Starting phenix.real_space_refine on Sat Jun 6 11:56:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10rx_75424/06_2026/10rx_75424_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/10rx_75424/06_2026/10rx_75424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10rx_75424/06_2026/10rx_75424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10rx_75424/06_2026/10rx_75424.map" model { file = "/net/cci-nas-00/data/ceres_data/10rx_75424/06_2026/10rx_75424_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10rx_75424/06_2026/10rx_75424_trim.cif" } resolution = 2.51 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 28 5.16 5 C 8876 2.51 5 N 2104 2.21 5 O 2324 1.98 5 H 13116 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26464 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6421 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "B" Number of atoms: 6421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6421 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "C" Number of atoms: 6421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6421 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "D" Number of atoms: 6421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6421 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "A" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 235 Unusual residues: {'PCW': 9} Classifications: {'RNA': 1, 'undetermined': 9} Modifications used: {'rna3p': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-2': 6, 'PCW:plan-4': 4, 'PCW:plan-1': 4, 'PCW:plan-3': 5} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Unusual residues: {'PCW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-4': 4, 'PCW:plan-1': 4, 'PCW:plan-2': 5, 'PCW:plan-3': 5} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Unusual residues: {'PCW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-4': 4, 'PCW:plan-1': 4, 'PCW:plan-2': 5, 'PCW:plan-3': 5} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 155 Unusual residues: {'PCW': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-4': 4, 'PCW:plan-1': 4, 'PCW:plan-2': 4, 'PCW:plan-3': 5} Unresolved non-hydrogen planarities: 61 Time building chain proxies: 5.10, per 1000 atoms: 0.19 Number of scatterers: 26464 At special positions: 0 Unit cell: (105.3, 105.3, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 16 15.00 O 2324 8.00 N 2104 7.00 C 8876 6.00 H 13116 1.00 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: 2.34 Conformation dependent library (CDL) restraints added in 790.5 milliseconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 72.2% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 9 through 36 removed outlier: 3.788A pdb=" N LEU A 13 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 43 through 64 removed outlier: 4.000A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 80 through 87 removed outlier: 4.492A pdb=" N ASP A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 113 through 126 removed outlier: 4.267A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 159 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 Processing helix chain 'A' and resid 227 through 246 Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 300 through 303 removed outlier: 3.591A pdb=" N LYS A 303 " --> pdb=" O PRO A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.517A pdb=" N LEU A 371 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 403 removed outlier: 3.856A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'B' and resid 10 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 43 through 64 removed outlier: 4.000A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 80 through 87 removed outlier: 4.492A pdb=" N ASP B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 113 through 126 removed outlier: 4.267A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 159 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 Processing helix chain 'B' and resid 227 through 246 Processing helix chain 'B' and resid 249 through 268 Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 294 through 299 Processing helix chain 'B' and resid 300 through 303 removed outlier: 3.591A pdb=" N LYS B 303 " --> pdb=" O PRO B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.516A pdb=" N LEU B 371 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 403 removed outlier: 3.856A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 414 Processing helix chain 'C' and resid 10 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 43 through 64 removed outlier: 4.000A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 80 through 87 removed outlier: 4.491A pdb=" N ASP C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 113 through 126 removed outlier: 4.267A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 159 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 Processing helix chain 'C' and resid 227 through 246 Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 280 through 293 Processing helix chain 'C' and resid 294 through 299 Processing helix chain 'C' and resid 300 through 303 removed outlier: 3.591A pdb=" N LYS C 303 " --> pdb=" O PRO C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 303' Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.517A pdb=" N LEU C 371 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 403 removed outlier: 3.856A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 414 Processing helix chain 'D' and resid 10 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 37 through 40 Processing helix chain 'D' and resid 43 through 64 removed outlier: 4.000A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 80 through 87 removed outlier: 4.492A pdb=" N ASP D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 113 through 126 removed outlier: 4.267A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 159 Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 249 through 268 Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 294 through 299 Processing helix chain 'D' and resid 300 through 303 removed outlier: 3.591A pdb=" N LYS D 303 " --> pdb=" O PRO D 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.517A pdb=" N LEU D 371 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.856A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 322 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.441A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 322 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.440A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 322 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.441A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 322 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.440A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) 852 hydrogen bonds defined for protein. 2436 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: 6.57 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13108 1.03 - 1.23: 47 1.23 - 1.42: 5345 1.42 - 1.62: 8160 1.62 - 1.81: 76 Bond restraints: 26736 Sorted by residual: bond pdb=" C4 CMP C 501 " pdb=" C5 CMP C 501 " ideal model delta sigma weight residual 1.490 1.333 0.157 2.00e-02 2.50e+03 6.12e+01 bond pdb=" C4 CMP D 501 " pdb=" C5 CMP D 501 " ideal model delta sigma weight residual 1.490 1.334 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" C4 CMP A 501 " pdb=" C5 CMP A 501 " ideal model delta sigma weight residual 1.490 1.334 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" C4 CMP B 501 " pdb=" C5 CMP B 501 " ideal model delta sigma weight residual 1.490 1.334 0.156 2.00e-02 2.50e+03 6.10e+01 bond pdb=" O2P CMP D 501 " pdb=" P CMP D 501 " ideal model delta sigma weight residual 1.510 1.643 -0.133 2.00e-02 2.50e+03 4.44e+01 ... (remaining 26731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.25: 47955 5.25 - 10.51: 121 10.51 - 15.76: 40 15.76 - 21.01: 0 21.01 - 26.27: 8 Bond angle restraints: 48124 Sorted by residual: angle pdb=" C19 PCW A 504 " pdb=" C20 PCW A 504 " pdb=" C21 PCW A 504 " ideal model delta sigma weight residual 127.82 154.09 -26.27 3.00e+00 1.11e-01 7.67e+01 angle pdb=" C19 PCW C 503 " pdb=" C20 PCW C 503 " pdb=" C21 PCW C 503 " ideal model delta sigma weight residual 127.82 154.07 -26.25 3.00e+00 1.11e-01 7.66e+01 angle pdb=" C19 PCW D 503 " pdb=" C20 PCW D 503 " pdb=" C21 PCW D 503 " ideal model delta sigma weight residual 127.82 154.07 -26.25 3.00e+00 1.11e-01 7.65e+01 angle pdb=" C19 PCW B 502 " pdb=" C20 PCW B 502 " pdb=" C21 PCW B 502 " ideal model delta sigma weight residual 127.82 154.05 -26.23 3.00e+00 1.11e-01 7.64e+01 angle pdb=" C19 PCW D 502 " pdb=" C20 PCW D 502 " pdb=" C21 PCW D 502 " ideal model delta sigma weight residual 127.82 154.04 -26.22 3.00e+00 1.11e-01 7.64e+01 ... (remaining 48119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.34: 12108 32.34 - 64.69: 540 64.69 - 97.03: 28 97.03 - 129.38: 8 129.38 - 161.72: 16 Dihedral angle restraints: 12700 sinusoidal: 7252 harmonic: 5448 Sorted by residual: dihedral pdb=" N PCW C 509 " pdb=" C4 PCW C 509 " pdb=" C5 PCW C 509 " pdb=" O4P PCW C 509 " ideal model delta sinusoidal sigma weight residual -66.66 95.06 -161.72 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" N PCW A 502 " pdb=" C4 PCW A 502 " pdb=" C5 PCW A 502 " pdb=" O4P PCW A 502 " ideal model delta sinusoidal sigma weight residual -66.66 95.05 -161.71 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" N PCW B 509 " pdb=" C4 PCW B 509 " pdb=" C5 PCW B 509 " pdb=" O4P PCW B 509 " ideal model delta sinusoidal sigma weight residual -66.66 95.05 -161.71 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 12697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1561 0.039 - 0.078: 433 0.078 - 0.118: 113 0.118 - 0.157: 5 0.157 - 0.196: 8 Chirality restraints: 2120 Sorted by residual: chirality pdb=" C2 PCW B 502 " pdb=" C1 PCW B 502 " pdb=" C3 PCW B 502 " pdb=" O2 PCW B 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.20 2.00e-01 2.50e+01 9.61e-01 chirality pdb=" C2 PCW D 502 " pdb=" C1 PCW D 502 " pdb=" C3 PCW D 502 " pdb=" O2 PCW D 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" C2 PCW C 509 " pdb=" C1 PCW C 509 " pdb=" C3 PCW C 509 " pdb=" O2 PCW C 509 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 2117 not shown) Planarity restraints: 3704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 89 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO D 90 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 89 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO C 90 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 89 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 90 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " 0.024 5.00e-02 4.00e+02 ... (remaining 3701 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 9463 2.36 - 2.92: 62149 2.92 - 3.48: 73810 3.48 - 4.04: 97714 4.04 - 4.60: 147877 Nonbonded interactions: 391013 Sorted by model distance: nonbonded pdb=" OD1 ASP C 92 " pdb=" H LEU C 93 " model vdw 1.799 2.450 nonbonded pdb=" OD1 ASP B 92 " pdb=" H LEU B 93 " model vdw 1.799 2.450 nonbonded pdb=" OD1 ASP D 92 " pdb=" H LEU D 93 " model vdw 1.799 2.450 nonbonded pdb=" OD1 ASP A 92 " pdb=" H LEU A 93 " model vdw 1.799 2.450 nonbonded pdb=" HH TYR D 25 " pdb=" OD1 ASP D 47 " model vdw 1.830 2.450 ... (remaining 391008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 501 or (resid 502 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O11 o \ r name O2 or name O3 or name O31 or name O3P or name P )) or (resid 503 and (nam \ e C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C23 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name O11 or name O2 or name O3 or name O31 or name O3P or name \ P )) or (resid 504 and (name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40)) or resid 505 or (resid 506 and (name C36 \ or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name \ C43 or name C44 or name C45)))) selection = (chain 'B' and (resid 9 through 501 or (resid 502 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O11 o \ r name O2 or name O3 or name O31 or name O3P or name P )) or (resid 503 and (nam \ e C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C23 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name O11 or name O2 or name O3 or name O31 or name O3P or name \ P )) or (resid 504 and (name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40)) or resid 505 through 506)) selection = (chain 'C' and (resid 9 through 501 or (resid 502 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O11 o \ r name O2 or name O3 or name O31 or name O3P or name P )) or (resid 503 and (nam \ e C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C23 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name O11 or name O2 or name O3 or name O31 or name O3P or name \ P )) or (resid 504 and (name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40)) or resid 505 through 506)) selection = (chain 'D' and (resid 9 through 501 or (resid 502 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O11 o \ r name O2 or name O3 or name O31 or name O3P or name P )) or (resid 503 and (nam \ e C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C23 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name O11 or name O2 or name O3 or name O31 or name O3P or name \ P )) or (resid 504 and (name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40)) or resid 505 through 506)) } 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: 0.010 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.530 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.011 0.157 13620 Z= 0.528 Angle : 1.263 26.267 18388 Z= 0.483 Chirality : 0.039 0.196 2120 Planarity : 0.004 0.044 2228 Dihedral : 19.625 161.723 5316 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.22 % Allowed : 14.31 % Favored : 85.47 % 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: 2.60 (0.22), residues: 1564 helix: 2.51 (0.16), residues: 1048 sheet: -2.77 (0.54), residues: 68 loop : 0.67 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 399 TYR 0.009 0.001 TYR C 245 PHE 0.008 0.001 PHE C 365 TRP 0.007 0.001 TRP D 264 HIS 0.002 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.01057 / 0.53 (13620) covalent geometry : angle 1.26319 / 0.48 (18388) hydrogen bonds : bond 0.08964 / 6.57 ( 852) hydrogen bonds : angle 4.70111 / 3.45 ( 2436) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.8862 (tt) cc_final: 0.8612 (pp) outliers start: 3 outliers final: 3 residues processed: 66 average time/residue: 0.9697 time to fit residues: 72.6887 Evaluate side-chains 54 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain D residue 47 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.094247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069389 restraints weight = 88822.329| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.68 r_work: 0.2966 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13620 Z= 0.124 Angle : 0.550 7.546 18388 Z= 0.263 Chirality : 0.037 0.125 2120 Planarity : 0.004 0.040 2228 Dihedral : 17.627 143.131 2334 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.37 % Allowed : 13.35 % Favored : 86.28 % 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: 2.68 (0.22), residues: 1564 helix: 2.59 (0.16), residues: 1056 sheet: -2.54 (0.48), residues: 68 loop : 0.55 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 399 TYR 0.010 0.001 TYR A 128 PHE 0.008 0.001 PHE A 242 TRP 0.006 0.001 TRP B 264 HIS 0.002 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13620) covalent geometry : angle 0.55042 / 0.26 (18388) hydrogen bonds : bond 0.03600 / 2.43 ( 852) hydrogen bonds : angle 4.15359 / 3.07 ( 2436) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.8842 (tt) cc_final: 0.8607 (pp) outliers start: 5 outliers final: 4 residues processed: 55 average time/residue: 1.0870 time to fit residues: 67.1047 Evaluate side-chains 52 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain D residue 47 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.092244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.067072 restraints weight = 88966.007| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.67 r_work: 0.2918 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13620 Z= 0.172 Angle : 0.551 8.719 18388 Z= 0.268 Chirality : 0.038 0.121 2120 Planarity : 0.004 0.038 2228 Dihedral : 16.462 138.566 2334 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.74 % Allowed : 13.57 % Favored : 85.69 % 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: 2.80 (0.22), residues: 1564 helix: 2.73 (0.16), residues: 1024 sheet: -2.18 (0.49), residues: 68 loop : 0.59 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 399 TYR 0.012 0.001 TYR A 245 PHE 0.010 0.001 PHE C 64 TRP 0.007 0.001 TRP C 264 HIS 0.002 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (13620) covalent geometry : angle 0.55087 / 0.27 (18388) hydrogen bonds : bond 0.03750 / 2.53 ( 852) hydrogen bonds : angle 4.05860 / 3.01 ( 2436) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.672 Fit side-chains REVERT: A 55 ILE cc_start: 0.8855 (tt) cc_final: 0.8595 (pp) REVERT: A 334 MET cc_start: 0.7802 (tpp) cc_final: 0.7216 (tpp) REVERT: B 265 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8423 (pp20) REVERT: B 334 MET cc_start: 0.7797 (tpp) cc_final: 0.7325 (tpp) REVERT: C 334 MET cc_start: 0.7841 (tpp) cc_final: 0.7275 (tpp) REVERT: D 265 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8391 (pp20) REVERT: D 334 MET cc_start: 0.7745 (tpp) cc_final: 0.7242 (tpp) outliers start: 10 outliers final: 2 residues processed: 55 average time/residue: 1.2372 time to fit residues: 75.5019 Evaluate side-chains 45 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain D residue 265 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 8 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 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 = 0.3654 r_free = 0.3654 target = 0.092418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067566 restraints weight = 88621.652| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.65 r_work: 0.2931 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13620 Z= 0.135 Angle : 0.525 8.262 18388 Z= 0.254 Chirality : 0.037 0.122 2120 Planarity : 0.004 0.041 2228 Dihedral : 15.293 139.115 2330 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.37 % Allowed : 13.42 % Favored : 86.21 % 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: 2.91 (0.22), residues: 1564 helix: 2.81 (0.16), residues: 1024 sheet: -2.09 (0.49), residues: 68 loop : 0.63 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 399 TYR 0.013 0.001 TYR A 128 PHE 0.006 0.001 PHE A 242 TRP 0.006 0.001 TRP C 264 HIS 0.002 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (13620) covalent geometry : angle 0.52455 / 0.25 (18388) hydrogen bonds : bond 0.03466 / 2.30 ( 852) hydrogen bonds : angle 3.95658 / 2.94 ( 2436) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.705 Fit side-chains REVERT: A 55 ILE cc_start: 0.8855 (tt) cc_final: 0.8600 (pp) REVERT: A 334 MET cc_start: 0.7732 (tpp) cc_final: 0.7192 (tpp) REVERT: B 334 MET cc_start: 0.7716 (tpp) cc_final: 0.7168 (tpp) REVERT: C 265 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8375 (pp20) REVERT: C 334 MET cc_start: 0.7783 (tpp) cc_final: 0.7261 (tpp) REVERT: D 334 MET cc_start: 0.7648 (tpp) cc_final: 0.7107 (tpp) outliers start: 5 outliers final: 1 residues processed: 48 average time/residue: 1.4530 time to fit residues: 76.6330 Evaluate side-chains 42 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain C residue 265 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 131 optimal weight: 0.0570 chunk 30 optimal weight: 0.7980 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.092800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.068001 restraints weight = 88003.493| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.63 r_work: 0.2945 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13620 Z= 0.108 Angle : 0.507 8.256 18388 Z= 0.245 Chirality : 0.037 0.123 2120 Planarity : 0.004 0.050 2228 Dihedral : 14.815 143.469 2328 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.29 % Allowed : 13.42 % Favored : 86.28 % 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: 3.14 (0.22), residues: 1564 helix: 2.87 (0.16), residues: 1044 sheet: -2.02 (0.49), residues: 68 loop : 0.93 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 399 TYR 0.017 0.001 TYR B 128 PHE 0.005 0.001 PHE A 242 TRP 0.006 0.001 TRP A 264 HIS 0.001 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (13620) covalent geometry : angle 0.50657 / 0.24 (18388) hydrogen bonds : bond 0.03256 / 2.17 ( 852) hydrogen bonds : angle 3.87132 / 2.87 ( 2436) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.818 Fit side-chains REVERT: A 55 ILE cc_start: 0.8857 (tt) cc_final: 0.8607 (pp) REVERT: A 334 MET cc_start: 0.7782 (tpp) cc_final: 0.7260 (tpp) REVERT: B 334 MET cc_start: 0.7746 (tpp) cc_final: 0.7222 (tpp) REVERT: C 334 MET cc_start: 0.7771 (tpp) cc_final: 0.7265 (tpp) outliers start: 4 outliers final: 1 residues processed: 46 average time/residue: 1.4666 time to fit residues: 74.3763 Evaluate side-chains 42 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.091774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.066715 restraints weight = 88625.577| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.67 r_work: 0.2912 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13620 Z= 0.162 Angle : 0.531 8.376 18388 Z= 0.258 Chirality : 0.038 0.118 2120 Planarity : 0.004 0.065 2228 Dihedral : 14.892 141.027 2328 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.44 % Allowed : 13.27 % Favored : 86.28 % 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: 3.14 (0.22), residues: 1564 helix: 2.85 (0.16), residues: 1044 sheet: -1.82 (0.50), residues: 68 loop : 0.94 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 399 TYR 0.011 0.001 TYR A 245 PHE 0.006 0.001 PHE A 365 TRP 0.006 0.001 TRP C 264 HIS 0.003 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (13620) covalent geometry : angle 0.53069 / 0.26 (18388) hydrogen bonds : bond 0.03508 / 2.34 ( 852) hydrogen bonds : angle 3.88332 / 2.88 ( 2436) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.624 Fit side-chains REVERT: A 55 ILE cc_start: 0.8853 (tt) cc_final: 0.8595 (pp) REVERT: C 334 MET cc_start: 0.7723 (tpp) cc_final: 0.7181 (tpp) outliers start: 6 outliers final: 1 residues processed: 49 average time/residue: 1.1802 time to fit residues: 64.7480 Evaluate side-chains 43 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 113 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.091921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.067017 restraints weight = 88169.427| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.67 r_work: 0.2927 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13620 Z= 0.119 Angle : 0.519 8.218 18388 Z= 0.249 Chirality : 0.037 0.123 2120 Planarity : 0.004 0.044 2228 Dihedral : 14.637 143.571 2328 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.29 % Allowed : 13.35 % Favored : 86.36 % 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: 3.22 (0.22), residues: 1564 helix: 2.93 (0.16), residues: 1044 sheet: -1.76 (0.50), residues: 68 loop : 0.93 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 399 TYR 0.017 0.001 TYR A 128 PHE 0.005 0.001 PHE A 242 TRP 0.005 0.001 TRP A 264 HIS 0.002 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13620) covalent geometry : angle 0.51932 / 0.25 (18388) hydrogen bonds : bond 0.03290 / 2.19 ( 852) hydrogen bonds : angle 3.81165 / 2.83 ( 2436) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.716 Fit side-chains REVERT: A 55 ILE cc_start: 0.8869 (tt) cc_final: 0.8616 (pp) outliers start: 4 outliers final: 1 residues processed: 46 average time/residue: 1.1515 time to fit residues: 59.7479 Evaluate side-chains 42 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 138 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.091560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.066506 restraints weight = 88682.458| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.67 r_work: 0.2914 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13620 Z= 0.149 Angle : 0.530 8.311 18388 Z= 0.256 Chirality : 0.037 0.119 2120 Planarity : 0.004 0.037 2228 Dihedral : 14.699 142.168 2328 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.59 % Allowed : 12.68 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.17 (0.22), residues: 1564 helix: 2.88 (0.16), residues: 1048 sheet: -1.58 (0.51), residues: 68 loop : 0.88 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 399 TYR 0.016 0.001 TYR D 128 PHE 0.005 0.001 PHE A 365 TRP 0.005 0.001 TRP A 264 HIS 0.002 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (13620) covalent geometry : angle 0.53044 / 0.26 (18388) hydrogen bonds : bond 0.03402 / 2.27 ( 852) hydrogen bonds : angle 3.81190 / 2.83 ( 2436) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.714 Fit side-chains REVERT: A 55 ILE cc_start: 0.8856 (tt) cc_final: 0.8599 (pp) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 1.0387 time to fit residues: 59.1565 Evaluate side-chains 46 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.091306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.066199 restraints weight = 88968.004| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.68 r_work: 0.2910 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13620 Z= 0.144 Angle : 0.530 8.254 18388 Z= 0.255 Chirality : 0.037 0.121 2120 Planarity : 0.004 0.034 2228 Dihedral : 14.677 143.540 2328 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.74 % Allowed : 12.61 % Favored : 86.65 % 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: 3.19 (0.22), residues: 1564 helix: 2.88 (0.16), residues: 1048 sheet: -1.44 (0.52), residues: 68 loop : 0.89 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 399 TYR 0.010 0.001 TYR A 128 PHE 0.005 0.001 PHE C 242 TRP 0.005 0.001 TRP B 264 HIS 0.002 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (13620) covalent geometry : angle 0.53019 / 0.26 (18388) hydrogen bonds : bond 0.03376 / 2.25 ( 852) hydrogen bonds : angle 3.77475 / 2.80 ( 2436) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.749 Fit side-chains REVERT: A 26 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: A 55 ILE cc_start: 0.8855 (tt) cc_final: 0.8595 (pp) REVERT: B 26 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: C 26 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: C 334 MET cc_start: 0.7946 (mmm) cc_final: 0.7675 (tpp) REVERT: D 26 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7585 (m-80) outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 1.0275 time to fit residues: 59.7539 Evaluate side-chains 50 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 127 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.091720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.066855 restraints weight = 88480.422| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.67 r_work: 0.2922 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13620 Z= 0.113 Angle : 0.516 8.173 18388 Z= 0.247 Chirality : 0.037 0.123 2120 Planarity : 0.003 0.034 2228 Dihedral : 14.393 143.886 2328 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.37 % Allowed : 12.91 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.27 (0.22), residues: 1564 helix: 2.95 (0.16), residues: 1048 sheet: -1.55 (0.51), residues: 68 loop : 0.92 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 399 TYR 0.015 0.001 TYR A 128 PHE 0.005 0.001 PHE A 242 TRP 0.005 0.001 TRP A 264 HIS 0.002 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (13620) covalent geometry : angle 0.51602 / 0.25 (18388) hydrogen bonds : bond 0.03207 / 2.14 ( 852) hydrogen bonds : angle 3.73234 / 2.76 ( 2436) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.566 Fit side-chains REVERT: A 55 ILE cc_start: 0.8854 (tt) cc_final: 0.8596 (pp) REVERT: C 277 LYS cc_start: 0.8839 (mmpt) cc_final: 0.8636 (mmtm) REVERT: C 334 MET cc_start: 0.7909 (mmm) cc_final: 0.6864 (ttp) outliers start: 5 outliers final: 5 residues processed: 47 average time/residue: 1.2219 time to fit residues: 64.2490 Evaluate side-chains 46 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 42 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 116 optimal weight: 0.4980 chunk 147 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.091907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.067104 restraints weight = 87899.549| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.66 r_work: 0.2929 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13620 Z= 0.108 Angle : 0.510 8.185 18388 Z= 0.244 Chirality : 0.037 0.122 2120 Planarity : 0.003 0.034 2228 Dihedral : 14.151 143.718 2328 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.66 % Allowed : 12.54 % Favored : 86.80 % 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: 3.35 (0.22), residues: 1564 helix: 3.01 (0.16), residues: 1048 sheet: -1.54 (0.51), residues: 68 loop : 0.98 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 399 TYR 0.007 0.001 TYR C 11 PHE 0.005 0.001 PHE A 242 TRP 0.006 0.001 TRP A 264 HIS 0.001 0.000 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (13620) covalent geometry : angle 0.51003 / 0.24 (18388) hydrogen bonds : bond 0.03126 / 2.08 ( 852) hydrogen bonds : angle 3.68562 / 2.73 ( 2436) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9453.17 seconds wall clock time: 160 minutes 18.13 seconds (9618.13 seconds total)