Starting phenix.real_space_refine on Sun Oct 25 03:17:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7o_72662/10_2026/9y7o_72662.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7o_72662/10_2026/9y7o_72662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y7o_72662/10_2026/9y7o_72662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7o_72662/10_2026/9y7o_72662.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y7o_72662/10_2026/9y7o_72662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7o_72662/10_2026/9y7o_72662.map" } resolution = 3.01 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= 0.009 sd= 0.074 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 12 5.49 5 S 96 5.16 5 C 10076 2.51 5 N 2424 2.21 5 O 2768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15376 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3770 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 6, 'TRANS': 453} Chain breaks: 2 Chain: "C" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3770 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 6, 'TRANS': 453} Chain breaks: 2 Chain: "B" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3770 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 6, 'TRANS': 453} Chain breaks: 2 Chain: "D" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3770 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 6, 'TRANS': 453} Chain breaks: 2 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'AQV': 1, 'EUJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'AQV': 1, 'EUJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'AQV': 1, 'EUJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'AQV': 1, 'EUJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.56, per 1000 atoms: 0.23 Number of scatterers: 15376 At special positions: 0 Unit cell: (97.94, 97.94, 116.2, 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 96 16.00 P 12 15.00 O 2768 8.00 N 2424 7.00 C 10076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS A 243 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 190 " distance=2.03 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 243 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 190 " distance=2.03 Simple disulfide: pdb=" SG CYS D 243 " - pdb=" SG CYS D 274 " distance=2.03 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: 0.91 Conformation dependent library (CDL) restraints added in 597.7 milliseconds 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 8 sheets defined 71.5% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 38 through 49 removed outlier: 3.528A pdb=" N PHE A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.539A pdb=" N GLY A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.580A pdb=" N ARG A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 201 removed outlier: 4.143A pdb=" N GLU A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 207 removed outlier: 3.933A pdb=" N TRP A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.953A pdb=" N HIS A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 237' Processing helix chain 'A' and resid 291 through 330 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 345 through 370 Processing helix chain 'A' and resid 375 through 392 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 400 through 440 removed outlier: 4.475A pdb=" N LEU A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 443 through 447 removed outlier: 4.113A pdb=" N GLU A 447 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 476 through 520 removed outlier: 4.101A pdb=" N LEU A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 518 " --> pdb=" O LYS A 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.784A pdb=" N GLY C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 140 Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.590A pdb=" N ARG C 158 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 201 removed outlier: 4.138A pdb=" N GLU C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 removed outlier: 3.935A pdb=" N TRP C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 206 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.951A pdb=" N HIS C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 237 " --> pdb=" O GLN C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 237' Processing helix chain 'C' and resid 291 through 330 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 345 through 370 Processing helix chain 'C' and resid 375 through 392 Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'C' and resid 400 through 440 removed outlier: 4.476A pdb=" N LEU C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Proline residue: C 415 - end of helix Processing helix chain 'C' and resid 443 through 447 removed outlier: 4.158A pdb=" N GLU C 447 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 476 through 520 removed outlier: 4.099A pdb=" N LEU C 499 " --> pdb=" O ILE C 495 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER C 500 " --> pdb=" O TYR C 496 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 518 " --> pdb=" O LYS C 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 51 through 60 Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.787A pdb=" N GLY B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.590A pdb=" N ARG B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 201 removed outlier: 4.138A pdb=" N GLU B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 207 removed outlier: 3.931A pdb=" N TRP B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 206 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.952A pdb=" N HIS B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 237' Processing helix chain 'B' and resid 291 through 330 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 345 through 370 Processing helix chain 'B' and resid 375 through 392 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 400 through 440 removed outlier: 4.475A pdb=" N LEU B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Proline residue: B 415 - end of helix Processing helix chain 'B' and resid 443 through 447 removed outlier: 4.139A pdb=" N GLU B 447 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 476 through 520 removed outlier: 4.099A pdb=" N LEU B 499 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER B 500 " --> pdb=" O TYR B 496 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 518 " --> pdb=" O LYS B 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 49 removed outlier: 3.502A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 60 Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.782A pdb=" N GLY D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 140 Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.590A pdb=" N ARG D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 201 removed outlier: 4.140A pdb=" N GLU D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 207 removed outlier: 3.930A pdb=" N TRP D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 206 " --> pdb=" O PRO D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.952A pdb=" N HIS D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER D 237 " --> pdb=" O GLN D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 232 through 237' Processing helix chain 'D' and resid 291 through 330 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 341 through 343 No H-bonds generated for 'chain 'D' and resid 341 through 343' Processing helix chain 'D' and resid 345 through 370 Processing helix chain 'D' and resid 375 through 392 Processing helix chain 'D' and resid 393 through 398 Processing helix chain 'D' and resid 400 through 440 removed outlier: 4.476A pdb=" N LEU D 406 " --> pdb=" O THR D 402 " (cutoff:3.500A) Proline residue: D 415 - end of helix Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 476 through 520 removed outlier: 4.103A pdb=" N LEU D 499 " --> pdb=" O ILE D 495 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N SER D 500 " --> pdb=" O TYR D 496 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 518 " --> pdb=" O LYS D 514 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.510A pdb=" N GLU A 268 " --> pdb=" O GLN A 247 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS A 243 " --> pdb=" O GLU A 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.510A pdb=" N GLU A 268 " --> pdb=" O GLN A 247 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS A 243 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 218 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR A 168 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 220 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.514A pdb=" N GLU C 268 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N CYS C 243 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.514A pdb=" N GLU C 268 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N CYS C 243 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU C 218 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TYR C 168 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 220 " --> pdb=" O GLN C 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.513A pdb=" N GLU B 268 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N CYS B 243 " --> pdb=" O GLU B 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.513A pdb=" N GLU B 268 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N CYS B 243 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 218 " --> pdb=" O TYR B 168 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR B 168 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 220 " --> pdb=" O GLN B 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.512A pdb=" N GLU D 268 " --> pdb=" O GLN D 247 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N CYS D 243 " --> pdb=" O GLU D 272 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.512A pdb=" N GLU D 268 " --> pdb=" O GLN D 247 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N CYS D 243 " --> pdb=" O GLU D 272 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU D 218 " --> pdb=" O TYR D 168 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR D 168 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D 220 " --> pdb=" O GLN D 166 " (cutoff:3.500A) 1194 hydrogen bonds defined for protein. 3465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2557 1.32 - 1.45: 4331 1.45 - 1.57: 8668 1.57 - 1.69: 40 1.69 - 1.81: 132 Bond restraints: 15728 Sorted by residual: bond pdb=" O3 EUJ D 601 " pdb=" P3 EUJ D 601 " ideal model delta sigma weight residual 1.727 1.609 0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" O3 EUJ A 601 " pdb=" P3 EUJ A 601 " ideal model delta sigma weight residual 1.727 1.609 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" O3 EUJ B 601 " pdb=" P3 EUJ B 601 " ideal model delta sigma weight residual 1.727 1.609 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" O3 EUJ C 601 " pdb=" P3 EUJ C 601 " ideal model delta sigma weight residual 1.727 1.609 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" O12 EUJ A 601 " pdb=" P1 EUJ A 601 " ideal model delta sigma weight residual 1.497 1.601 -0.104 2.00e-02 2.50e+03 2.71e+01 ... (remaining 15723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 20955 2.48 - 4.97: 245 4.97 - 7.45: 64 7.45 - 9.93: 16 9.93 - 12.42: 20 Bond angle restraints: 21300 Sorted by residual: angle pdb=" O11 EUJ C 601 " pdb=" P1 EUJ C 601 " pdb=" O12 EUJ C 601 " ideal model delta sigma weight residual 121.88 109.46 12.42 3.00e+00 1.11e-01 1.71e+01 angle pdb=" O11 EUJ B 601 " pdb=" P1 EUJ B 601 " pdb=" O12 EUJ B 601 " ideal model delta sigma weight residual 121.88 109.46 12.42 3.00e+00 1.11e-01 1.71e+01 angle pdb=" O11 EUJ D 601 " pdb=" P1 EUJ D 601 " pdb=" O12 EUJ D 601 " ideal model delta sigma weight residual 121.88 109.50 12.38 3.00e+00 1.11e-01 1.70e+01 angle pdb=" O11 EUJ A 601 " pdb=" P1 EUJ A 601 " pdb=" O12 EUJ A 601 " ideal model delta sigma weight residual 121.88 109.60 12.28 3.00e+00 1.11e-01 1.67e+01 angle pdb=" C5 EUJ C 601 " pdb=" O5 EUJ C 601 " pdb=" P5 EUJ C 601 " ideal model delta sigma weight residual 113.41 124.82 -11.41 3.00e+00 1.11e-01 1.45e+01 ... (remaining 21295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.85: 8847 28.85 - 57.70: 432 57.70 - 86.54: 85 86.54 - 115.39: 40 115.39 - 144.24: 32 Dihedral angle restraints: 9436 sinusoidal: 3996 harmonic: 5440 Sorted by residual: dihedral pdb=" C2C EUJ A 601 " pdb=" C1C EUJ A 601 " pdb=" O13 EUJ A 601 " pdb=" P1 EUJ A 601 " ideal model delta sinusoidal sigma weight residual 93.25 -122.51 -144.24 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" C2C EUJ D 601 " pdb=" C1C EUJ D 601 " pdb=" O13 EUJ D 601 " pdb=" P1 EUJ D 601 " ideal model delta sinusoidal sigma weight residual 93.25 -128.20 -138.55 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" C2C EUJ B 601 " pdb=" C1C EUJ B 601 " pdb=" O13 EUJ B 601 " pdb=" P1 EUJ B 601 " ideal model delta sinusoidal sigma weight residual 93.25 -128.30 -138.45 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 9433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.978: 2408 0.978 - 1.957: 0 1.957 - 2.935: 0 2.935 - 3.913: 0 3.913 - 4.891: 4 Chirality restraints: 2412 Sorted by residual: chirality pdb=" C4 EUJ B 601 " pdb=" C3 EUJ B 601 " pdb=" C5 EUJ B 601 " pdb=" O4 EUJ B 601 " both_signs ideal model delta sigma weight residual False 2.45 -2.44 4.89 2.00e-01 2.50e+01 5.98e+02 chirality pdb=" C4 EUJ D 601 " pdb=" C3 EUJ D 601 " pdb=" C5 EUJ D 601 " pdb=" O4 EUJ D 601 " both_signs ideal model delta sigma weight residual False 2.45 -2.44 4.89 2.00e-01 2.50e+01 5.98e+02 chirality pdb=" C4 EUJ C 601 " pdb=" C3 EUJ C 601 " pdb=" C5 EUJ C 601 " pdb=" O4 EUJ C 601 " both_signs ideal model delta sigma weight residual False 2.45 -2.44 4.89 2.00e-01 2.50e+01 5.98e+02 ... (remaining 2409 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 440 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 441 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 440 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO D 441 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 441 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 441 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 440 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO C 441 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 441 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 441 " -0.021 5.00e-02 4.00e+02 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2546 2.76 - 3.29: 14480 3.29 - 3.83: 25801 3.83 - 4.36: 31682 4.36 - 4.90: 54612 Nonbonded interactions: 129121 Sorted by model distance: nonbonded pdb=" NZ LYS B 72 " pdb=" OD1 ASP B 354 " model vdw 2.224 3.120 nonbonded pdb=" NZ LYS C 72 " pdb=" OD1 ASP C 354 " model vdw 2.225 3.120 nonbonded pdb=" NZ LYS D 72 " pdb=" OD1 ASP D 354 " model vdw 2.225 3.120 nonbonded pdb=" O PHE D 469 " pdb=" NH2 ARG D 484 " model vdw 2.245 3.120 nonbonded pdb=" O PHE C 469 " pdb=" NH2 ARG C 484 " model vdw 2.246 3.120 ... (remaining 129116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.560 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.070 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 : 0.007 0.118 15736 Z= 0.313 Angle : 0.764 12.416 21316 Z= 0.330 Chirality : 0.204 4.891 2412 Planarity : 0.003 0.038 2580 Dihedral : 20.857 144.238 5900 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.19), residues: 1816 helix: 1.57 (0.15), residues: 1144 sheet: -0.26 (0.36), residues: 228 loop : -0.70 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 395 TYR 0.019 0.001 TYR C 486 PHE 0.020 0.001 PHE B 494 TRP 0.010 0.001 TRP B 390 HIS 0.003 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.31 (15728) covalent geometry : angle 0.76473 / 0.33 (21300) SS BOND : bond 0.00114 / 0.07 ( 8) SS BOND : angle 0.21121 / 0.12 ( 16) hydrogen bonds : bond 0.15810 / 10.95 ( 1098) hydrogen bonds : angle 7.26763 / 5.23 ( 3465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.566 Fit side-chains REVERT: A 211 PHE cc_start: 0.8822 (m-80) cc_final: 0.8579 (m-80) REVERT: A 212 ARG cc_start: 0.7903 (mmp-170) cc_final: 0.7565 (mtp85) REVERT: C 212 ARG cc_start: 0.7907 (mmp-170) cc_final: 0.7571 (mtp85) REVERT: B 212 ARG cc_start: 0.7906 (mmp-170) cc_final: 0.7572 (mtp85) REVERT: B 451 ILE cc_start: 0.8496 (mt) cc_final: 0.8271 (mt) REVERT: D 211 PHE cc_start: 0.8815 (m-80) cc_final: 0.8579 (m-80) REVERT: D 212 ARG cc_start: 0.7896 (mmp-170) cc_final: 0.7572 (mtp85) REVERT: D 451 ILE cc_start: 0.8486 (mt) cc_final: 0.8253 (mt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1291 time to fit residues: 34.3147 Evaluate side-chains 153 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN A 518 GLN C 518 GLN B 518 GLN D 518 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.168059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106882 restraints weight = 14068.968| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.86 r_work: 0.2922 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15736 Z= 0.245 Angle : 0.602 7.218 21316 Z= 0.305 Chirality : 0.044 0.201 2412 Planarity : 0.004 0.044 2580 Dihedral : 21.292 155.455 2364 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.36 % Allowed : 5.86 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.19), residues: 1816 helix: 1.87 (0.15), residues: 1136 sheet: -0.25 (0.33), residues: 228 loop : -0.27 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.020 0.002 TYR B 428 PHE 0.019 0.002 PHE B 494 TRP 0.012 0.002 TRP B 390 HIS 0.004 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.24 (15728) covalent geometry : angle 0.60223 / 0.31 (21300) SS BOND : bond 0.00100 / 0.06 ( 8) SS BOND : angle 0.46222 / 0.26 ( 16) hydrogen bonds : bond 0.05726 / 3.97 ( 1098) hydrogen bonds : angle 5.34228 / 3.78 ( 3465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 174 time to evaluate : 0.546 Fit side-chains REVERT: A 212 ARG cc_start: 0.7756 (mmp-170) cc_final: 0.7093 (mtp85) REVERT: C 212 ARG cc_start: 0.7754 (mmp-170) cc_final: 0.7096 (mtp85) REVERT: B 212 ARG cc_start: 0.7757 (mmp-170) cc_final: 0.7094 (mtp85) REVERT: D 212 ARG cc_start: 0.7729 (mmp-170) cc_final: 0.7103 (mtp85) outliers start: 6 outliers final: 5 residues processed: 175 average time/residue: 0.1277 time to fit residues: 33.4774 Evaluate side-chains 166 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain D residue 224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: [86, 24, 53, 181, 15, 158, 14, 115, 58, 25, 85] chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 53 optimal weight: 0.0970 chunk 181 optimal weight: 1.9990 chunk 15 optimal weight: 0.0470 chunk 158 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 25 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS A 518 GLN C 518 GLN B 518 GLN D 518 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.168697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.107082 restraints weight = 14411.583| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.97 r_work: 0.3001 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15736 Z= 0.128 Angle : 0.492 7.048 21316 Z= 0.250 Chirality : 0.039 0.228 2412 Planarity : 0.003 0.040 2580 Dihedral : 20.189 174.199 2364 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.30 % Allowed : 7.12 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.19), residues: 1816 helix: 2.24 (0.15), residues: 1132 sheet: -0.12 (0.32), residues: 236 loop : -0.27 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 484 TYR 0.014 0.001 TYR B 428 PHE 0.012 0.001 PHE B 494 TRP 0.008 0.001 TRP B 390 HIS 0.002 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (15728) covalent geometry : angle 0.49246 / 0.25 (21300) SS BOND : bond 0.00102 / 0.06 ( 8) SS BOND : angle 0.40528 / 0.23 ( 16) hydrogen bonds : bond 0.04608 / 3.17 ( 1098) hydrogen bonds : angle 4.83247 / 3.42 ( 3465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 172 time to evaluate : 0.568 Fit side-chains REVERT: A 212 ARG cc_start: 0.7693 (mmp-170) cc_final: 0.7011 (mtp85) REVERT: A 242 ASP cc_start: 0.7023 (m-30) cc_final: 0.6658 (m-30) REVERT: C 212 ARG cc_start: 0.7671 (mmp-170) cc_final: 0.6981 (mtp85) REVERT: C 242 ASP cc_start: 0.7007 (m-30) cc_final: 0.6650 (m-30) REVERT: B 212 ARG cc_start: 0.7679 (mmp-170) cc_final: 0.6984 (mtp85) REVERT: D 212 ARG cc_start: 0.7684 (mmp-170) cc_final: 0.7009 (mtp85) outliers start: 5 outliers final: 5 residues processed: 172 average time/residue: 0.1350 time to fit residues: 34.3702 Evaluate side-chains 159 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain D residue 112 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: [176, 156, 48, 170, 43, 116, 14, 89, 97, 104, 63] chunk 176 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS A 518 GLN C 192 HIS C 518 GLN B 518 GLN D 518 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.167508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.106393 restraints weight = 14296.728| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.93 r_work: 0.3039 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15736 Z= 0.128 Angle : 0.486 6.877 21316 Z= 0.246 Chirality : 0.039 0.183 2412 Planarity : 0.003 0.038 2580 Dihedral : 18.174 165.349 2364 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.30 % Allowed : 9.63 % Favored : 90.07 % 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 are not related in a simple way. whole: 2.19 (0.20), residues: 1816 helix: 2.45 (0.15), residues: 1132 sheet: 0.02 (0.34), residues: 220 loop : -0.36 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 238 TYR 0.014 0.001 TYR C 428 PHE 0.015 0.001 PHE A 210 TRP 0.007 0.001 TRP B 390 HIS 0.002 0.000 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (15728) covalent geometry : angle 0.48578 / 0.25 (21300) SS BOND : bond 0.00067 / 0.04 ( 8) SS BOND : angle 0.38048 / 0.22 ( 16) hydrogen bonds : bond 0.04497 / 3.10 ( 1098) hydrogen bonds : angle 4.62404 / 3.27 ( 3465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 173 time to evaluate : 0.563 Fit side-chains REVERT: A 212 ARG cc_start: 0.7685 (mmp-170) cc_final: 0.7002 (mtp85) REVERT: A 214 ASP cc_start: 0.7551 (t0) cc_final: 0.7344 (t0) REVERT: A 242 ASP cc_start: 0.6971 (m-30) cc_final: 0.6557 (m-30) REVERT: C 212 ARG cc_start: 0.7666 (mmp-170) cc_final: 0.6983 (mtp85) REVERT: C 214 ASP cc_start: 0.7529 (t0) cc_final: 0.7322 (t0) REVERT: C 242 ASP cc_start: 0.6996 (m-30) cc_final: 0.6647 (m-30) REVERT: B 212 ARG cc_start: 0.7674 (mmp-170) cc_final: 0.6972 (mtp85) REVERT: B 214 ASP cc_start: 0.7519 (t0) cc_final: 0.7309 (t0) REVERT: D 212 ARG cc_start: 0.7694 (mmp-170) cc_final: 0.6996 (mtp85) REVERT: D 214 ASP cc_start: 0.7579 (t0) cc_final: 0.7379 (t0) outliers start: 5 outliers final: 4 residues processed: 174 average time/residue: 0.1303 time to fit residues: 33.6587 Evaluate side-chains 167 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain D residue 112 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: [81, 8, 38, 35, 136, 100, 41, 99, 116, 110, 88] chunk 81 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 99 optimal weight: 0.0060 chunk 116 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS A 518 GLN C 61 GLN C 192 HIS C 518 GLN B 61 GLN B 518 GLN D 61 GLN D 518 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.165096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103253 restraints weight = 14429.126| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.93 r_work: 0.2997 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15736 Z= 0.159 Angle : 0.498 7.028 21316 Z= 0.254 Chirality : 0.039 0.139 2412 Planarity : 0.003 0.038 2580 Dihedral : 17.387 141.535 2364 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.54 % Allowed : 10.41 % Favored : 89.06 % 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: 2.13 (0.19), residues: 1816 helix: 2.40 (0.15), residues: 1132 sheet: 0.04 (0.34), residues: 220 loop : -0.38 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 310 TYR 0.015 0.001 TYR B 486 PHE 0.018 0.001 PHE B 210 TRP 0.008 0.001 TRP B 390 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (15728) covalent geometry : angle 0.49811 / 0.25 (21300) SS BOND : bond 0.00089 / 0.05 ( 8) SS BOND : angle 0.25652 / 0.15 ( 16) hydrogen bonds : bond 0.04826 / 3.35 ( 1098) hydrogen bonds : angle 4.72478 / 3.34 ( 3465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.464 Fit side-chains REVERT: A 212 ARG cc_start: 0.7725 (mmp-170) cc_final: 0.7050 (mtp85) REVERT: A 242 ASP cc_start: 0.7097 (m-30) cc_final: 0.6636 (m-30) REVERT: C 212 ARG cc_start: 0.7711 (mmp-170) cc_final: 0.7030 (mtp85) REVERT: C 242 ASP cc_start: 0.7059 (m-30) cc_final: 0.6691 (m-30) REVERT: B 212 ARG cc_start: 0.7704 (mmp-170) cc_final: 0.7024 (mtp85) REVERT: B 214 ASP cc_start: 0.7600 (t0) cc_final: 0.7328 (t0) REVERT: D 212 ARG cc_start: 0.7721 (mmp-170) cc_final: 0.7039 (mtp85) outliers start: 9 outliers final: 9 residues processed: 169 average time/residue: 0.1325 time to fit residues: 32.9046 Evaluate side-chains 171 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 224 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: [80, 84, 50, 172, 157, 146, 120, 173, 2, 163, 183] chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 0.0020 chunk 50 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 157 optimal weight: 0.0980 chunk 146 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS C 192 HIS C 518 GLN B 518 GLN D 518 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.165632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.104305 restraints weight = 14306.996| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.91 r_work: 0.2965 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15736 Z= 0.147 Angle : 0.478 6.970 21316 Z= 0.246 Chirality : 0.039 0.137 2412 Planarity : 0.003 0.038 2580 Dihedral : 16.938 138.147 2364 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.72 % Allowed : 11.00 % Favored : 88.28 % 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: 2.17 (0.19), residues: 1816 helix: 2.44 (0.15), residues: 1132 sheet: 0.01 (0.34), residues: 220 loop : -0.36 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 310 TYR 0.015 0.001 TYR B 428 PHE 0.021 0.001 PHE D 210 TRP 0.007 0.001 TRP B 390 HIS 0.002 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (15728) covalent geometry : angle 0.47845 / 0.25 (21300) SS BOND : bond 0.00084 / 0.05 ( 8) SS BOND : angle 0.21350 / 0.12 ( 16) hydrogen bonds : bond 0.04683 / 3.24 ( 1098) hydrogen bonds : angle 4.65312 / 3.29 ( 3465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.608 Fit side-chains REVERT: A 214 ASP cc_start: 0.7610 (t0) cc_final: 0.7389 (t0) REVERT: A 242 ASP cc_start: 0.7086 (m-30) cc_final: 0.6619 (m-30) REVERT: C 212 ARG cc_start: 0.7702 (mmp-170) cc_final: 0.7022 (mtp85) REVERT: C 214 ASP cc_start: 0.7628 (t0) cc_final: 0.7405 (t0) REVERT: C 242 ASP cc_start: 0.7062 (m-30) cc_final: 0.6690 (m-30) REVERT: B 212 ARG cc_start: 0.7701 (mmp-170) cc_final: 0.7021 (mtp85) REVERT: B 214 ASP cc_start: 0.7617 (t0) cc_final: 0.7391 (t0) REVERT: D 214 ASP cc_start: 0.7640 (t0) cc_final: 0.7425 (t0) outliers start: 12 outliers final: 12 residues processed: 164 average time/residue: 0.1118 time to fit residues: 28.2131 Evaluate side-chains 169 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 224 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: [102, 91, 117, 136, 34, 111, 105, 118, 176, 153, 40] chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS C 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.165631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103079 restraints weight = 14182.357| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.94 r_work: 0.2977 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15736 Z= 0.180 Angle : 0.506 7.060 21316 Z= 0.260 Chirality : 0.040 0.142 2412 Planarity : 0.003 0.039 2580 Dihedral : 16.842 139.615 2364 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.84 % Allowed : 11.30 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.19), residues: 1816 helix: 2.34 (0.15), residues: 1132 sheet: -0.05 (0.34), residues: 220 loop : -0.41 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 484 TYR 0.016 0.001 TYR D 428 PHE 0.022 0.001 PHE A 210 TRP 0.009 0.001 TRP B 390 HIS 0.002 0.001 HIS D 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (15728) covalent geometry : angle 0.50656 / 0.26 (21300) SS BOND : bond 0.00099 / 0.05 ( 8) SS BOND : angle 0.22646 / 0.13 ( 16) hydrogen bonds : bond 0.05012 / 3.48 ( 1098) hydrogen bonds : angle 4.77714 / 3.37 ( 3465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.441 Fit side-chains REVERT: A 242 ASP cc_start: 0.7133 (m-30) cc_final: 0.6624 (m-30) REVERT: C 242 ASP cc_start: 0.7157 (m-30) cc_final: 0.6654 (m-30) outliers start: 14 outliers final: 14 residues processed: 162 average time/residue: 0.1237 time to fit residues: 30.0341 Evaluate side-chains 169 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 224 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: [74, 145, 183, 164, 59, 112, 8, 108, 105, 92, 127] chunk 74 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 105 optimal weight: 0.0040 chunk 92 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS C 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.164185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.102586 restraints weight = 14352.490| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.90 r_work: 0.2990 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15736 Z= 0.165 Angle : 0.490 7.032 21316 Z= 0.253 Chirality : 0.039 0.139 2412 Planarity : 0.003 0.040 2580 Dihedral : 16.740 141.336 2364 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.78 % Allowed : 12.14 % Favored : 87.08 % 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: 2.07 (0.19), residues: 1816 helix: 2.37 (0.14), residues: 1132 sheet: -0.04 (0.34), residues: 220 loop : -0.40 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 484 TYR 0.016 0.001 TYR B 428 PHE 0.023 0.001 PHE A 210 TRP 0.008 0.001 TRP B 390 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (15728) covalent geometry : angle 0.49049 / 0.25 (21300) SS BOND : bond 0.00083 / 0.05 ( 8) SS BOND : angle 0.17459 / 0.10 ( 16) hydrogen bonds : bond 0.04856 / 3.37 ( 1098) hydrogen bonds : angle 4.71925 / 3.33 ( 3465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.463 Fit side-chains REVERT: A 242 ASP cc_start: 0.7147 (m-30) cc_final: 0.6657 (m-30) REVERT: C 242 ASP cc_start: 0.7114 (m-30) cc_final: 0.6616 (m-30) outliers start: 13 outliers final: 13 residues processed: 160 average time/residue: 0.1202 time to fit residues: 28.7584 Evaluate side-chains 165 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 224 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: [34, 139, 97, 71, 57, 103, 151, 146, 75, 144, 99] chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS C 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.168186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.106392 restraints weight = 14262.948| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.95 r_work: 0.3003 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15736 Z= 0.119 Angle : 0.445 6.894 21316 Z= 0.232 Chirality : 0.037 0.136 2412 Planarity : 0.003 0.039 2580 Dihedral : 16.593 143.425 2364 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.66 % Allowed : 12.86 % Favored : 86.48 % 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: 2.28 (0.20), residues: 1816 helix: 2.53 (0.15), residues: 1132 sheet: 0.05 (0.34), residues: 220 loop : -0.35 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 310 TYR 0.013 0.001 TYR D 428 PHE 0.024 0.001 PHE D 210 TRP 0.005 0.001 TRP B 390 HIS 0.002 0.000 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (15728) covalent geometry : angle 0.44486 / 0.23 (21300) SS BOND : bond 0.00077 / 0.04 ( 8) SS BOND : angle 0.18050 / 0.10 ( 16) hydrogen bonds : bond 0.04393 / 3.03 ( 1098) hydrogen bonds : angle 4.50682 / 3.18 ( 3465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.541 Fit side-chains REVERT: A 242 ASP cc_start: 0.6998 (m-30) cc_final: 0.6558 (m-30) REVERT: C 214 ASP cc_start: 0.7606 (t0) cc_final: 0.7398 (t0) REVERT: C 242 ASP cc_start: 0.6970 (m-30) cc_final: 0.6535 (m-30) REVERT: B 214 ASP cc_start: 0.7594 (t0) cc_final: 0.7379 (t0) REVERT: D 214 ASP cc_start: 0.7592 (t0) cc_final: 0.7388 (t0) outliers start: 11 outliers final: 10 residues processed: 161 average time/residue: 0.1143 time to fit residues: 28.0693 Evaluate side-chains 162 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: [121, 181, 147, 135, 124, 104, 170, 142, 157, 180, 62] chunk 121 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 157 optimal weight: 0.0970 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS C 192 HIS B 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.170874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110752 restraints weight = 14195.608| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.92 r_work: 0.3068 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 0.002 0.031 15736 Z= 0.114 Angle : 0.434 6.803 21316 Z= 0.228 Chirality : 0.037 0.134 2412 Planarity : 0.003 0.038 2580 Dihedral : 16.500 147.258 2364 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.54 % Allowed : 13.16 % Favored : 86.30 % 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 are not related in a simple way. whole: 2.40 (0.20), residues: 1816 helix: 2.63 (0.14), residues: 1132 sheet: 0.10 (0.34), residues: 220 loop : -0.29 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 212 TYR 0.012 0.001 TYR B 428 PHE 0.025 0.001 PHE D 210 TRP 0.005 0.001 TRP A 390 HIS 0.002 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (15728) covalent geometry : angle 0.43407 / 0.23 (21300) SS BOND : bond 0.00055 / 0.03 ( 8) SS BOND : angle 0.19732 / 0.11 ( 16) hydrogen bonds : bond 0.04305 / 2.97 ( 1098) hydrogen bonds : angle 4.39538 / 3.10 ( 3465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3632 Ramachandran restraints generated. 1816 Oldfield, 0 Emsley, 1816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.457 Fit side-chains REVERT: C 212 ARG cc_start: 0.7667 (mmp-170) cc_final: 0.7010 (mtp-110) REVERT: B 212 ARG cc_start: 0.7670 (mmp-170) cc_final: 0.7012 (mtp-110) REVERT: D 212 ARG cc_start: 0.7653 (mmp-170) cc_final: 0.6967 (mtp-110) outliers start: 9 outliers final: 9 residues processed: 168 average time/residue: 0.1213 time to fit residues: 30.6331 Evaluate side-chains 160 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: [22, 178, 175, 61, 6, 45, 106, 77, 52, 24, 63] chunk 22 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 61 optimal weight: 0.0370 chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS A 518 GLN C 192 HIS B 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.166175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104562 restraints weight = 14183.389| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.91 r_work: 0.2967 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15736 Z= 0.169 Angle : 0.493 7.044 21316 Z= 0.256 Chirality : 0.039 0.140 2412 Planarity : 0.003 0.039 2580 Dihedral : 16.486 149.324 2364 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.54 % Allowed : 13.40 % Favored : 86.06 % 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: 2.20 (0.20), residues: 1816 helix: 2.47 (0.15), residues: 1132 sheet: -0.01 (0.34), residues: 220 loop : -0.34 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.016 0.001 TYR B 428 PHE 0.029 0.001 PHE A 210 TRP 0.009 0.001 TRP B 390 HIS 0.002 0.001 HIS D 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (15728) covalent geometry : angle 0.49303 / 0.26 (21300) SS BOND : bond 0.00097 / 0.05 ( 8) SS BOND : angle 0.23668 / 0.13 ( 16) hydrogen bonds : bond 0.04921 / 3.41 ( 1098) hydrogen bonds : angle 4.66546 / 3.29 ( 3465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3991.10 seconds wall clock time: 69 minutes 11.26 seconds (4151.26 seconds total)