Starting phenix.real_space_refine on Wed Sep 17 12:07:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jjb_61522/09_2025/9jjb_61522.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jjb_61522/09_2025/9jjb_61522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jjb_61522/09_2025/9jjb_61522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jjb_61522/09_2025/9jjb_61522.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jjb_61522/09_2025/9jjb_61522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jjb_61522/09_2025/9jjb_61522.map" } resolution = 2.68 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= 0.016 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 24 5.16 5 C 5178 2.51 5 N 1502 2.21 5 O 1574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8280 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3647 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 26, 'TRANS': 463} Chain breaks: 6 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 469 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain breaks: 1 Chain: "B" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3647 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 26, 'TRANS': 463} Chain breaks: 6 Chain: "D" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 469 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain breaks: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'9EF': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'9EF': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.18, per 1000 atoms: 0.26 Number of scatterers: 8280 At special positions: 0 Unit cell: (92.22, 107.3, 66.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 2 15.00 O 1574 8.00 N 1502 7.00 C 5178 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 444.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 46.6% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 103 through 109 removed outlier: 3.611A pdb=" N ALA A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.548A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.794A pdb=" N ARG A 136 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 157 removed outlier: 3.641A pdb=" N ARG A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 removed outlier: 4.095A pdb=" N THR A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 4.560A pdb=" N ILE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 213 Processing helix chain 'A' and resid 229 through 240 removed outlier: 4.005A pdb=" N ALA A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 304 through 320 removed outlier: 3.535A pdb=" N GLN A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.834A pdb=" N THR A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 387 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 484 through 501 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'C' and resid 955 through 960 Processing helix chain 'C' and resid 963 through 967 removed outlier: 3.864A pdb=" N VAL C 967 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 977 Processing helix chain 'C' and resid 979 through 992 removed outlier: 3.692A pdb=" N ALA C 992 " --> pdb=" O ASP C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1006 Processing helix chain 'C' and resid 1008 through 1014 removed outlier: 3.534A pdb=" N GLU C1014 " --> pdb=" O ALA C1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 54 Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.654A pdb=" N ALA B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 128 removed outlier: 3.542A pdb=" N ARG B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.793A pdb=" N ARG B 136 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 156 Processing helix chain 'B' and resid 165 through 171 removed outlier: 4.297A pdb=" N THR B 169 " --> pdb=" O HIS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 removed outlier: 4.555A pdb=" N ILE B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 213 Processing helix chain 'B' and resid 229 through 240 removed outlier: 3.984A pdb=" N ALA B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 304 through 320 removed outlier: 3.539A pdb=" N GLN B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.834A pdb=" N THR B 366 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 374 through 387 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 484 through 501 Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 533 through 545 Processing helix chain 'D' and resid 955 through 960 Processing helix chain 'D' and resid 963 through 967 removed outlier: 3.864A pdb=" N VAL D 967 " --> pdb=" O ALA D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 973 through 977 Processing helix chain 'D' and resid 979 through 992 removed outlier: 3.693A pdb=" N ALA D 992 " --> pdb=" O ASP D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1006 Processing helix chain 'D' and resid 1008 through 1014 removed outlier: 3.537A pdb=" N GLU D1014 " --> pdb=" O ALA D1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 412 through 414 removed outlier: 5.717A pdb=" N LEU A 359 " --> pdb=" O ARG A 413 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 328 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN A 444 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 291 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N HIS A 446 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER A 289 " --> pdb=" O HIS A 446 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL A 448 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 284 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 268 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU A 34 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU A 266 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N CYS A 36 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY A 264 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 224 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N MET A 191 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 142 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL A 193 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 144 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N MET B 191 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 142 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL B 193 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 144 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 224 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY B 264 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N CYS B 36 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 266 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU B 34 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 268 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 284 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL B 448 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER B 289 " --> pdb=" O HIS B 446 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N HIS B 446 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 291 " --> pdb=" O ASN B 444 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN B 444 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 328 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU B 359 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.612A pdb=" N ALA A 419 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 478 through 482 Processing sheet with id=AA5, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AA6, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.613A pdb=" N ALA B 419 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 478 through 482 380 hydrogen bonds defined for protein. 1074 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: 1.26 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2826 1.34 - 1.46: 1038 1.46 - 1.57: 4528 1.57 - 1.69: 2 1.69 - 1.81: 36 Bond restraints: 8430 Sorted by residual: bond pdb=" OAR 9EF C1101 " pdb=" PAW 9EF C1101 " ideal model delta sigma weight residual 1.676 1.610 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" OAR 9EF D1101 " pdb=" PAW 9EF D1101 " ideal model delta sigma weight residual 1.676 1.610 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" N HIS A 166 " pdb=" CA HIS A 166 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.32e-02 5.74e+03 5.42e+00 bond pdb=" N HIS A 165 " pdb=" CA HIS A 165 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.28e-02 6.10e+03 5.27e+00 bond pdb=" N HIS B 165 " pdb=" CA HIS B 165 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.37e-02 5.33e+03 5.15e+00 ... (remaining 8425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 11248 1.53 - 3.06: 152 3.06 - 4.60: 40 4.60 - 6.13: 12 6.13 - 7.66: 8 Bond angle restraints: 11460 Sorted by residual: angle pdb=" CA HIS A 166 " pdb=" CB HIS A 166 " pdb=" CG HIS A 166 " ideal model delta sigma weight residual 113.80 118.84 -5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" N HIS B 165 " pdb=" CA HIS B 165 " pdb=" C HIS B 165 " ideal model delta sigma weight residual 113.72 108.54 5.18 1.30e+00 5.92e-01 1.59e+01 angle pdb=" N HIS A 165 " pdb=" CA HIS A 165 " pdb=" C HIS A 165 " ideal model delta sigma weight residual 113.88 108.98 4.90 1.23e+00 6.61e-01 1.58e+01 angle pdb=" N HIS B 166 " pdb=" CA HIS B 166 " pdb=" C HIS B 166 " ideal model delta sigma weight residual 113.23 108.83 4.40 1.24e+00 6.50e-01 1.26e+01 angle pdb=" N VAL B 92 " pdb=" CA VAL B 92 " pdb=" C VAL B 92 " ideal model delta sigma weight residual 112.43 109.20 3.23 9.20e-01 1.18e+00 1.23e+01 ... (remaining 11455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 4575 21.72 - 43.43: 355 43.43 - 65.15: 73 65.15 - 86.86: 9 86.86 - 108.58: 4 Dihedral angle restraints: 5016 sinusoidal: 1922 harmonic: 3094 Sorted by residual: dihedral pdb=" CAK 9EF D1101 " pdb=" CAJ 9EF D1101 " pdb=" NAO 9EF D1101 " pdb=" CAS 9EF D1101 " ideal model delta sinusoidal sigma weight residual 81.61 -169.81 -108.58 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" CAK 9EF C1101 " pdb=" CAJ 9EF C1101 " pdb=" NAO 9EF C1101 " pdb=" CAS 9EF C1101 " ideal model delta sinusoidal sigma weight residual 81.61 179.66 -98.05 1 3.00e+01 1.11e-03 1.22e+01 dihedral pdb=" CB GLU B 524 " pdb=" CG GLU B 524 " pdb=" CD GLU B 524 " pdb=" OE1 GLU B 524 " ideal model delta sinusoidal sigma weight residual 0.00 -88.33 88.33 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 5013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 978 0.036 - 0.073: 228 0.073 - 0.109: 89 0.109 - 0.145: 21 0.145 - 0.181: 4 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA MET B 168 " pdb=" N MET B 168 " pdb=" C MET B 168 " pdb=" CB MET B 168 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA ASP A 90 " pdb=" N ASP A 90 " pdb=" C ASP A 90 " pdb=" CB ASP A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CA ASP B 90 " pdb=" N ASP B 90 " pdb=" C ASP B 90 " pdb=" CB ASP B 90 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 1317 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 322 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO B 323 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 323 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 323 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 322 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A 323 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 111 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO B 112 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.019 5.00e-02 4.00e+02 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 4 2.14 - 2.83: 2656 2.83 - 3.52: 10918 3.52 - 4.21: 19085 4.21 - 4.90: 34917 Nonbonded interactions: 67580 Sorted by model distance: nonbonded pdb=" OG SER D 980 " pdb=" OAG 9EF D1101 " model vdw 1.453 3.040 nonbonded pdb=" OG SER C 980 " pdb=" OAG 9EF C1101 " model vdw 1.483 3.040 nonbonded pdb=" OG SER D 980 " pdb=" PAW 9EF D1101 " model vdw 1.557 3.400 nonbonded pdb=" OG SER C 980 " pdb=" PAW 9EF C1101 " model vdw 1.558 3.400 nonbonded pdb=" OG SER A 200 " pdb=" O GLY A 373 " model vdw 2.230 3.040 ... (remaining 67575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = 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: 11.870 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.330 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.002 0.066 8432 Z= 0.144 Angle : 0.518 7.661 11460 Z= 0.282 Chirality : 0.039 0.181 1320 Planarity : 0.004 0.051 1498 Dihedral : 15.924 108.579 3024 Min Nonbonded Distance : 1.453 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.53 % Allowed : 18.28 % Favored : 80.19 % 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 aren not related in a simple way. whole: 1.12 (0.26), residues: 1066 helix: 1.93 (0.26), residues: 454 sheet: 1.02 (0.44), residues: 140 loop : -0.51 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 91 TYR 0.005 0.001 TYR B 151 PHE 0.004 0.000 PHE B 88 TRP 0.005 0.000 TRP B 48 HIS 0.010 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8430) covalent geometry : angle 0.51753 (11460) hydrogen bonds : bond 0.15676 ( 380) hydrogen bonds : angle 5.98395 ( 1074) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.307 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.7246 time to fit residues: 76.9844 Evaluate side-chains 101 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.0570 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.171158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125687 restraints weight = 8225.523| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.77 r_work: 0.3357 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8432 Z= 0.134 Angle : 0.541 6.848 11460 Z= 0.271 Chirality : 0.042 0.151 1320 Planarity : 0.005 0.048 1498 Dihedral : 7.093 102.177 1248 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.78 % Favored : 98.03 % Rotamer: Outliers : 4.01 % Allowed : 16.98 % Favored : 79.01 % 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 aren not related in a simple way. whole: 1.04 (0.25), residues: 1066 helix: 2.01 (0.25), residues: 460 sheet: 0.84 (0.46), residues: 120 loop : -0.64 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 91 TYR 0.019 0.002 TYR B 155 PHE 0.007 0.001 PHE B 95 TRP 0.009 0.001 TRP A 48 HIS 0.007 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8430) covalent geometry : angle 0.54075 (11460) hydrogen bonds : bond 0.04479 ( 380) hydrogen bonds : angle 4.05584 ( 1074) Misc. bond : bond 0.00081 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.304 Fit side-chains REVERT: A 49 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6696 (tt0) REVERT: B 49 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6672 (tt0) REVERT: B 156 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.6443 (mtt180) outliers start: 34 outliers final: 17 residues processed: 95 average time/residue: 0.8368 time to fit residues: 83.2847 Evaluate side-chains 89 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain D residue 970 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 42 optimal weight: 0.0050 chunk 96 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 957 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.172750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.128473 restraints weight = 8079.318| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.70 r_work: 0.3385 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8432 Z= 0.100 Angle : 0.473 6.394 11460 Z= 0.238 Chirality : 0.040 0.150 1320 Planarity : 0.004 0.054 1498 Dihedral : 6.498 97.688 1243 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.31 % Favored : 98.50 % Rotamer: Outliers : 3.42 % Allowed : 17.81 % Favored : 78.77 % 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 aren not related in a simple way. whole: 1.20 (0.26), residues: 1066 helix: 2.22 (0.25), residues: 460 sheet: 0.49 (0.42), residues: 140 loop : -0.56 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 910 TYR 0.016 0.001 TYR B 155 PHE 0.005 0.001 PHE B 88 TRP 0.010 0.001 TRP B 48 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8430) covalent geometry : angle 0.47334 (11460) hydrogen bonds : bond 0.03641 ( 380) hydrogen bonds : angle 3.76701 ( 1074) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.308 Fit side-chains REVERT: A 49 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6772 (tt0) REVERT: A 168 MET cc_start: 0.7355 (tmt) cc_final: 0.7144 (ppp) REVERT: A 372 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: B 49 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6750 (tt0) REVERT: B 156 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6541 (mtt180) REVERT: B 168 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7227 (ttm) REVERT: B 372 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6669 (mp0) outliers start: 29 outliers final: 14 residues processed: 98 average time/residue: 0.7867 time to fit residues: 80.9757 Evaluate side-chains 94 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain D residue 970 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 957 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.164987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120581 restraints weight = 8349.535| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.73 r_work: 0.3279 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8432 Z= 0.239 Angle : 0.682 9.254 11460 Z= 0.340 Chirality : 0.047 0.162 1320 Planarity : 0.006 0.051 1498 Dihedral : 7.233 92.024 1242 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.06 % Favored : 97.75 % Rotamer: Outliers : 5.42 % Allowed : 16.27 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.25), residues: 1066 helix: 1.57 (0.24), residues: 462 sheet: 0.50 (0.45), residues: 120 loop : -0.85 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 542 TYR 0.021 0.003 TYR B 316 PHE 0.010 0.002 PHE A 95 TRP 0.009 0.002 TRP A 48 HIS 0.007 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 8430) covalent geometry : angle 0.68168 (11460) hydrogen bonds : bond 0.05895 ( 380) hydrogen bonds : angle 4.24499 ( 1074) Misc. bond : bond 0.00213 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 69 time to evaluate : 0.257 Fit side-chains REVERT: A 49 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6762 (tt0) REVERT: A 314 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.5607 (ptt180) REVERT: A 372 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: A 524 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: B 49 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6746 (tt0) REVERT: B 156 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6572 (mtt180) REVERT: B 168 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7276 (ttm) REVERT: B 314 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.5619 (ptt180) REVERT: B 372 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: B 524 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: B 926 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7171 (tp30) outliers start: 46 outliers final: 24 residues processed: 100 average time/residue: 0.7832 time to fit residues: 82.1094 Evaluate side-chains 101 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain D residue 958 VAL Chi-restraints excluded: chain D residue 970 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 0.0010 chunk 42 optimal weight: 0.0470 chunk 46 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.0170 overall best weight: 0.3522 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.172693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128752 restraints weight = 8224.816| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.74 r_work: 0.3386 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 8432 Z= 0.084 Angle : 0.457 5.770 11460 Z= 0.232 Chirality : 0.040 0.152 1320 Planarity : 0.004 0.055 1498 Dihedral : 6.398 94.406 1242 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.78 % Favored : 98.03 % Rotamer: Outliers : 3.66 % Allowed : 18.28 % Favored : 78.07 % 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 aren not related in a simple way. whole: 0.97 (0.26), residues: 1066 helix: 2.12 (0.25), residues: 462 sheet: 0.40 (0.46), residues: 120 loop : -0.77 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 91 TYR 0.013 0.001 TYR B 155 PHE 0.006 0.001 PHE B 88 TRP 0.012 0.001 TRP B 122 HIS 0.004 0.001 HIS C 957 Details of bonding type rmsd covalent geometry : bond 0.00174 ( 8430) covalent geometry : angle 0.45721 (11460) hydrogen bonds : bond 0.03146 ( 380) hydrogen bonds : angle 3.72636 ( 1074) Misc. bond : bond 0.00021 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.323 Fit side-chains REVERT: A 49 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6706 (tt0) REVERT: A 372 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: A 926 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7110 (tp30) REVERT: B 49 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6682 (tt0) REVERT: B 156 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6531 (mtt180) REVERT: B 372 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: B 926 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7164 (tp30) outliers start: 31 outliers final: 16 residues processed: 104 average time/residue: 0.7562 time to fit residues: 82.7069 Evaluate side-chains 96 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain D residue 970 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.0060 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.0370 chunk 102 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 0.3674 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.173356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129564 restraints weight = 8215.656| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.74 r_work: 0.3396 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 8432 Z= 0.083 Angle : 0.458 6.938 11460 Z= 0.228 Chirality : 0.040 0.150 1320 Planarity : 0.004 0.057 1498 Dihedral : 6.231 90.953 1242 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.53 % Favored : 97.37 % Rotamer: Outliers : 3.54 % Allowed : 19.46 % Favored : 77.00 % 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 aren not related in a simple way. whole: 1.15 (0.26), residues: 1066 helix: 2.33 (0.25), residues: 462 sheet: 0.35 (0.46), residues: 120 loop : -0.71 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 910 TYR 0.012 0.001 TYR B 155 PHE 0.006 0.001 PHE B 88 TRP 0.010 0.001 TRP B 48 HIS 0.003 0.001 HIS D 957 Details of bonding type rmsd covalent geometry : bond 0.00175 ( 8430) covalent geometry : angle 0.45756 (11460) hydrogen bonds : bond 0.03118 ( 380) hydrogen bonds : angle 3.60060 ( 1074) Misc. bond : bond 0.00021 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.321 Fit side-chains REVERT: A 49 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6697 (tt0) REVERT: A 372 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: B 49 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6685 (tt0) REVERT: B 168 MET cc_start: 0.8137 (ttm) cc_final: 0.7920 (ttp) REVERT: B 372 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6721 (mp0) outliers start: 30 outliers final: 20 residues processed: 96 average time/residue: 0.8222 time to fit residues: 82.7045 Evaluate side-chains 94 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain D residue 970 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.170842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126637 restraints weight = 8281.967| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.75 r_work: 0.3361 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8432 Z= 0.106 Angle : 0.503 9.663 11460 Z= 0.248 Chirality : 0.041 0.151 1320 Planarity : 0.005 0.057 1498 Dihedral : 6.408 89.569 1242 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.78 % Favored : 98.12 % Rotamer: Outliers : 3.42 % Allowed : 19.22 % Favored : 77.36 % 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 aren not related in a simple way. whole: 1.06 (0.26), residues: 1066 helix: 2.23 (0.25), residues: 462 sheet: 0.40 (0.46), residues: 120 loop : -0.75 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 910 TYR 0.013 0.001 TYR B 316 PHE 0.006 0.001 PHE B 95 TRP 0.009 0.001 TRP B 48 HIS 0.004 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8430) covalent geometry : angle 0.50313 (11460) hydrogen bonds : bond 0.03720 ( 380) hydrogen bonds : angle 3.68944 ( 1074) Misc. bond : bond 0.00052 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.344 Fit side-chains REVERT: A 49 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6705 (tt0) REVERT: A 372 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: B 49 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: B 168 MET cc_start: 0.8202 (ttm) cc_final: 0.7864 (ttp) REVERT: B 372 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6812 (mp0) outliers start: 29 outliers final: 21 residues processed: 92 average time/residue: 0.8470 time to fit residues: 81.6220 Evaluate side-chains 93 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain D residue 970 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.0030 chunk 78 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 overall best weight: 0.4350 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.173304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129370 restraints weight = 8216.030| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.74 r_work: 0.3392 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 8432 Z= 0.086 Angle : 0.462 7.534 11460 Z= 0.229 Chirality : 0.040 0.150 1320 Planarity : 0.004 0.057 1498 Dihedral : 6.233 89.001 1242 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.88 % Favored : 98.03 % Rotamer: Outliers : 3.42 % Allowed : 19.46 % Favored : 77.12 % 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 aren not related in a simple way. whole: 1.15 (0.26), residues: 1066 helix: 2.35 (0.25), residues: 462 sheet: 0.33 (0.46), residues: 120 loop : -0.71 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 910 TYR 0.011 0.001 TYR B 155 PHE 0.006 0.001 PHE B 88 TRP 0.010 0.001 TRP B 48 HIS 0.003 0.001 HIS C 957 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 8430) covalent geometry : angle 0.46209 (11460) hydrogen bonds : bond 0.03168 ( 380) hydrogen bonds : angle 3.59228 ( 1074) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.373 Fit side-chains REVERT: A 49 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: A 168 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7510 (ttp) REVERT: A 372 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: B 49 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6701 (tt0) REVERT: B 168 MET cc_start: 0.8163 (ttm) cc_final: 0.7948 (ttp) REVERT: B 372 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6799 (mp0) outliers start: 29 outliers final: 21 residues processed: 93 average time/residue: 0.7697 time to fit residues: 75.2934 Evaluate side-chains 96 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain D residue 970 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.0670 chunk 74 optimal weight: 0.0970 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 13 optimal weight: 0.0370 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.173986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129931 restraints weight = 8225.928| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.75 r_work: 0.3398 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 8432 Z= 0.085 Angle : 0.458 7.701 11460 Z= 0.227 Chirality : 0.040 0.148 1320 Planarity : 0.004 0.058 1498 Dihedral : 6.169 88.138 1242 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.42 % Allowed : 19.58 % Favored : 77.00 % 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 aren not related in a simple way. whole: 1.19 (0.26), residues: 1066 helix: 2.36 (0.25), residues: 462 sheet: 0.35 (0.46), residues: 120 loop : -0.68 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 910 TYR 0.011 0.001 TYR B 155 PHE 0.005 0.001 PHE A 88 TRP 0.010 0.001 TRP B 48 HIS 0.003 0.001 HIS C 957 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 8430) covalent geometry : angle 0.45820 (11460) hydrogen bonds : bond 0.03111 ( 380) hydrogen bonds : angle 3.56084 ( 1074) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.385 Fit side-chains REVERT: A 49 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6741 (tt0) REVERT: A 168 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7529 (ttp) REVERT: A 372 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: B 49 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6733 (tt0) REVERT: B 168 MET cc_start: 0.8146 (ttm) cc_final: 0.7946 (ttp) REVERT: B 372 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6736 (mp0) outliers start: 29 outliers final: 21 residues processed: 96 average time/residue: 0.7609 time to fit residues: 76.6451 Evaluate side-chains 99 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain D residue 970 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.171664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127262 restraints weight = 8153.774| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.75 r_work: 0.3364 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8432 Z= 0.104 Angle : 0.491 7.262 11460 Z= 0.244 Chirality : 0.041 0.150 1320 Planarity : 0.005 0.058 1498 Dihedral : 6.364 88.729 1242 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.42 % Allowed : 19.58 % Favored : 77.00 % 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 aren not related in a simple way. whole: 1.11 (0.26), residues: 1066 helix: 2.26 (0.25), residues: 462 sheet: 0.37 (0.46), residues: 120 loop : -0.68 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 910 TYR 0.012 0.001 TYR B 316 PHE 0.005 0.001 PHE A 95 TRP 0.009 0.001 TRP A 48 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8430) covalent geometry : angle 0.49121 (11460) hydrogen bonds : bond 0.03621 ( 380) hydrogen bonds : angle 3.65519 ( 1074) Misc. bond : bond 0.00051 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.332 Fit side-chains REVERT: A 49 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6712 (tt0) REVERT: A 314 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.5542 (ptt180) REVERT: A 372 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: A 542 ARG cc_start: 0.7107 (tpp-160) cc_final: 0.6554 (mtp85) REVERT: B 49 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6708 (tt0) REVERT: B 168 MET cc_start: 0.8187 (ttm) cc_final: 0.7936 (ttp) REVERT: B 372 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: B 542 ARG cc_start: 0.7096 (tpp-160) cc_final: 0.6532 (mtp85) outliers start: 29 outliers final: 19 residues processed: 92 average time/residue: 0.8472 time to fit residues: 81.4992 Evaluate side-chains 92 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain D residue 970 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.171474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126979 restraints weight = 8235.021| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.75 r_work: 0.3359 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8432 Z= 0.104 Angle : 0.492 7.511 11460 Z= 0.244 Chirality : 0.041 0.152 1320 Planarity : 0.005 0.058 1498 Dihedral : 6.374 88.327 1241 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.30 % Allowed : 19.81 % Favored : 76.89 % 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 aren not related in a simple way. whole: 1.10 (0.26), residues: 1066 helix: 2.26 (0.25), residues: 462 sheet: 0.38 (0.46), residues: 120 loop : -0.71 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 910 TYR 0.012 0.001 TYR B 316 PHE 0.006 0.001 PHE B 88 TRP 0.009 0.001 TRP B 48 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8430) covalent geometry : angle 0.49156 (11460) hydrogen bonds : bond 0.03607 ( 380) hydrogen bonds : angle 3.67091 ( 1074) Misc. bond : bond 0.00048 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.56 seconds wall clock time: 59 minutes 41.40 seconds (3581.40 seconds total)