: 2.34 (0.13), residues: 1532 sheet: -0.03 (0.46), residues: 108 loop : -1.19 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 492 TYR 0.012 0.001 TYR B 277 PHE 0.009 0.001 PHE C 222 TRP 0.008 0.001 TRP D 330 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (16904) covalent geometry : angle 0.56198 / 0.27 (22932) hydrogen bonds : bond 0.03959 / 2.64 ( 1205) hydrogen bonds : angle 4.11587 / 2.97 ( 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: 34 poor density : 216 time to evaluate : 0.691 Fit side-chains REVERT: A 336 MET cc_start: 0.8680 (ptp) cc_final: 0.8112 (ptp) REVERT: B 101 MET cc_start: 0.7744 (mmt) cc_final: 0.7305 (mmt) REVERT: B 270 ARG cc_start: 0.5237 (OUTLIER) cc_final: 0.4736 (ptp-170) REVERT: B 336 MET cc_start: 0.8346 (ptp) cc_final: 0.7967 (ptp) REVERT: C 101 MET cc_start: 0.7676 (mmm) cc_final: 0.7406 (mmt) REVERT: C 270 ARG cc_start: 0.5187 (OUTLIER) cc_final: 0.4836 (ptp-170) REVERT: C 336 MET cc_start: 0.8503 (ptp) cc_final: 0.8112 (ptp) REVERT: D 101 MET cc_start: 0.7701 (mmm) cc_final: 0.7391 (mmt) REVERT: D 270 ARG cc_start: 0.5284 (OUTLIER) cc_final: 0.4795 (ptp-170) REVERT: D 336 MET cc_start: 0.8339 (ptp) cc_final: 0.7961 (ptp) outliers start: 34 outliers final: 26 residues processed: 232 average time/residue: 0.1237 time to fit residues: 44.6575 Evaluate side-chains 230 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 419 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 172 THR 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 328 ASP 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 172 THR 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 473 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 172 THR 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 473 MET 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: 0.1980 chunk 206 optimal weight: 0.7980 chunk 59 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.177494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.129893 restraints weight = 7836.079| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.27 r_work: 0.3478 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16904 Z= 0.124 Angle : 0.566 9.329 22932 Z= 0.269 Chirality : 0.039 0.156 2604 Planarity : 0.003 0.032 2864 Dihedral : 3.974 30.701 2356 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.95 % Allowed : 11.07 % Favored : 86.98 % 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: 2.25 (0.18), residues: 2108 helix: 2.35 (0.13), residues: 1532 sheet: -0.01 (0.46), residues: 108 loop : -1.16 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 492 TYR 0.012 0.001 TYR B 277 PHE 0.022 0.001 PHE D 109 TRP 0.010 0.001 TRP A 175 HIS 0.003 0.001 HIS B 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16904) covalent geometry : angle 0.56634 / 0.27 (22932) hydrogen bonds : bond 0.04060 / 2.70 ( 1205) hydrogen bonds : angle 4.12698 / 2.98 ( 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 244 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.665 Fit side-chains REVERT: A 336 MET cc_start: 0.8790 (ptp) cc_final: 0.8239 (ptp) REVERT: B 101 MET cc_start: 0.7779 (mmt) cc_final: 0.7334 (mmt) REVERT: B 270 ARG cc_start: 0.5461 (OUTLIER) cc_final: 0.4976 (ptp-170) REVERT: B 336 MET cc_start: 0.8367 (ptp) cc_final: 0.7993 (ptp) REVERT: C 101 MET cc_start: 0.7708 (mmm) cc_final: 0.7429 (mmt) REVERT: C 270 ARG cc_start: 0.5386 (OUTLIER) cc_final: 0.5025 (ptp-170) REVERT: C 336 MET cc_start: 0.8494 (ptp) cc_final: 0.8106 (ptp) REVERT: D 101 MET cc_start: 0.7735 (mmm) cc_final: 0.7418 (mmt) REVERT: D 270 ARG cc_start: 0.5439 (OUTLIER) cc_final: 0.4942 (ptp-170) REVERT: D 336 MET cc_start: 0.8368 (ptp) cc_final: 0.7995 (ptp) outliers start: 32 outliers final: 28 residues processed: 226 average time/residue: 0.1259 time to fit residues: 44.4558 Evaluate side-chains 240 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 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 172 THR 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 328 ASP 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 172 THR 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 473 MET Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 172 THR 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 473 MET 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: 2.9990 chunk 156 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 59 optimal weight: 0.0570 chunk 60 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.178171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130217 restraints weight = 7709.778| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.30 r_work: 0.3486 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2267 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= 0.119 Angle : 0.559 8.952 22932 Z= 0.265 Chirality : 0.039 0.154 2604 Planarity : 0.003 0.032 2864 Dihedral : 3.941 30.461 2356 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.89 % Allowed : 11.37 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.26 (0.18), residues: 2108 helix: 2.41 (0.13), residues: 1532 sheet: -0.59 (0.49), residues: 84 loop : -1.15 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 492 TYR 0.012 0.001 TYR B 277 PHE 0.021 0.001 PHE B 109 TRP 0.008 0.001 TRP D 330 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (16904) covalent geometry : angle 0.55890 / 0.26 (22932) hydrogen bonds : bond 0.03939 / 2.62 ( 1205) hydrogen bonds : angle 4.09933 / 2.96 ( 3531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4545.63 seconds wall clock time: 78 minutes 22.84 seconds (4702.84 seconds total)