Starting phenix.real_space_refine on Fri Oct 10 23:16:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtn_37837/10_2025/8wtn_37837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtn_37837/10_2025/8wtn_37837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wtn_37837/10_2025/8wtn_37837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtn_37837/10_2025/8wtn_37837.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wtn_37837/10_2025/8wtn_37837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtn_37837/10_2025/8wtn_37837.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.322 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 64 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 S 42 5.16 5 C 6294 2.51 5 N 1632 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9714 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4825 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 23, 'TRANS': 590} Chain breaks: 3 Chain: "B" Number of atoms: 4825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4825 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 23, 'TRANS': 590} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.10, per 1000 atoms: 0.22 Number of scatterers: 9714 At special positions: 0 Unit cell: (98.44, 78.2, 137.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 2 22.97 S 42 16.00 P 4 15.00 O 1740 8.00 N 1632 7.00 C 6294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 646 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS B 646 " - pdb=" SG CYS B 687 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 317.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 55.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.634A pdb=" N LEU A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 199 through 215 Processing helix chain 'A' and resid 236 through 246 removed outlier: 3.817A pdb=" N ASP A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'A' and resid 319 through 327 removed outlier: 4.059A pdb=" N PHE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 354 through 368 removed outlier: 3.793A pdb=" N PHE A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 368 " --> pdb=" O TRP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 430 through 445 removed outlier: 3.524A pdb=" N LEU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.703A pdb=" N VAL A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 474 through 495 removed outlier: 3.638A pdb=" N GLN A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE A 493 " --> pdb=" O MET A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 499 removed outlier: 3.700A pdb=" N ALA A 499 " --> pdb=" O CYS A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 500 through 514 removed outlier: 3.705A pdb=" N LEU A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLU A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 509 " --> pdb=" O GLN A 505 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 512 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 532 through 552 removed outlier: 3.689A pdb=" N THR A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TRP A 549 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 551 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 581 removed outlier: 3.748A pdb=" N PHE A 562 " --> pdb=" O MET A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 605 removed outlier: 3.629A pdb=" N VAL A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 640 removed outlier: 3.832A pdb=" N GLN A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 654 removed outlier: 4.087A pdb=" N LEU A 653 " --> pdb=" O GLY A 650 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 654 " --> pdb=" O VAL A 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 650 through 654' Processing helix chain 'A' and resid 666 through 675 removed outlier: 3.865A pdb=" N SER A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 704 through 732 Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.637A pdb=" N LEU B 134 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 199 through 215 Processing helix chain 'B' and resid 236 through 246 removed outlier: 3.817A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'B' and resid 319 through 327 removed outlier: 4.068A pdb=" N PHE B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLY B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 344 through 347 Processing helix chain 'B' and resid 354 through 368 removed outlier: 3.779A pdb=" N PHE B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 363 " --> pdb=" O GLU B 359 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET B 367 " --> pdb=" O LYS B 363 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 368 " --> pdb=" O TRP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 399 Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.524A pdb=" N LEU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 436 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.703A pdb=" N VAL B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 474 through 495 removed outlier: 3.639A pdb=" N GLN B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE B 493 " --> pdb=" O MET B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 499 removed outlier: 3.703A pdb=" N ALA B 499 " --> pdb=" O CYS B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 500 through 514 removed outlier: 3.654A pdb=" N LEU B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLU B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 512 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 531 Processing helix chain 'B' and resid 532 through 552 removed outlier: 3.689A pdb=" N THR B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TRP B 549 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 551 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 581 removed outlier: 3.724A pdb=" N PHE B 562 " --> pdb=" O MET B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 605 removed outlier: 3.645A pdb=" N VAL B 596 " --> pdb=" O TYR B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 640 removed outlier: 3.831A pdb=" N GLN B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 654 removed outlier: 3.796A pdb=" N LEU B 653 " --> pdb=" O GLY B 650 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 654 " --> pdb=" O VAL B 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 650 through 654' Processing helix chain 'B' and resid 666 through 673 Processing helix chain 'B' and resid 674 through 677 Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.569A pdb=" N VAL B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 732 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 109 removed outlier: 6.112A pdb=" N TYR A 80 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 170 removed outlier: 5.977A pdb=" N ALA A 168 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 312 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.426A pdb=" N THR A 689 " --> pdb=" O PHE A 647 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 113 through 116 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 109 removed outlier: 6.109A pdb=" N TYR B 80 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 167 through 170 removed outlier: 5.981A pdb=" N ALA B 168 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE B 312 " --> pdb=" O PHE B 304 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3080 1.36 - 1.51: 2962 1.51 - 1.65: 3802 1.65 - 1.80: 46 1.80 - 1.94: 34 Bond restraints: 9924 Sorted by residual: bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" O3B ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sigma weight residual 1.510 1.426 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O3B ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sigma weight residual 1.510 1.427 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 ADP B 801 " pdb=" C6 ADP B 801 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 9919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.27: 13414 7.27 - 14.54: 10 14.54 - 21.81: 4 21.81 - 29.08: 4 29.08 - 36.35: 2 Bond angle restraints: 13434 Sorted by residual: angle pdb=" O2 VO4 B 802 " pdb=" V VO4 B 802 " pdb=" O4 VO4 B 802 " ideal model delta sigma weight residual 109.47 73.12 36.35 3.00e+00 1.11e-01 1.47e+02 angle pdb=" O2 VO4 A 802 " pdb=" V VO4 A 802 " pdb=" O4 VO4 A 802 " ideal model delta sigma weight residual 109.47 73.13 36.34 3.00e+00 1.11e-01 1.47e+02 angle pdb=" O3 VO4 A 802 " pdb=" V VO4 A 802 " pdb=" O4 VO4 A 802 " ideal model delta sigma weight residual 109.47 85.14 24.33 3.00e+00 1.11e-01 6.58e+01 angle pdb=" O3 VO4 B 802 " pdb=" V VO4 B 802 " pdb=" O4 VO4 B 802 " ideal model delta sigma weight residual 109.47 85.16 24.32 3.00e+00 1.11e-01 6.57e+01 angle pdb=" PA ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sigma weight residual 120.50 142.94 -22.44 3.00e+00 1.11e-01 5.59e+01 ... (remaining 13429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.95: 5558 23.95 - 47.91: 279 47.91 - 71.86: 21 71.86 - 95.81: 6 95.81 - 119.77: 4 Dihedral angle restraints: 5868 sinusoidal: 2348 harmonic: 3520 Sorted by residual: dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 59.77 -119.77 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" O2A ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PA ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 59.73 -119.73 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" O1B ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " pdb=" PA ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 50.99 -110.99 1 2.00e+01 2.50e-03 3.26e+01 ... (remaining 5865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1432 0.089 - 0.178: 112 0.178 - 0.267: 2 0.267 - 0.356: 2 0.356 - 0.445: 2 Chirality restraints: 1550 Sorted by residual: chirality pdb=" CB ILE B 620 " pdb=" CA ILE B 620 " pdb=" CG1 ILE B 620 " pdb=" CG2 ILE B 620 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CB ILE A 620 " pdb=" CA ILE A 620 " pdb=" CG1 ILE A 620 " pdb=" CG2 ILE A 620 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CB VAL B 502 " pdb=" CA VAL B 502 " pdb=" CG1 VAL B 502 " pdb=" CG2 VAL B 502 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1547 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 120 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ILE A 120 " -0.056 2.00e-02 2.50e+03 pdb=" O ILE A 120 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU A 121 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 120 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ILE B 120 " -0.056 2.00e-02 2.50e+03 pdb=" O ILE B 120 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 121 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 657 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO B 658 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 658 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 658 " 0.039 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2439 2.78 - 3.31: 8411 3.31 - 3.84: 16126 3.84 - 4.37: 20429 4.37 - 4.90: 34043 Nonbonded interactions: 81448 Sorted by model distance: nonbonded pdb=" O PHE B 510 " pdb=" OG1 THR B 514 " model vdw 2.256 3.040 nonbonded pdb=" O PHE A 510 " pdb=" OG1 THR A 514 " model vdw 2.256 3.040 nonbonded pdb=" O MET A 452 " pdb=" OG1 THR A 456 " model vdw 2.259 3.040 nonbonded pdb=" O MET B 452 " pdb=" OG1 THR B 456 " model vdw 2.259 3.040 nonbonded pdb=" O1B ADP B 801 " pdb=" O3 VO4 B 802 " model vdw 2.294 3.040 ... (remaining 81443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.440 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:8.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.013 0.806 9930 Z= 1.190 Angle : 1.150 36.349 13438 Z= 0.540 Chirality : 0.052 0.445 1550 Planarity : 0.007 0.071 1664 Dihedral : 14.110 119.767 3594 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.66 (0.16), residues: 1212 helix: -4.28 (0.08), residues: 688 sheet: -2.00 (0.49), residues: 80 loop : -2.82 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 206 TYR 0.019 0.002 TYR B 592 PHE 0.020 0.002 PHE A 75 TRP 0.008 0.002 TRP A 429 HIS 0.005 0.001 HIS A 528 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 9924) covalent geometry : angle 1.14963 (13434) SS BOND : bond 0.00364 ( 2) SS BOND : angle 1.42733 ( 4) hydrogen bonds : bond 0.29231 ( 450) hydrogen bonds : angle 10.40386 ( 1317) Misc. bond : bond 0.57736 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.7576 (mtpp) cc_final: 0.7305 (mmtp) REVERT: A 511 MET cc_start: 0.7627 (mtm) cc_final: 0.7402 (mmt) REVERT: B 110 ASN cc_start: 0.7948 (m-40) cc_final: 0.7622 (t160) REVERT: B 511 MET cc_start: 0.7624 (mtm) cc_final: 0.7403 (mmt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.5939 time to fit residues: 90.3322 Evaluate side-chains 116 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 248 HIS A 289 HIS A 336 GLN A 528 HIS A 611 ASN A 733 ASN B 110 ASN B 248 HIS B 289 HIS B 336 GLN B 528 HIS B 587 HIS B 611 ASN B 733 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.192499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124700 restraints weight = 8793.016| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.51 r_work: 0.2786 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9930 Z= 0.193 Angle : 0.690 7.197 13438 Z= 0.354 Chirality : 0.043 0.238 1550 Planarity : 0.005 0.054 1664 Dihedral : 8.863 147.095 1348 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.37 % Allowed : 8.71 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.21), residues: 1212 helix: -1.80 (0.17), residues: 674 sheet: -2.41 (0.44), residues: 86 loop : -2.08 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.013 0.002 TYR A 630 PHE 0.018 0.002 PHE A 75 TRP 0.012 0.001 TRP B 572 HIS 0.004 0.001 HIS B 528 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 9924) covalent geometry : angle 0.68941 (13434) SS BOND : bond 0.00170 ( 2) SS BOND : angle 1.05512 ( 4) hydrogen bonds : bond 0.04341 ( 450) hydrogen bonds : angle 4.85043 ( 1317) Misc. bond : bond 0.00090 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.394 Fit side-chains REVERT: A 164 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7682 (mmtp) REVERT: A 301 ARG cc_start: 0.8282 (ttm170) cc_final: 0.8038 (ttm170) REVERT: A 511 MET cc_start: 0.8448 (mtm) cc_final: 0.7850 (mmt) REVERT: A 588 VAL cc_start: 0.8286 (p) cc_final: 0.7939 (t) REVERT: A 594 ILE cc_start: 0.8801 (mt) cc_final: 0.8594 (mm) REVERT: A 680 MET cc_start: 0.7159 (mmt) cc_final: 0.6672 (mmm) REVERT: B 300 ASP cc_start: 0.8059 (m-30) cc_final: 0.7730 (m-30) REVERT: B 301 ARG cc_start: 0.8290 (ttm170) cc_final: 0.8046 (ttm170) REVERT: B 511 MET cc_start: 0.8431 (mtm) cc_final: 0.7830 (mmt) REVERT: B 588 VAL cc_start: 0.8283 (p) cc_final: 0.7952 (t) REVERT: B 594 ILE cc_start: 0.8811 (mt) cc_final: 0.8603 (mm) REVERT: B 666 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7347 (mmm) outliers start: 25 outliers final: 9 residues processed: 131 average time/residue: 0.6976 time to fit residues: 97.3518 Evaluate side-chains 122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 666 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.190774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3316 r_free = 0.3316 target = 0.120904 restraints weight = 8743.393| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.62 r_work: 0.2784 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9930 Z= 0.215 Angle : 0.681 7.440 13438 Z= 0.347 Chirality : 0.044 0.234 1550 Planarity : 0.004 0.052 1664 Dihedral : 8.566 142.866 1348 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 3.79 % Allowed : 10.51 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.23), residues: 1212 helix: -0.67 (0.19), residues: 698 sheet: -2.13 (0.48), residues: 86 loop : -1.92 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 116 TYR 0.014 0.001 TYR A 630 PHE 0.019 0.002 PHE B 75 TRP 0.011 0.001 TRP B 572 HIS 0.004 0.001 HIS B 528 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 9924) covalent geometry : angle 0.68117 (13434) SS BOND : bond 0.00219 ( 2) SS BOND : angle 0.98539 ( 4) hydrogen bonds : bond 0.04197 ( 450) hydrogen bonds : angle 4.43663 ( 1317) Misc. bond : bond 0.00081 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 0.293 Fit side-chains REVERT: A 164 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7771 (mmtp) REVERT: A 175 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8515 (mp) REVERT: A 236 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: A 301 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7973 (ttm170) REVERT: A 367 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6986 (pmm) REVERT: A 511 MET cc_start: 0.8386 (mtm) cc_final: 0.7770 (mmt) REVERT: A 588 VAL cc_start: 0.8280 (p) cc_final: 0.7954 (t) REVERT: A 680 MET cc_start: 0.7080 (mmt) cc_final: 0.6556 (mmm) REVERT: B 175 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8506 (mp) REVERT: B 301 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7969 (ttm170) REVERT: B 389 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.5864 (mptm) REVERT: B 511 MET cc_start: 0.8372 (mtm) cc_final: 0.7754 (mmt) REVERT: B 588 VAL cc_start: 0.8291 (p) cc_final: 0.7950 (t) REVERT: B 666 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7408 (mmm) REVERT: B 680 MET cc_start: 0.7009 (mmm) cc_final: 0.6738 (mmm) outliers start: 40 outliers final: 18 residues processed: 135 average time/residue: 0.5387 time to fit residues: 78.5763 Evaluate side-chains 132 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 666 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 116 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.187135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.117217 restraints weight = 8875.881| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.95 r_work: 0.2788 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9930 Z= 0.170 Angle : 0.636 7.096 13438 Z= 0.324 Chirality : 0.043 0.224 1550 Planarity : 0.004 0.050 1664 Dihedral : 8.242 141.521 1348 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.22 % Allowed : 12.22 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.24), residues: 1212 helix: -0.04 (0.20), residues: 696 sheet: -2.11 (0.50), residues: 86 loop : -1.80 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 444 TYR 0.013 0.001 TYR A 630 PHE 0.017 0.001 PHE B 75 TRP 0.011 0.001 TRP A 572 HIS 0.003 0.001 HIS A 528 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9924) covalent geometry : angle 0.63562 (13434) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.83715 ( 4) hydrogen bonds : bond 0.03665 ( 450) hydrogen bonds : angle 4.13699 ( 1317) Misc. bond : bond 0.00065 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.365 Fit side-chains REVERT: A 162 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7491 (ttp) REVERT: A 164 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7656 (mmtp) REVERT: A 175 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 236 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: A 301 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7825 (ttm170) REVERT: A 367 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7009 (pmm) REVERT: A 511 MET cc_start: 0.8337 (mtm) cc_final: 0.7704 (mmt) REVERT: A 588 VAL cc_start: 0.8163 (p) cc_final: 0.7815 (t) REVERT: A 666 MET cc_start: 0.7220 (mmm) cc_final: 0.6722 (ttp) REVERT: A 680 MET cc_start: 0.7102 (mmt) cc_final: 0.6598 (mmm) REVERT: B 175 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8496 (mp) REVERT: B 301 ARG cc_start: 0.8276 (ttm170) cc_final: 0.7779 (ttm170) REVERT: B 389 LYS cc_start: 0.6081 (OUTLIER) cc_final: 0.5625 (mptm) REVERT: B 511 MET cc_start: 0.8320 (mtm) cc_final: 0.7681 (mmt) REVERT: B 588 VAL cc_start: 0.8181 (p) cc_final: 0.7827 (t) REVERT: B 666 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7322 (mmm) REVERT: B 680 MET cc_start: 0.6957 (mmm) cc_final: 0.6666 (mmm) outliers start: 34 outliers final: 16 residues processed: 121 average time/residue: 0.6261 time to fit residues: 81.5777 Evaluate side-chains 122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 666 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 63 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.181503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.107345 restraints weight = 9088.172| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.76 r_work: 0.2808 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9930 Z= 0.137 Angle : 0.603 6.985 13438 Z= 0.307 Chirality : 0.041 0.212 1550 Planarity : 0.004 0.050 1664 Dihedral : 7.938 138.576 1348 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.03 % Allowed : 12.78 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.25), residues: 1212 helix: 0.41 (0.21), residues: 686 sheet: -1.99 (0.52), residues: 86 loop : -1.73 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 444 TYR 0.012 0.001 TYR A 630 PHE 0.015 0.001 PHE B 75 TRP 0.011 0.001 TRP B 572 HIS 0.002 0.001 HIS B 528 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9924) covalent geometry : angle 0.60253 (13434) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.76533 ( 4) hydrogen bonds : bond 0.03360 ( 450) hydrogen bonds : angle 3.92583 ( 1317) Misc. bond : bond 0.00047 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.355 Fit side-chains REVERT: A 162 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7400 (ttp) REVERT: A 164 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7608 (mmtp) REVERT: A 175 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 196 ARG cc_start: 0.7881 (ptm160) cc_final: 0.6683 (tpt-90) REVERT: A 301 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7786 (ttm170) REVERT: A 367 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7171 (pmm) REVERT: A 511 MET cc_start: 0.8288 (mtm) cc_final: 0.7643 (mmt) REVERT: A 588 VAL cc_start: 0.8089 (p) cc_final: 0.7740 (t) REVERT: A 666 MET cc_start: 0.7354 (mmm) cc_final: 0.6706 (ttp) REVERT: A 680 MET cc_start: 0.7140 (mmt) cc_final: 0.6661 (mmm) REVERT: B 175 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8447 (mp) REVERT: B 196 ARG cc_start: 0.8030 (ptm160) cc_final: 0.6747 (tpt-90) REVERT: B 301 ARG cc_start: 0.8207 (ttm170) cc_final: 0.7779 (ttm170) REVERT: B 389 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5651 (mptm) REVERT: B 511 MET cc_start: 0.8266 (mtm) cc_final: 0.7614 (mmt) REVERT: B 588 VAL cc_start: 0.8107 (p) cc_final: 0.7750 (t) REVERT: B 666 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7385 (mmm) outliers start: 32 outliers final: 18 residues processed: 131 average time/residue: 0.5868 time to fit residues: 82.3382 Evaluate side-chains 127 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 666 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 36 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 26 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.188216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117505 restraints weight = 8934.597| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.67 r_work: 0.2825 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9930 Z= 0.162 Angle : 0.630 9.610 13438 Z= 0.317 Chirality : 0.042 0.208 1550 Planarity : 0.004 0.045 1664 Dihedral : 7.950 138.024 1348 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 3.03 % Allowed : 14.02 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.25), residues: 1212 helix: 0.41 (0.20), residues: 698 sheet: -1.92 (0.53), residues: 86 loop : -1.69 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 116 TYR 0.013 0.001 TYR A 630 PHE 0.016 0.001 PHE B 75 TRP 0.011 0.001 TRP B 572 HIS 0.003 0.001 HIS A 528 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9924) covalent geometry : angle 0.62986 (13434) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.78829 ( 4) hydrogen bonds : bond 0.03563 ( 450) hydrogen bonds : angle 3.92328 ( 1317) Misc. bond : bond 0.00054 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.299 Fit side-chains REVERT: A 164 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7630 (mmtp) REVERT: A 196 ARG cc_start: 0.7909 (ptm160) cc_final: 0.6724 (tpt-90) REVERT: A 236 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: A 301 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7830 (ttm170) REVERT: A 367 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7264 (pmm) REVERT: A 511 MET cc_start: 0.8304 (mtm) cc_final: 0.7678 (mmt) REVERT: A 588 VAL cc_start: 0.8188 (p) cc_final: 0.7878 (t) REVERT: A 666 MET cc_start: 0.7509 (mmm) cc_final: 0.6755 (ttp) REVERT: A 680 MET cc_start: 0.7175 (mmt) cc_final: 0.6690 (mmm) REVERT: B 196 ARG cc_start: 0.8027 (ptm160) cc_final: 0.6746 (tpt-90) REVERT: B 301 ARG cc_start: 0.8274 (ttm170) cc_final: 0.7839 (ttm170) REVERT: B 389 LYS cc_start: 0.6267 (OUTLIER) cc_final: 0.5742 (mptm) REVERT: B 511 MET cc_start: 0.8299 (mtm) cc_final: 0.7681 (mmt) REVERT: B 588 VAL cc_start: 0.8231 (p) cc_final: 0.7912 (t) REVERT: B 666 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7390 (mmm) outliers start: 32 outliers final: 19 residues processed: 121 average time/residue: 0.5873 time to fit residues: 76.3606 Evaluate side-chains 120 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 666 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 81 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS B 289 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.189751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.119702 restraints weight = 8894.189| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.66 r_work: 0.2903 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9930 Z= 0.126 Angle : 0.596 8.685 13438 Z= 0.300 Chirality : 0.041 0.207 1550 Planarity : 0.004 0.049 1664 Dihedral : 7.781 137.271 1348 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 3.41 % Allowed : 14.39 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.25), residues: 1212 helix: 0.72 (0.21), residues: 688 sheet: -1.87 (0.53), residues: 86 loop : -1.69 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 116 TYR 0.011 0.001 TYR A 630 PHE 0.014 0.001 PHE B 75 TRP 0.011 0.001 TRP A 572 HIS 0.002 0.001 HIS A 528 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9924) covalent geometry : angle 0.59635 (13434) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.69956 ( 4) hydrogen bonds : bond 0.03203 ( 450) hydrogen bonds : angle 3.78885 ( 1317) Misc. bond : bond 0.00044 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.411 Fit side-chains REVERT: A 175 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 196 ARG cc_start: 0.7890 (ptm160) cc_final: 0.6678 (tpt-90) REVERT: A 367 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7191 (pmm) REVERT: A 511 MET cc_start: 0.8330 (mtm) cc_final: 0.7670 (mmt) REVERT: A 588 VAL cc_start: 0.8149 (p) cc_final: 0.7855 (t) REVERT: A 680 MET cc_start: 0.7144 (mmt) cc_final: 0.6658 (mmm) REVERT: B 196 ARG cc_start: 0.8054 (ptm160) cc_final: 0.6747 (tpt-90) REVERT: B 300 ASP cc_start: 0.7952 (m-30) cc_final: 0.7578 (m-30) REVERT: B 389 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5698 (mptm) REVERT: B 511 MET cc_start: 0.8237 (mtm) cc_final: 0.7615 (mmt) REVERT: B 588 VAL cc_start: 0.8163 (p) cc_final: 0.7854 (t) REVERT: B 666 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7323 (mmm) outliers start: 36 outliers final: 19 residues processed: 126 average time/residue: 0.5553 time to fit residues: 75.5842 Evaluate side-chains 120 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 666 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 81 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.187247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116937 restraints weight = 8934.520| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.66 r_work: 0.2860 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9930 Z= 0.179 Angle : 0.643 8.586 13438 Z= 0.323 Chirality : 0.043 0.202 1550 Planarity : 0.004 0.053 1664 Dihedral : 7.895 136.999 1348 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 3.22 % Allowed : 15.53 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.25), residues: 1212 helix: 0.55 (0.20), residues: 700 sheet: -1.84 (0.54), residues: 86 loop : -1.68 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 444 TYR 0.013 0.001 TYR B 630 PHE 0.017 0.001 PHE B 75 TRP 0.011 0.001 TRP A 572 HIS 0.003 0.001 HIS B 528 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9924) covalent geometry : angle 0.64247 (13434) SS BOND : bond 0.00220 ( 2) SS BOND : angle 0.80971 ( 4) hydrogen bonds : bond 0.03661 ( 450) hydrogen bonds : angle 3.90758 ( 1317) Misc. bond : bond 0.00063 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.389 Fit side-chains REVERT: A 175 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8366 (mp) REVERT: A 236 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: A 301 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7716 (ttm110) REVERT: A 367 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7258 (pmm) REVERT: A 389 LYS cc_start: 0.6320 (tttm) cc_final: 0.5808 (mptm) REVERT: A 511 MET cc_start: 0.8341 (mtm) cc_final: 0.7691 (mmt) REVERT: A 588 VAL cc_start: 0.8204 (p) cc_final: 0.7905 (t) REVERT: A 645 GLU cc_start: 0.7867 (tp30) cc_final: 0.6752 (pt0) REVERT: A 666 MET cc_start: 0.7234 (mmm) cc_final: 0.6824 (ttp) REVERT: A 680 MET cc_start: 0.7150 (mmt) cc_final: 0.6649 (mmm) REVERT: B 175 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8385 (mp) REVERT: B 301 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7711 (ttm110) REVERT: B 389 LYS cc_start: 0.6228 (OUTLIER) cc_final: 0.5719 (mptm) REVERT: B 433 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8173 (ttpt) REVERT: B 511 MET cc_start: 0.8322 (mtm) cc_final: 0.7667 (mmt) REVERT: B 588 VAL cc_start: 0.8271 (p) cc_final: 0.7958 (t) REVERT: B 666 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7393 (mmm) outliers start: 34 outliers final: 22 residues processed: 126 average time/residue: 0.5812 time to fit residues: 78.7773 Evaluate side-chains 127 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 666 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 44 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN B 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.187482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117288 restraints weight = 8881.387| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.65 r_work: 0.2802 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9930 Z= 0.168 Angle : 0.638 8.421 13438 Z= 0.320 Chirality : 0.043 0.204 1550 Planarity : 0.004 0.060 1664 Dihedral : 7.869 136.759 1348 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 3.41 % Allowed : 15.53 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.25), residues: 1212 helix: 0.59 (0.20), residues: 702 sheet: -1.81 (0.54), residues: 86 loop : -1.64 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 116 TYR 0.013 0.001 TYR B 630 PHE 0.016 0.001 PHE B 75 TRP 0.011 0.001 TRP A 572 HIS 0.003 0.001 HIS A 528 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9924) covalent geometry : angle 0.63819 (13434) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.76623 ( 4) hydrogen bonds : bond 0.03561 ( 450) hydrogen bonds : angle 3.88278 ( 1317) Misc. bond : bond 0.00057 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.373 Fit side-chains REVERT: A 140 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.6817 (t0) REVERT: A 175 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8355 (mp) REVERT: A 236 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: A 301 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7570 (ttm110) REVERT: A 367 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7245 (pmm) REVERT: A 389 LYS cc_start: 0.6410 (tttm) cc_final: 0.5885 (mptm) REVERT: A 433 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8110 (ttpt) REVERT: A 511 MET cc_start: 0.8356 (mtm) cc_final: 0.7657 (mmt) REVERT: A 588 VAL cc_start: 0.8288 (p) cc_final: 0.7969 (t) REVERT: A 645 GLU cc_start: 0.7918 (tp30) cc_final: 0.6804 (pt0) REVERT: A 666 MET cc_start: 0.7400 (mmm) cc_final: 0.6991 (ttp) REVERT: A 680 MET cc_start: 0.7138 (mmt) cc_final: 0.6659 (mmm) REVERT: B 164 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.6908 (mmtp) REVERT: B 175 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8384 (mp) REVERT: B 300 ASP cc_start: 0.7953 (m-30) cc_final: 0.7593 (m-30) REVERT: B 301 ARG cc_start: 0.8158 (ttm170) cc_final: 0.7570 (ttm110) REVERT: B 389 LYS cc_start: 0.6259 (OUTLIER) cc_final: 0.5738 (mptm) REVERT: B 511 MET cc_start: 0.8350 (mtm) cc_final: 0.7648 (mmt) REVERT: B 588 VAL cc_start: 0.8303 (p) cc_final: 0.7966 (t) REVERT: B 666 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7424 (mmm) outliers start: 36 outliers final: 18 residues processed: 126 average time/residue: 0.5565 time to fit residues: 75.5181 Evaluate side-chains 126 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 666 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN B 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.187660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.117542 restraints weight = 8876.502| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.66 r_work: 0.2871 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9930 Z= 0.182 Angle : 0.919 59.175 13438 Z= 0.523 Chirality : 0.042 0.218 1550 Planarity : 0.004 0.055 1664 Dihedral : 7.865 136.807 1348 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 2.75 % Allowed : 16.38 % Favored : 80.87 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.25), residues: 1212 helix: 0.62 (0.20), residues: 702 sheet: -1.81 (0.54), residues: 86 loop : -1.64 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 444 TYR 0.013 0.001 TYR B 630 PHE 0.016 0.001 PHE B 75 TRP 0.011 0.001 TRP B 572 HIS 0.003 0.001 HIS A 528 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9924) covalent geometry : angle 0.91874 (13434) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.78213 ( 4) hydrogen bonds : bond 0.03519 ( 450) hydrogen bonds : angle 3.87636 ( 1317) Misc. bond : bond 0.00052 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.441 Fit side-chains REVERT: A 140 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7651 (m110) REVERT: A 175 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8369 (mp) REVERT: A 236 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: A 301 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7599 (ttm110) REVERT: A 367 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7278 (pmm) REVERT: A 389 LYS cc_start: 0.6448 (tttm) cc_final: 0.5925 (mptm) REVERT: A 433 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8149 (ttpt) REVERT: A 511 MET cc_start: 0.8362 (mtm) cc_final: 0.7677 (mmt) REVERT: A 588 VAL cc_start: 0.8281 (p) cc_final: 0.7965 (t) REVERT: A 645 GLU cc_start: 0.7934 (tp30) cc_final: 0.6832 (pt0) REVERT: A 666 MET cc_start: 0.7396 (mmm) cc_final: 0.6998 (ttp) REVERT: A 680 MET cc_start: 0.7183 (mmt) cc_final: 0.6707 (mmm) REVERT: B 164 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.6930 (mmtp) REVERT: B 175 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8405 (mp) REVERT: B 300 ASP cc_start: 0.7959 (m-30) cc_final: 0.7603 (m-30) REVERT: B 301 ARG cc_start: 0.8175 (ttm170) cc_final: 0.7594 (ttm110) REVERT: B 389 LYS cc_start: 0.6301 (OUTLIER) cc_final: 0.5779 (mptm) REVERT: B 511 MET cc_start: 0.8360 (mtm) cc_final: 0.7671 (mmt) REVERT: B 588 VAL cc_start: 0.8301 (p) cc_final: 0.7967 (t) REVERT: B 666 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7429 (mmm) outliers start: 29 outliers final: 19 residues processed: 120 average time/residue: 0.5965 time to fit residues: 77.0252 Evaluate side-chains 128 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 433 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 666 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 63 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN B 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.187676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.120392 restraints weight = 8854.857| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.89 r_work: 0.2819 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.592 9930 Z= 0.495 Angle : 0.837 43.699 13438 Z= 0.553 Chirality : 0.045 0.712 1550 Planarity : 0.006 0.177 1664 Dihedral : 7.865 136.807 1348 Min Nonbonded Distance : 1.594 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 2.65 % Allowed : 16.48 % Favored : 80.87 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.25), residues: 1212 helix: 0.62 (0.20), residues: 702 sheet: -1.81 (0.54), residues: 86 loop : -1.64 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 444 TYR 0.013 0.001 TYR B 630 PHE 0.016 0.001 PHE B 75 TRP 0.011 0.001 TRP B 572 HIS 0.003 0.001 HIS A 528 Details of bonding type rmsd covalent geometry : bond 0.00984 ( 9924) covalent geometry : angle 0.83743 (13434) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.78209 ( 4) hydrogen bonds : bond 0.03519 ( 450) hydrogen bonds : angle 3.87636 ( 1317) Misc. bond : bond 0.00052 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3664.78 seconds wall clock time: 63 minutes 10.69 seconds (3790.69 seconds total)