Starting phenix.real_space_refine on Thu Jul 2 02:37:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mx2_24070/07_2026/7mx2_24070.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mx2_24070/07_2026/7mx2_24070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mx2_24070/07_2026/7mx2_24070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mx2_24070/07_2026/7mx2_24070.map" model { file = "/net/cci-nas-00/data/ceres_data/7mx2_24070/07_2026/7mx2_24070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mx2_24070/07_2026/7mx2_24070.cif" } resolution = 3.64 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= 0.004 sd= 0.093 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 40 5.16 5 C 3978 2.51 5 N 1078 2.21 5 O 1060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 6159 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 4515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 4515 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 209} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 617} Chain breaks: 5 Unresolved non-hydrogen bonds: 730 Unresolved non-hydrogen angles: 895 Unresolved non-hydrogen dihedrals: 586 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'ASP:plan': 23, 'GLN:plan1': 13, 'GLU:plan': 38, 'ARG:plan': 11, 'HIS:plan': 4, 'ASN:plan1': 10, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 411 Chain: "C" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 451 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1115 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 148} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 8, 'ASP:plan': 7, 'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 91 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Classifications: {'peptide': 4} Link IDs: {'PTRANS': 1, 'TRANS': 2} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CMC': 1} Classifications: {'undetermined': 1} 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: 1.63, per 1000 atoms: 0.26 Number of scatterers: 6159 At special positions: 0 Unit cell: (80.64, 99.12, 106.68, 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 40 16.00 P 3 15.00 O 1060 8.00 N 1078 7.00 C 3978 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 383.1 milliseconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 59.7% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'B' and resid 32 through 41 removed outlier: 3.631A pdb=" N GLU B 38 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.991A pdb=" N LYS B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 121 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 143 through 168 Processing helix chain 'B' and resid 189 through 211 removed outlier: 3.587A pdb=" N ARG B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 252 Processing helix chain 'B' and resid 255 through 260 removed outlier: 3.977A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.641A 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 260 through 278 removed outlier: 4.511A pdb=" N LEU B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 269 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 340 Processing helix chain 'B' and resid 341 through 344 Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 364 through 376 Processing helix chain 'B' and resid 388 through 400 Processing helix chain 'B' and resid 414 through 440 removed outlier: 4.342A 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 442 through 476 removed outlier: 4.321A pdb=" N ARG B 447 " --> pdb=" O ARG B 443 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASP B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU B 455 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 510 removed outlier: 3.671A pdb=" N GLY B 507 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 528 removed outlier: 3.729A pdb=" N TRP B 523 " --> pdb=" O TYR B 519 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 547 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 625 removed outlier: 3.502A pdb=" N SER B 625 " --> pdb=" O PRO B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 642 removed outlier: 3.652A pdb=" N GLU B 639 " --> pdb=" O LEU B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 646 removed outlier: 3.583A pdb=" N TYR B 646 " --> pdb=" O LEU B 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 643 through 646' Processing helix chain 'B' and resid 651 through 672 Processing helix chain 'B' and resid 677 through 699 removed outlier: 3.511A pdb=" N ILE B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Proline residue: B 689 - end of helix removed outlier: 3.621A pdb=" N GLY B 699 " --> pdb=" O LYS B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 48 Processing helix chain 'C' and resid 105 through 109 removed outlier: 3.782A pdb=" N ILE C 109 " --> pdb=" O GLY C 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 223 through 235 Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.610A pdb=" N TYR A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 291 through 294 removed outlier: 3.518A 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 Processing helix chain 'A' and resid 326 through 337 removed outlier: 3.561A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) 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 'C' and resid 69 through 70 removed outlier: 3.799A pdb=" N CYS C 69 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 214 through 217 removed outlier: 6.762A pdb=" N ALA A 267 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU A 287 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A 269 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 281 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS A 275 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 317 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU A 321 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N MET A 286 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 12.710A pdb=" N GLU A 323 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 13.736A pdb=" N ALA A 288 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA A 354 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ARG A 343 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG A 356 " --> pdb=" O ASP A 341 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1107 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: 0.67 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 959 1.30 - 1.43: 1680 1.43 - 1.56: 3587 1.56 - 1.69: 5 1.69 - 1.82: 64 Bond restraints: 6295 Sorted by residual: bond pdb=" O3B CMC D 501 " pdb=" P3B CMC D 501 " ideal model delta sigma weight residual 1.728 1.613 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" O3A CMC D 501 " pdb=" P2A CMC D 501 " ideal model delta sigma weight residual 1.658 1.559 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O6A CMC D 501 " pdb=" P2A CMC D 501 " ideal model delta sigma weight residual 1.637 1.548 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" O3A CMC D 501 " pdb=" P1A CMC D 501 " 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 D 501 " pdb=" P1A CMC D 501 " ideal model delta sigma weight residual 1.652 1.566 0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 6290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.84: 8598 6.84 - 13.68: 15 13.68 - 20.51: 0 20.51 - 27.35: 1 27.35 - 34.19: 1 Bond angle restraints: 8615 Sorted by residual: angle pdb=" C1 CMC D 501 " pdb=" C2 CMC D 501 " pdb=" O21 CMC D 501 " ideal model delta sigma weight residual 113.40 79.21 34.19 3.00e+00 1.11e-01 1.30e+02 angle pdb=" P1A CMC D 501 " pdb=" O3A CMC D 501 " pdb=" P2A CMC D 501 " ideal model delta sigma weight residual 128.09 107.43 20.66 3.00e+00 1.11e-01 4.74e+01 angle pdb=" CA PRO B 653 " pdb=" N PRO B 653 " pdb=" CD PRO B 653 " ideal model delta sigma weight residual 112.00 103.26 8.74 1.40e+00 5.10e-01 3.90e+01 angle pdb=" CG ARG A 294 " pdb=" CD ARG A 294 " pdb=" NE ARG A 294 " ideal model delta sigma weight residual 112.00 123.33 -11.33 2.20e+00 2.07e-01 2.65e+01 angle pdb=" O1A CMC D 501 " pdb=" P1A CMC D 501 " pdb=" O3A CMC D 501 " ideal model delta sigma weight residual 111.52 98.57 12.95 3.00e+00 1.11e-01 1.86e+01 ... (remaining 8610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.86: 3503 26.86 - 53.73: 214 53.73 - 80.59: 12 80.59 - 107.45: 2 107.45 - 134.31: 1 Dihedral angle restraints: 3732 sinusoidal: 1157 harmonic: 2575 Sorted by residual: dihedral pdb=" CG ARG A 294 " pdb=" CD ARG A 294 " pdb=" NE ARG A 294 " pdb=" CZ ARG A 294 " ideal model delta sinusoidal sigma weight residual 90.00 6.24 83.76 2 1.50e+01 4.44e-03 2.11e+01 dihedral pdb=" CAP CMC D 501 " pdb=" CBP CMC D 501 " pdb=" CCP CMC D 501 " pdb=" O6A CMC D 501 " ideal model delta sinusoidal sigma weight residual 70.77 -63.54 134.31 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" CA GLY B 55 " pdb=" C GLY B 55 " pdb=" N LEU B 56 " pdb=" CA LEU B 56 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 887 0.056 - 0.112: 131 0.112 - 0.168: 11 0.168 - 0.223: 2 0.223 - 0.279: 2 Chirality restraints: 1033 Sorted by residual: chirality pdb=" CA MET D 402 " pdb=" N MET D 402 " pdb=" C MET D 402 " pdb=" CB MET D 402 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C4B CMC D 501 " pdb=" C3B CMC D 501 " pdb=" C5B CMC D 501 " pdb=" O4B CMC D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CAP CMC D 501 " pdb=" C9P CMC D 501 " pdb=" CBP CMC D 501 " pdb=" OAP CMC D 501 " both_signs ideal model delta sigma weight residual False -2.38 -2.57 0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 1030 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P CMC D 501 " 0.268 2.00e-02 2.50e+03 2.31e-01 6.68e+02 pdb=" C9P CMC D 501 " -0.012 2.00e-02 2.50e+03 pdb=" CAP CMC D 501 " 0.145 2.00e-02 2.50e+03 pdb=" N8P CMC D 501 " -0.417 2.00e-02 2.50e+03 pdb=" O9P CMC D 501 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P CMC D 501 " -0.073 2.00e-02 2.50e+03 6.23e-02 4.85e+01 pdb=" C5P CMC D 501 " -0.010 2.00e-02 2.50e+03 pdb=" C6P CMC D 501 " 0.029 2.00e-02 2.50e+03 pdb=" N4P CMC D 501 " 0.103 2.00e-02 2.50e+03 pdb=" O5P CMC D 501 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 652 " -0.080 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO B 653 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO B 653 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 653 " -0.062 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 32 2.60 - 3.17: 5142 3.17 - 3.75: 9514 3.75 - 4.32: 11600 4.32 - 4.90: 20020 Nonbonded interactions: 46308 Sorted by model distance: nonbonded pdb=" O2B CMC D 501 " pdb=" O9A CMC D 501 " model vdw 2.021 3.040 nonbonded pdb=" OH TYR A 283 " pdb=" OE1 GLU A 321 " model vdw 2.248 3.040 nonbonded pdb=" O LYS B 96 " pdb=" OH TYR B 134 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR A 239 " pdb=" N LEU D 403 " model vdw 2.297 3.120 nonbonded pdb=" O SER B 124 " pdb=" OG1 THR B 128 " model vdw 2.313 3.040 ... (remaining 46303 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 group one per residue 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: 0.690 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.140 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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 : 0.005 0.127 6296 Z= 0.279 Angle : 0.844 34.190 8615 Z= 0.380 Chirality : 0.042 0.279 1033 Planarity : 0.009 0.231 1094 Dihedral : 16.141 134.314 2052 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.40 % Allowed : 22.95 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.47 (0.30), residues: 855 helix: 2.69 (0.24), residues: 471 sheet: -1.67 (0.67), residues: 53 loop : -1.21 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A 294 TYR 0.010 0.001 TYR B 616 PHE 0.015 0.001 PHE B 432 TRP 0.007 0.001 TRP B 119 HIS 0.003 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 ( 6295) covalent geometry : angle 0.84395 / 0.38 ( 8615) hydrogen bonds : bond 0.15738 / 10.76 ( 382) hydrogen bonds : angle 5.07190 / 3.76 ( 1107) Misc. bond : bond 0.12743 / 6.71 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.253 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 103 average time/residue: 0.0547 time to fit residues: 8.4180 Evaluate side-chains 97 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.111374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091769 restraints weight = 11260.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.094826 restraints weight = 5997.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096955 restraints weight = 3960.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098350 restraints weight = 2985.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098702 restraints weight = 2463.819| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6296 Z= 0.116 Angle : 0.520 8.241 8615 Z= 0.266 Chirality : 0.039 0.190 1033 Planarity : 0.004 0.066 1094 Dihedral : 8.817 143.608 989 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.79 % Rotamer: Outliers : 3.79 % Allowed : 20.36 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.60 (0.30), residues: 855 helix: 2.76 (0.24), residues: 479 sheet: -1.44 (0.62), residues: 62 loop : -1.19 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 294 TYR 0.013 0.001 TYR A 348 PHE 0.013 0.001 PHE B 432 TRP 0.007 0.001 TRP B 523 HIS 0.003 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 6295) covalent geometry : angle 0.51954 / 0.27 ( 8615) hydrogen bonds : bond 0.03986 / 2.78 ( 382) hydrogen bonds : angle 3.89078 / 2.83 ( 1107) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.245 Fit side-chains REVERT: B 329 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8898 (m-80) REVERT: B 653 PRO cc_start: 0.8355 (Cg_exo) cc_final: 0.8146 (Cg_endo) outliers start: 19 outliers final: 14 residues processed: 119 average time/residue: 0.0494 time to fit residues: 9.0596 Evaluate side-chains 107 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 281 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 65 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.108577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.088930 restraints weight = 11493.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.091943 restraints weight = 6134.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094005 restraints weight = 4058.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095391 restraints weight = 3071.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.096277 restraints weight = 2539.714| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6296 Z= 0.161 Angle : 0.531 6.590 8615 Z= 0.272 Chirality : 0.040 0.207 1033 Planarity : 0.004 0.062 1094 Dihedral : 8.671 138.435 989 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.91 % Rotamer: Outliers : 4.79 % Allowed : 20.16 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.50 (0.30), residues: 855 helix: 2.70 (0.24), residues: 478 sheet: -1.54 (0.60), residues: 62 loop : -1.24 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 294 TYR 0.016 0.001 TYR A 348 PHE 0.016 0.001 PHE B 432 TRP 0.006 0.001 TRP B 523 HIS 0.003 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 6295) covalent geometry : angle 0.53063 / 0.27 ( 8615) hydrogen bonds : bond 0.03844 / 2.69 ( 382) hydrogen bonds : angle 3.80385 / 2.73 ( 1107) Misc. bond : bond 0.00370 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.238 Fit side-chains REVERT: B 60 MET cc_start: 0.8274 (tpp) cc_final: 0.7890 (mtm) REVERT: B 329 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.9013 (m-80) REVERT: B 519 TYR cc_start: 0.9019 (p90) cc_final: 0.8656 (p90) REVERT: B 597 ASP cc_start: 0.8910 (t0) cc_final: 0.8509 (t0) outliers start: 24 outliers final: 13 residues processed: 111 average time/residue: 0.0512 time to fit residues: 8.6562 Evaluate side-chains 104 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 281 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 chunk 17 optimal weight: 0.0980 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 49 optimal weight: 0.0470 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.112500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.093028 restraints weight = 11301.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.096063 restraints weight = 5959.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.098214 restraints weight = 3930.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099581 restraints weight = 2950.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100549 restraints weight = 2437.409| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6296 Z= 0.094 Angle : 0.480 7.118 8615 Z= 0.243 Chirality : 0.038 0.208 1033 Planarity : 0.003 0.056 1094 Dihedral : 8.329 132.786 989 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.63 % Favored : 96.26 % Rotamer: Outliers : 3.59 % Allowed : 22.36 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.71 (0.30), residues: 855 helix: 2.87 (0.24), residues: 480 sheet: -1.33 (0.61), residues: 62 loop : -1.22 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 294 TYR 0.013 0.001 TYR B 520 PHE 0.024 0.001 PHE B 54 TRP 0.007 0.001 TRP B 119 HIS 0.003 0.000 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 ( 6295) covalent geometry : angle 0.48005 / 0.24 ( 8615) hydrogen bonds : bond 0.03057 / 2.12 ( 382) hydrogen bonds : angle 3.52252 / 2.51 ( 1107) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.249 Fit side-chains REVERT: B 60 MET cc_start: 0.8138 (tpp) cc_final: 0.7760 (mtm) REVERT: B 329 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8856 (m-80) REVERT: B 519 TYR cc_start: 0.8957 (p90) cc_final: 0.8662 (p90) REVERT: B 597 ASP cc_start: 0.8779 (t0) cc_final: 0.8396 (t0) REVERT: B 627 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.6457 (tmm) outliers start: 18 outliers final: 13 residues processed: 122 average time/residue: 0.0541 time to fit residues: 9.9335 Evaluate side-chains 112 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 42 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.108630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.088804 restraints weight = 11605.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.091747 restraints weight = 6263.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.093805 restraints weight = 4188.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.095110 restraints weight = 3174.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.096157 restraints weight = 2650.193| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6296 Z= 0.166 Angle : 0.529 7.336 8615 Z= 0.269 Chirality : 0.040 0.205 1033 Planarity : 0.003 0.055 1094 Dihedral : 8.221 130.631 989 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.44 % Favored : 95.44 % Rotamer: Outliers : 4.59 % Allowed : 22.36 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.63 (0.30), residues: 855 helix: 2.79 (0.24), residues: 478 sheet: -1.45 (0.59), residues: 62 loop : -1.17 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 294 TYR 0.015 0.001 TYR B 520 PHE 0.020 0.001 PHE B 54 TRP 0.007 0.001 TRP B 523 HIS 0.003 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 6295) covalent geometry : angle 0.52874 / 0.27 ( 8615) hydrogen bonds : bond 0.03619 / 2.54 ( 382) hydrogen bonds : angle 3.70705 / 2.64 ( 1107) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.148 Fit side-chains REVERT: B 60 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7972 (mtm) REVERT: B 329 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.9027 (m-80) REVERT: B 519 TYR cc_start: 0.9070 (p90) cc_final: 0.8799 (p90) REVERT: B 597 ASP cc_start: 0.8923 (t0) cc_final: 0.8460 (t0) REVERT: B 627 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.6525 (tmm) REVERT: D 402 MET cc_start: 0.7850 (mtt) cc_final: 0.7575 (ttt) outliers start: 23 outliers final: 16 residues processed: 111 average time/residue: 0.0442 time to fit residues: 7.5644 Evaluate side-chains 117 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.107419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.087717 restraints weight = 11489.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.090608 restraints weight = 6248.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092642 restraints weight = 4199.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094047 restraints weight = 3187.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.094664 restraints weight = 2643.819| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6296 Z= 0.192 Angle : 0.552 7.939 8615 Z= 0.282 Chirality : 0.041 0.213 1033 Planarity : 0.004 0.053 1094 Dihedral : 8.307 128.764 989 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 4.19 % Allowed : 22.36 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.53 (0.30), residues: 855 helix: 2.67 (0.24), residues: 478 sheet: -1.16 (0.62), residues: 52 loop : -1.25 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 294 TYR 0.017 0.002 TYR B 520 PHE 0.021 0.001 PHE B 54 TRP 0.006 0.001 TRP A 251 HIS 0.004 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 ( 6295) covalent geometry : angle 0.55173 / 0.28 ( 8615) hydrogen bonds : bond 0.03884 / 2.73 ( 382) hydrogen bonds : angle 3.80930 / 2.72 ( 1107) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.297 Fit side-chains REVERT: B 60 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8027 (mtm) REVERT: B 432 PHE cc_start: 0.8266 (m-80) cc_final: 0.8024 (m-80) REVERT: B 597 ASP cc_start: 0.8993 (t0) cc_final: 0.8528 (t0) REVERT: B 627 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6427 (tmm) outliers start: 21 outliers final: 16 residues processed: 110 average time/residue: 0.0484 time to fit residues: 8.1900 Evaluate side-chains 112 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 281 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.109625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.089938 restraints weight = 11411.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092990 restraints weight = 6147.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.095051 restraints weight = 4060.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096421 restraints weight = 3074.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097066 restraints weight = 2547.855| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6296 Z= 0.121 Angle : 0.508 8.542 8615 Z= 0.256 Chirality : 0.039 0.217 1033 Planarity : 0.003 0.050 1094 Dihedral : 8.183 127.161 989 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.91 % Rotamer: Outliers : 3.79 % Allowed : 23.75 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.70 (0.30), residues: 855 helix: 2.81 (0.24), residues: 479 sheet: -1.05 (0.62), residues: 52 loop : -1.18 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 294 TYR 0.022 0.001 TYR B 519 PHE 0.024 0.001 PHE B 54 TRP 0.007 0.001 TRP B 119 HIS 0.003 0.000 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 6295) covalent geometry : angle 0.50823 / 0.26 ( 8615) hydrogen bonds : bond 0.03355 / 2.33 ( 382) hydrogen bonds : angle 3.59121 / 2.55 ( 1107) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.313 Fit side-chains REVERT: B 60 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.8005 (mtm) REVERT: B 597 ASP cc_start: 0.8903 (t0) cc_final: 0.8438 (t0) REVERT: B 627 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6469 (tmm) outliers start: 19 outliers final: 16 residues processed: 109 average time/residue: 0.0499 time to fit residues: 8.3592 Evaluate side-chains 113 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 281 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.108842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.089184 restraints weight = 11452.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092165 restraints weight = 6179.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094226 restraints weight = 4107.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.095586 restraints weight = 3112.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096398 restraints weight = 2582.724| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 : 0.004 0.038 6296 Z= 0.146 Angle : 0.536 9.324 8615 Z= 0.267 Chirality : 0.040 0.214 1033 Planarity : 0.003 0.049 1094 Dihedral : 8.155 126.961 989 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.33 % Favored : 95.56 % Rotamer: Outliers : 4.79 % Allowed : 22.55 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.70 (0.30), residues: 855 helix: 2.79 (0.24), residues: 478 sheet: -1.02 (0.62), residues: 52 loop : -1.15 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 294 TYR 0.024 0.001 TYR B 519 PHE 0.024 0.001 PHE B 54 TRP 0.006 0.001 TRP A 251 HIS 0.003 0.000 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 6295) covalent geometry : angle 0.53586 / 0.27 ( 8615) hydrogen bonds : bond 0.03469 / 2.42 ( 382) hydrogen bonds : angle 3.64447 / 2.59 ( 1107) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.229 Fit side-chains REVERT: B 60 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8034 (mtm) REVERT: B 597 ASP cc_start: 0.8915 (t0) cc_final: 0.8645 (t0) REVERT: B 627 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.6464 (tmm) REVERT: C 103 MET cc_start: 0.8536 (tmm) cc_final: 0.8290 (tmm) outliers start: 24 outliers final: 18 residues processed: 113 average time/residue: 0.0461 time to fit residues: 8.0770 Evaluate side-chains 116 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 319 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.107668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.088011 restraints weight = 11532.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090951 restraints weight = 6214.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093014 restraints weight = 4135.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.094377 restraints weight = 3126.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.095358 restraints weight = 2595.998| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6296 Z= 0.175 Angle : 0.554 8.617 8615 Z= 0.278 Chirality : 0.041 0.219 1033 Planarity : 0.003 0.049 1094 Dihedral : 8.211 126.695 989 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.68 % Favored : 95.20 % Rotamer: Outliers : 4.59 % Allowed : 22.95 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.64 (0.30), residues: 855 helix: 2.76 (0.24), residues: 477 sheet: -1.06 (0.62), residues: 52 loop : -1.21 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 294 TYR 0.025 0.002 TYR B 519 PHE 0.024 0.001 PHE B 54 TRP 0.006 0.001 TRP A 251 HIS 0.003 0.000 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 6295) covalent geometry : angle 0.55361 / 0.28 ( 8615) hydrogen bonds : bond 0.03700 / 2.59 ( 382) hydrogen bonds : angle 3.71643 / 2.65 ( 1107) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.240 Fit side-chains REVERT: B 60 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8049 (mtm) REVERT: B 578 MET cc_start: 0.9065 (tpp) cc_final: 0.8858 (mmm) REVERT: B 597 ASP cc_start: 0.8934 (t0) cc_final: 0.8664 (t0) REVERT: B 627 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6498 (tmm) REVERT: C 103 MET cc_start: 0.8538 (tmm) cc_final: 0.8304 (tmm) outliers start: 23 outliers final: 17 residues processed: 111 average time/residue: 0.0455 time to fit residues: 7.7900 Evaluate side-chains 117 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 319 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.109022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.089418 restraints weight = 11412.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.092429 restraints weight = 6111.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094488 restraints weight = 4043.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.095841 restraints weight = 3063.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096817 restraints weight = 2541.160| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6296 Z= 0.132 Angle : 0.537 8.395 8615 Z= 0.267 Chirality : 0.040 0.223 1033 Planarity : 0.003 0.049 1094 Dihedral : 8.152 125.993 989 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.21 % Favored : 95.67 % Rotamer: Outliers : 3.79 % Allowed : 23.15 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.70 (0.30), residues: 855 helix: 2.80 (0.24), residues: 479 sheet: -0.96 (0.62), residues: 52 loop : -1.20 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 294 TYR 0.024 0.001 TYR B 519 PHE 0.025 0.001 PHE B 54 TRP 0.007 0.001 TRP A 251 HIS 0.003 0.000 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 6295) covalent geometry : angle 0.53684 / 0.27 ( 8615) hydrogen bonds : bond 0.03438 / 2.39 ( 382) hydrogen bonds : angle 3.58450 / 2.55 ( 1107) Misc. bond : bond 0.00003 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.261 Fit side-chains REVERT: B 60 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.8052 (mtm) REVERT: B 597 ASP cc_start: 0.8903 (t0) cc_final: 0.8623 (t0) REVERT: B 627 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.6487 (tmm) REVERT: C 103 MET cc_start: 0.8537 (tmm) cc_final: 0.8317 (tmm) REVERT: A 361 LEU cc_start: 0.9019 (mm) cc_final: 0.8789 (mt) outliers start: 19 outliers final: 16 residues processed: 111 average time/residue: 0.0532 time to fit residues: 8.8817 Evaluate side-chains 116 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 319 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.111135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.091458 restraints weight = 11370.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.094536 restraints weight = 6104.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.096632 restraints weight = 4040.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098055 restraints weight = 3052.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.098920 restraints weight = 2518.113| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6296 Z= 0.105 Angle : 0.523 8.022 8615 Z= 0.258 Chirality : 0.039 0.233 1033 Planarity : 0.003 0.048 1094 Dihedral : 7.974 125.613 989 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.91 % Rotamer: Outliers : 3.19 % Allowed : 23.35 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.82 (0.30), residues: 855 helix: 2.91 (0.24), residues: 480 sheet: -0.79 (0.64), residues: 50 loop : -1.21 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 294 TYR 0.024 0.001 TYR B 519 PHE 0.027 0.001 PHE B 54 TRP 0.006 0.001 TRP A 251 HIS 0.003 0.000 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 6295) covalent geometry : angle 0.52305 / 0.26 ( 8615) hydrogen bonds : bond 0.03050 / 2.11 ( 382) hydrogen bonds : angle 3.41602 / 2.40 ( 1107) Misc. bond : bond 0.00003 / 0.00 ( 1) =============================================================================== Job complete usr+sys time: 1034.48 seconds wall clock time: 18 minutes 35.19 seconds (1115.19 seconds total)