Starting phenix.real_space_refine on Thu Jul 2 01:00:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rb3_24393/07_2026/7rb3_24393_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rb3_24393/07_2026/7rb3_24393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rb3_24393/07_2026/7rb3_24393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rb3_24393/07_2026/7rb3_24393.map" model { file = "/net/cci-nas-00/data/ceres_data/7rb3_24393/07_2026/7rb3_24393_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rb3_24393/07_2026/7rb3_24393_neut.cif" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= -0.002 sd= 0.080 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 3 5.49 5 S 31 5.16 5 C 3297 2.51 5 N 906 2.21 5 O 873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5110 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4053 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 557} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 665 Unresolved non-hydrogen angles: 821 Unresolved non-hydrogen dihedrals: 523 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLU:plan': 32, 'GLN:plan1': 12, 'ASP:plan': 21, 'ASN:plan1': 10, 'PHE:plan': 1, 'TYR:plan': 3, 'ARG:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 336 Chain: "A" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 990 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain breaks: 2 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 9, 'ASP:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 121 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'CMC': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="CMC A 401 " pdbres="MET A 402 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'CMC:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.11, per 1000 atoms: 0.22 Number of scatterers: 5110 At special positions: 0 Unit cell: (65.52, 104.16, 104.16, 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 31 16.00 P 3 15.00 O 873 8.00 N 906 7.00 C 3297 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: 0.29 Conformation dependent library (CDL) restraints added in 142.2 milliseconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 65.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'B' and resid 85 through 91 removed outlier: 4.226A pdb=" N LYS B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 121 Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.871A pdb=" N HIS B 136 " --> pdb=" O CYS B 132 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 137' Processing helix chain 'B' and resid 138 through 141 Processing helix chain 'B' and resid 143 through 168 Processing helix chain 'B' and resid 189 through 211 removed outlier: 4.452A pdb=" N ARG B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 250 Processing helix chain 'B' and resid 255 through 260 removed outlier: 3.951A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 260' Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.577A pdb=" N VAL B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 341 removed outlier: 4.311A pdb=" N VAL B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 341 " --> pdb=" O LYS B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 345 removed outlier: 3.565A pdb=" N LEU B 345 " --> pdb=" O VAL B 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 342 through 345' Processing helix chain 'B' and resid 347 through 361 removed outlier: 3.798A pdb=" N GLN B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 376 Processing helix chain 'B' and resid 388 through 400 Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 417 through 441 removed outlier: 4.655A pdb=" N SER B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG B 430 " --> pdb=" O THR B 426 " (cutoff:3.500A) Proline residue: B 431 - end of helix Processing helix chain 'B' and resid 444 through 475 removed outlier: 4.487A pdb=" N ASP B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLU B 455 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 510 removed outlier: 3.746A pdb=" N GLY B 507 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 517 through 528 removed outlier: 3.575A pdb=" N PHE B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 548 Processing helix chain 'B' and resid 572 through 600 Processing helix chain 'B' and resid 611 through 620 Processing helix chain 'B' and resid 621 through 626 removed outlier: 3.569A pdb=" N VAL B 626 " --> pdb=" O PHE B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 642 Processing helix chain 'B' and resid 651 through 671 Processing helix chain 'B' and resid 677 through 698 Proline residue: B 689 - end of helix removed outlier: 3.566A pdb=" N VAL B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.873A pdb=" N LYS A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.792A pdb=" N TYR A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 294 removed outlier: 3.661A pdb=" N ARG A 294 " --> pdb=" O SER A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 297 through 313 removed outlier: 4.181A pdb=" N ALA A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 336 Processing sheet with id=AA1, first strand: chain 'B' and resid 381 through 382 Processing sheet with id=AA2, first strand: chain 'B' and resid 710 through 712 Processing sheet with id=AA3, first strand: chain 'A' and resid 214 through 216 removed outlier: 6.830A pdb=" N PHE A 256 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA A 267 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA A 258 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 263 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N VAL A 265 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL A 289 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 267 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 287 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 269 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU A 321 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N MET A 286 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 12.699A pdb=" N GLU A 323 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 13.785A pdb=" N ALA A 288 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 354 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARG A 343 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG A 356 " --> pdb=" O ASP A 341 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1017 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: 0.70 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1253 1.33 - 1.46: 1135 1.46 - 1.58: 2786 1.58 - 1.70: 1 1.70 - 1.82: 51 Bond restraints: 5226 Sorted by residual: bond pdb=" O3B CMC A 401 " pdb=" P3B CMC A 401 " ideal model delta sigma weight residual 1.728 1.612 0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" O3A CMC A 401 " pdb=" P2A CMC A 401 " ideal model delta sigma weight residual 1.658 1.559 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" O6A CMC A 401 " pdb=" P2A CMC A 401 " ideal model delta sigma weight residual 1.637 1.547 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" O3A CMC A 401 " pdb=" P1A CMC A 401 " ideal model delta sigma weight residual 1.630 1.541 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" O5B CMC A 401 " pdb=" P1A CMC A 401 " ideal model delta sigma weight residual 1.652 1.566 0.086 2.00e-02 2.50e+03 1.84e+01 ... (remaining 5221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.83: 7130 6.83 - 13.66: 14 13.66 - 20.50: 0 20.50 - 27.33: 1 27.33 - 34.16: 1 Bond angle restraints: 7146 Sorted by residual: angle pdb=" C1 CMC A 401 " pdb=" C2 CMC A 401 " pdb=" O21 CMC A 401 " ideal model delta sigma weight residual 113.40 79.24 34.16 3.00e+00 1.11e-01 1.30e+02 angle pdb=" P1A CMC A 401 " pdb=" O3A CMC A 401 " pdb=" P2A CMC A 401 " ideal model delta sigma weight residual 128.09 107.44 20.65 3.00e+00 1.11e-01 4.74e+01 angle pdb=" C PHE B 607 " pdb=" N GLU B 608 " pdb=" CA GLU B 608 " ideal model delta sigma weight residual 120.28 126.87 -6.59 1.44e+00 4.82e-01 2.09e+01 angle pdb=" N CYS B 420 " pdb=" CA CYS B 420 " pdb=" C CYS B 420 " ideal model delta sigma weight residual 114.04 108.47 5.57 1.24e+00 6.50e-01 2.02e+01 angle pdb=" N MET B 204 " pdb=" CA MET B 204 " pdb=" C MET B 204 " ideal model delta sigma weight residual 114.04 108.56 5.48 1.24e+00 6.50e-01 1.95e+01 ... (remaining 7141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.87: 2874 26.87 - 53.74: 183 53.74 - 80.61: 14 80.61 - 107.47: 5 107.47 - 134.34: 1 Dihedral angle restraints: 3077 sinusoidal: 923 harmonic: 2154 Sorted by residual: dihedral pdb=" C MET A 402 " pdb=" N MET A 402 " pdb=" CA MET A 402 " pdb=" CB MET A 402 " ideal model delta harmonic sigma weight residual -122.60 -111.25 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" CA SER A 220 " pdb=" C SER A 220 " pdb=" N GLU A 221 " pdb=" CA GLU A 221 " ideal model delta harmonic sigma weight residual 180.00 157.96 22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CAP CMC A 401 " pdb=" CBP CMC A 401 " pdb=" CCP CMC A 401 " pdb=" O6A CMC A 401 " ideal model delta sinusoidal sigma weight residual 70.77 -63.57 134.34 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 3074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 757 0.068 - 0.135: 76 0.135 - 0.203: 4 0.203 - 0.270: 3 0.270 - 0.338: 1 Chirality restraints: 841 Sorted by residual: chirality pdb=" CA MET A 402 " pdb=" N MET A 402 " pdb=" C MET A 402 " pdb=" CB MET A 402 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C4B CMC A 401 " pdb=" C3B CMC A 401 " pdb=" C5B CMC A 401 " pdb=" O4B CMC A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA GLU B 608 " pdb=" N GLU B 608 " pdb=" C GLU B 608 " pdb=" CB GLU B 608 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 838 not shown) Planarity restraints: 908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P CMC A 401 " -0.268 2.00e-02 2.50e+03 2.31e-01 6.69e+02 pdb=" C9P CMC A 401 " 0.012 2.00e-02 2.50e+03 pdb=" CAP CMC A 401 " -0.145 2.00e-02 2.50e+03 pdb=" N8P CMC A 401 " 0.417 2.00e-02 2.50e+03 pdb=" O9P CMC A 401 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P CMC A 401 " 0.073 2.00e-02 2.50e+03 6.20e-02 4.81e+01 pdb=" C5P CMC A 401 " 0.010 2.00e-02 2.50e+03 pdb=" C6P CMC A 401 " -0.029 2.00e-02 2.50e+03 pdb=" N4P CMC A 401 " -0.103 2.00e-02 2.50e+03 pdb=" O5P CMC A 401 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B CMC A 401 " 0.058 2.00e-02 2.50e+03 2.40e-02 1.58e+01 pdb=" C2A CMC A 401 " -0.007 2.00e-02 2.50e+03 pdb=" C4A CMC A 401 " -0.012 2.00e-02 2.50e+03 pdb=" C5A CMC A 401 " -0.007 2.00e-02 2.50e+03 pdb=" C6A CMC A 401 " -0.007 2.00e-02 2.50e+03 pdb=" C8A CMC A 401 " -0.010 2.00e-02 2.50e+03 pdb=" N1A CMC A 401 " 0.008 2.00e-02 2.50e+03 pdb=" N3A CMC A 401 " -0.016 2.00e-02 2.50e+03 pdb=" N6A CMC A 401 " 0.034 2.00e-02 2.50e+03 pdb=" N7A CMC A 401 " -0.011 2.00e-02 2.50e+03 pdb=" N9A CMC A 401 " -0.031 2.00e-02 2.50e+03 ... (remaining 905 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 27 2.60 - 3.17: 4276 3.17 - 3.75: 8008 3.75 - 4.32: 9974 4.32 - 4.90: 17024 Nonbonded interactions: 39309 Sorted by model distance: nonbonded pdb=" O2B CMC A 401 " pdb=" O9A CMC A 401 " model vdw 2.021 3.040 nonbonded pdb=" O TYR B 412 " pdb=" NZ LYS B 418 " model vdw 2.280 3.120 nonbonded pdb=" O LYS B 96 " pdb=" OH TYR B 134 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR A 348 " pdb=" O MET A 402 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR B 582 " pdb=" OE2 GLU B 679 " model vdw 2.391 3.040 ... (remaining 39304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.570 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.460 Find NCS groups from input model: 0.010 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.012 0.758 5228 Z= 1.103 Angle : 0.925 34.159 7146 Z= 0.429 Chirality : 0.045 0.338 841 Planarity : 0.009 0.231 908 Dihedral : 17.166 134.343 1669 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.30 % Allowed : 25.39 % Favored : 73.32 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 8.00 % 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: 1.44 (0.32), residues: 706 helix: 2.01 (0.25), residues: 449 sheet: -0.92 (0.71), residues: 57 loop : -0.90 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 294 TYR 0.024 0.002 TYR B 520 PHE 0.014 0.001 PHE B 607 TRP 0.007 0.001 TRP B 491 HIS 0.005 0.001 HIS B 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.27 ( 5226) covalent geometry : angle 0.92489 / 0.43 ( 7146) hydrogen bonds : bond 0.14679 / 10.31 ( 350) hydrogen bonds : angle 5.07717 / 3.82 ( 1017) Misc. bond : bond 0.54734 / 28.70 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.131 Fit side-chains REVERT: A 301 ASN cc_start: 0.8692 (m-40) cc_final: 0.8486 (m110) outliers start: 5 outliers final: 2 residues processed: 120 average time/residue: 0.0393 time to fit residues: 6.6652 Evaluate side-chains 116 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 403 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.109906 restraints weight = 9635.936| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.92 r_work: 0.3315 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5228 Z= 0.123 Angle : 0.521 7.377 7146 Z= 0.258 Chirality : 0.038 0.139 841 Planarity : 0.003 0.044 908 Dihedral : 10.296 169.084 837 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.40 % Allowed : 20.21 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.88 (0.32), residues: 706 helix: 2.43 (0.25), residues: 447 sheet: -0.98 (0.71), residues: 51 loop : -0.83 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 294 TYR 0.024 0.001 TYR B 520 PHE 0.009 0.001 PHE B 620 TRP 0.008 0.001 TRP B 491 HIS 0.004 0.001 HIS B 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 5226) covalent geometry : angle 0.52096 / 0.26 ( 7146) hydrogen bonds : bond 0.03764 / 2.67 ( 350) hydrogen bonds : angle 3.61641 / 2.72 ( 1017) Misc. bond : bond 0.00065 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 231 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7990 (tt) REVERT: A 250 ASN cc_start: 0.8408 (m110) cc_final: 0.7748 (m110) outliers start: 17 outliers final: 13 residues processed: 130 average time/residue: 0.0432 time to fit residues: 8.0244 Evaluate side-chains 133 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 403 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 472 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109408 restraints weight = 9491.106| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.90 r_work: 0.3304 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5228 Z= 0.144 Angle : 0.508 6.876 7146 Z= 0.254 Chirality : 0.039 0.142 841 Planarity : 0.003 0.043 908 Dihedral : 10.046 168.911 837 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.40 % Allowed : 21.24 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.94 (0.32), residues: 706 helix: 2.47 (0.25), residues: 448 sheet: -0.92 (0.66), residues: 57 loop : -0.82 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 294 TYR 0.024 0.001 TYR B 520 PHE 0.012 0.001 PHE B 620 TRP 0.007 0.001 TRP B 491 HIS 0.004 0.001 HIS B 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 5226) covalent geometry : angle 0.50791 / 0.25 ( 7146) hydrogen bonds : bond 0.03621 / 2.58 ( 350) hydrogen bonds : angle 3.38965 / 2.53 ( 1017) Misc. bond : bond 0.00039 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.124 Fit side-chains REVERT: B 394 ASP cc_start: 0.8206 (t0) cc_final: 0.7719 (t0) REVERT: A 231 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8066 (tt) REVERT: A 250 ASN cc_start: 0.8408 (m110) cc_final: 0.7804 (m110) outliers start: 17 outliers final: 12 residues processed: 128 average time/residue: 0.0397 time to fit residues: 7.2336 Evaluate side-chains 130 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 231 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111444 restraints weight = 9463.431| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.87 r_work: 0.3333 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5228 Z= 0.104 Angle : 0.482 6.770 7146 Z= 0.238 Chirality : 0.038 0.127 841 Planarity : 0.003 0.040 908 Dihedral : 9.844 172.440 835 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.15 % Allowed : 23.32 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.14 (0.32), residues: 706 helix: 2.66 (0.25), residues: 445 sheet: -0.96 (0.66), residues: 51 loop : -0.75 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 294 TYR 0.022 0.001 TYR B 520 PHE 0.009 0.001 PHE B 620 TRP 0.008 0.001 TRP B 491 HIS 0.003 0.000 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 5226) covalent geometry : angle 0.48207 / 0.24 ( 7146) hydrogen bonds : bond 0.03092 / 2.18 ( 350) hydrogen bonds : angle 3.17794 / 2.36 ( 1017) Misc. bond : bond 0.00014 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.194 Fit side-chains REVERT: B 352 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 231 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8045 (tt) REVERT: A 250 ASN cc_start: 0.8428 (m110) cc_final: 0.7795 (m110) outliers start: 16 outliers final: 10 residues processed: 128 average time/residue: 0.0392 time to fit residues: 7.3004 Evaluate side-chains 131 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 59 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.108713 restraints weight = 9675.204| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.87 r_work: 0.3290 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5228 Z= 0.178 Angle : 0.538 8.784 7146 Z= 0.264 Chirality : 0.040 0.157 841 Planarity : 0.003 0.040 908 Dihedral : 9.714 168.789 835 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.96 % Allowed : 22.28 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.99 (0.32), residues: 706 helix: 2.54 (0.25), residues: 445 sheet: -1.01 (0.63), residues: 57 loop : -0.78 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 397 TYR 0.026 0.002 TYR B 520 PHE 0.014 0.001 PHE B 620 TRP 0.008 0.001 TRP B 523 HIS 0.003 0.001 HIS B 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 5226) covalent geometry : angle 0.53813 / 0.26 ( 7146) hydrogen bonds : bond 0.03681 / 2.63 ( 350) hydrogen bonds : angle 3.29139 / 2.44 ( 1017) Misc. bond : bond 0.00030 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.122 Fit side-chains REVERT: B 394 ASP cc_start: 0.8184 (t0) cc_final: 0.7723 (t0) REVERT: A 231 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8154 (tt) REVERT: A 250 ASN cc_start: 0.8454 (m110) cc_final: 0.7839 (m110) outliers start: 23 outliers final: 17 residues processed: 132 average time/residue: 0.0369 time to fit residues: 6.9945 Evaluate side-chains 134 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 361 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.0040 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 633 HIS B 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111240 restraints weight = 9693.683| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.88 r_work: 0.3332 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5228 Z= 0.097 Angle : 0.501 9.220 7146 Z= 0.240 Chirality : 0.038 0.126 841 Planarity : 0.003 0.039 908 Dihedral : 9.577 172.301 835 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.11 % Allowed : 25.91 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 (0.32), residues: 706 helix: 2.72 (0.25), residues: 445 sheet: -1.07 (0.64), residues: 51 loop : -0.76 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 619 TYR 0.022 0.001 TYR B 520 PHE 0.007 0.001 PHE B 620 TRP 0.008 0.001 TRP B 491 HIS 0.003 0.000 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 5226) covalent geometry : angle 0.50105 / 0.24 ( 7146) hydrogen bonds : bond 0.03006 / 2.12 ( 350) hydrogen bonds : angle 3.09345 / 2.29 ( 1017) Misc. bond : bond 0.00008 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.123 Fit side-chains REVERT: B 352 LEU cc_start: 0.8600 (mt) cc_final: 0.8354 (mt) REVERT: A 231 ILE cc_start: 0.8371 (mm) cc_final: 0.8092 (tt) REVERT: A 250 ASN cc_start: 0.8449 (m110) cc_final: 0.7818 (m110) REVERT: A 301 ASN cc_start: 0.8679 (m-40) cc_final: 0.8424 (m110) outliers start: 12 outliers final: 11 residues processed: 128 average time/residue: 0.0381 time to fit residues: 7.1762 Evaluate side-chains 130 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 29 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111945 restraints weight = 9656.095| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.87 r_work: 0.3341 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.002 0.028 5228 Z= 0.101 Angle : 0.502 9.479 7146 Z= 0.242 Chirality : 0.038 0.126 841 Planarity : 0.003 0.038 908 Dihedral : 9.354 172.845 835 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.63 % Allowed : 24.87 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.27 (0.32), residues: 706 helix: 2.79 (0.25), residues: 447 sheet: -0.97 (0.64), residues: 51 loop : -0.77 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 619 TYR 0.021 0.001 TYR B 520 PHE 0.009 0.001 PHE B 620 TRP 0.009 0.001 TRP B 491 HIS 0.002 0.000 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 5226) covalent geometry : angle 0.50156 / 0.24 ( 7146) hydrogen bonds : bond 0.02890 / 2.04 ( 350) hydrogen bonds : angle 2.98903 / 2.21 ( 1017) Misc. bond : bond 0.00011 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.138 Fit side-chains REVERT: B 352 LEU cc_start: 0.8604 (mt) cc_final: 0.8349 (mt) REVERT: A 231 ILE cc_start: 0.8383 (mm) cc_final: 0.8095 (tt) REVERT: A 250 ASN cc_start: 0.8469 (m110) cc_final: 0.7858 (m110) REVERT: A 301 ASN cc_start: 0.8698 (m-40) cc_final: 0.8441 (m110) outliers start: 14 outliers final: 13 residues processed: 133 average time/residue: 0.0380 time to fit residues: 7.2750 Evaluate side-chains 132 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 53 optimal weight: 0.0000 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 446 GLN ** 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 = 0.3632 r_free = 0.3632 target = 0.126401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112749 restraints weight = 9621.850| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.87 r_work: 0.3350 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5228 Z= 0.093 Angle : 0.495 9.409 7146 Z= 0.236 Chirality : 0.038 0.123 841 Planarity : 0.003 0.037 908 Dihedral : 9.221 173.239 835 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.15 % Allowed : 25.39 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.21 (0.32), residues: 706 helix: 2.71 (0.25), residues: 454 sheet: -0.92 (0.64), residues: 51 loop : -0.90 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.021 0.001 TYR B 520 PHE 0.008 0.001 PHE B 620 TRP 0.008 0.001 TRP B 491 HIS 0.002 0.000 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 ( 5226) covalent geometry : angle 0.49521 / 0.24 ( 7146) hydrogen bonds : bond 0.02772 / 1.95 ( 350) hydrogen bonds : angle 2.95149 / 2.17 ( 1017) Misc. bond : bond 0.00006 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.115 Fit side-chains REVERT: B 352 LEU cc_start: 0.8608 (mt) cc_final: 0.8370 (mt) REVERT: B 580 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8665 (mt0) REVERT: A 231 ILE cc_start: 0.8378 (mm) cc_final: 0.8090 (tt) REVERT: A 250 ASN cc_start: 0.8493 (m110) cc_final: 0.7844 (m110) REVERT: A 301 ASN cc_start: 0.8672 (m-40) cc_final: 0.8404 (m110) outliers start: 16 outliers final: 13 residues processed: 132 average time/residue: 0.0454 time to fit residues: 8.4462 Evaluate side-chains 133 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 325 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109252 restraints weight = 9523.699| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.85 r_work: 0.3296 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5228 Z= 0.171 Angle : 0.548 9.317 7146 Z= 0.268 Chirality : 0.040 0.161 841 Planarity : 0.003 0.036 908 Dihedral : 9.207 165.661 835 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.66 % Allowed : 24.61 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.14 (0.32), residues: 706 helix: 2.66 (0.24), residues: 447 sheet: -1.07 (0.63), residues: 57 loop : -0.71 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.026 0.002 TYR B 520 PHE 0.012 0.001 PHE B 620 TRP 0.009 0.001 TRP B 523 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 5226) covalent geometry : angle 0.54848 / 0.27 ( 7146) hydrogen bonds : bond 0.03555 / 2.54 ( 350) hydrogen bonds : angle 3.17290 / 2.33 ( 1017) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.122 Fit side-chains REVERT: B 394 ASP cc_start: 0.8183 (t0) cc_final: 0.7721 (t0) REVERT: A 231 ILE cc_start: 0.8445 (mm) cc_final: 0.8180 (tt) outliers start: 18 outliers final: 14 residues processed: 128 average time/residue: 0.0499 time to fit residues: 8.9667 Evaluate side-chains 128 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108793 restraints weight = 9601.694| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.86 r_work: 0.3287 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5228 Z= 0.184 Angle : 0.566 9.504 7146 Z= 0.274 Chirality : 0.040 0.157 841 Planarity : 0.003 0.036 908 Dihedral : 9.250 162.844 835 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.89 % Allowed : 25.13 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.98 (0.32), residues: 706 helix: 2.53 (0.24), residues: 447 sheet: -1.15 (0.62), residues: 57 loop : -0.77 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.026 0.002 TYR B 520 PHE 0.014 0.001 PHE B 620 TRP 0.006 0.001 TRP B 523 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 5226) covalent geometry : angle 0.56588 / 0.27 ( 7146) hydrogen bonds : bond 0.03665 / 2.63 ( 350) hydrogen bonds : angle 3.27165 / 2.41 ( 1017) Misc. bond : bond 0.00043 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.207 Fit side-chains REVERT: B 352 LEU cc_start: 0.8591 (mt) cc_final: 0.8304 (mt) REVERT: B 394 ASP cc_start: 0.8179 (t0) cc_final: 0.7709 (t0) REVERT: A 231 ILE cc_start: 0.8424 (mm) cc_final: 0.8170 (tt) outliers start: 15 outliers final: 15 residues processed: 121 average time/residue: 0.0450 time to fit residues: 7.6980 Evaluate side-chains 126 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110555 restraints weight = 9697.106| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.88 r_work: 0.3315 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5228 Z= 0.123 Angle : 0.526 9.630 7146 Z= 0.252 Chirality : 0.039 0.130 841 Planarity : 0.003 0.036 908 Dihedral : 9.148 165.804 835 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.63 % Allowed : 25.39 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 (0.32), residues: 706 helix: 2.55 (0.25), residues: 454 sheet: -1.23 (0.64), residues: 51 loop : -0.97 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.022 0.001 TYR B 520 PHE 0.011 0.001 PHE B 620 TRP 0.006 0.001 TRP B 491 HIS 0.003 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 5226) covalent geometry : angle 0.52627 / 0.25 ( 7146) hydrogen bonds : bond 0.03168 / 2.25 ( 350) hydrogen bonds : angle 3.12881 / 2.31 ( 1017) Misc. bond : bond 0.00015 / 0.01 ( 2) =============================================================================== Job complete usr+sys time: 1188.65 seconds wall clock time: 20 minutes 57.63 seconds (1257.63 seconds total)