Starting phenix.real_space_refine on Sun Jun 8 16:56:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtn_37837/06_2025/8wtn_37837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtn_37837/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wtn_37837/06_2025/8wtn_37837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtn_37837/06_2025/8wtn_37837.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtn_37837/06_2025/8wtn_37837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtn_37837/06_2025/8wtn_37837.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.61, per 1000 atoms: 0.68 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: 2.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.32 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: 3.19 Time building geometry restraints manager: 3.35 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: 0.05 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.890 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.002 TRP A 429 HIS 0.005 0.001 HIS A 528 PHE 0.020 0.002 PHE A 75 TYR 0.019 0.002 TYR B 592 ARG 0.002 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.29231 ( 450) hydrogen bonds : angle 10.40386 ( 1317) SS BOND : bond 0.00364 ( 2) SS BOND : angle 1.42733 ( 4) covalent geometry : bond 0.00604 ( 9924) covalent geometry : angle 1.14963 (13434) 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 : 1.207 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: 1.3474 time to fit residues: 206.7530 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 : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 0.2980 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 110 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 611 ASN A 733 ASN B 110 ASN B 248 HIS B 289 HIS B 336 GLN B 611 ASN B 733 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.187104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.120403 restraints weight = 8849.641| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.92 r_work: 0.2871 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9930 Z= 0.133 Angle : 0.642 7.374 13438 Z= 0.332 Chirality : 0.041 0.219 1550 Planarity : 0.005 0.054 1664 Dihedral : 8.686 147.019 1348 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.08 % Allowed : 9.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.21), residues: 1212 helix: -1.70 (0.17), residues: 664 sheet: -2.41 (0.44), residues: 86 loop : -2.20 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 572 HIS 0.002 0.000 HIS B 528 PHE 0.016 0.001 PHE A 75 TYR 0.015 0.002 TYR B 592 ARG 0.006 0.001 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 450) hydrogen bonds : angle 4.74375 ( 1317) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.93737 ( 4) covalent geometry : bond 0.00303 ( 9924) covalent geometry : angle 0.64221 (13434) Misc. bond : bond 0.00129 ( 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 141 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.878 Fit side-chains REVERT: A 164 LYS cc_start: 0.7721 (mtpp) cc_final: 0.7415 (mmtp) REVERT: A 300 ASP cc_start: 0.7911 (m-30) cc_final: 0.7559 (m-30) REVERT: A 389 LYS cc_start: 0.6122 (OUTLIER) cc_final: 0.5679 (mptm) REVERT: A 511 MET cc_start: 0.8252 (mtm) cc_final: 0.7596 (mmt) REVERT: A 588 VAL cc_start: 0.8049 (p) cc_final: 0.7714 (t) REVERT: A 666 MET cc_start: 0.7587 (mmm) cc_final: 0.7370 (mmm) REVERT: A 680 MET cc_start: 0.7047 (mmt) cc_final: 0.6555 (mmm) REVERT: B 300 ASP cc_start: 0.7923 (m-30) cc_final: 0.7571 (m-30) REVERT: B 301 ARG cc_start: 0.8175 (ttm170) cc_final: 0.7958 (ttm170) REVERT: B 444 ARG cc_start: 0.7664 (ttp-170) cc_final: 0.7462 (mtm110) REVERT: B 511 MET cc_start: 0.8238 (mtm) cc_final: 0.7587 (mmt) REVERT: B 588 VAL cc_start: 0.8043 (p) cc_final: 0.7714 (t) REVERT: B 666 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7258 (mmm) outliers start: 22 outliers final: 6 residues processed: 128 average time/residue: 1.7067 time to fit residues: 236.7336 Evaluate side-chains 118 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 613 ASP 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 43 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS B 528 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.191814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3509 r_free = 0.3509 target = 0.135982 restraints weight = 8775.968| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.21 r_work: 0.2856 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9930 Z= 0.189 Angle : 0.654 7.206 13438 Z= 0.334 Chirality : 0.043 0.222 1550 Planarity : 0.004 0.051 1664 Dihedral : 8.357 142.376 1348 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.31 % Allowed : 10.32 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.24), residues: 1212 helix: -0.57 (0.19), residues: 698 sheet: -2.16 (0.48), residues: 86 loop : -1.95 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.004 0.001 HIS B 528 PHE 0.019 0.001 PHE A 75 TYR 0.013 0.001 TYR B 630 ARG 0.008 0.001 ARG A 444 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 450) hydrogen bonds : angle 4.33534 ( 1317) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.92742 ( 4) covalent geometry : bond 0.00459 ( 9924) covalent geometry : angle 0.65426 (13434) Misc. bond : bond 0.00075 ( 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 148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.945 Fit side-chains REVERT: A 164 LYS cc_start: 0.7813 (mtpp) cc_final: 0.7539 (mmtp) REVERT: A 175 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8510 (mp) REVERT: A 300 ASP cc_start: 0.7943 (m-30) cc_final: 0.7634 (m-30) REVERT: A 301 ARG cc_start: 0.8263 (ttm170) cc_final: 0.7886 (ttm110) REVERT: A 367 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7027 (pmm) REVERT: A 389 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.5953 (mptm) REVERT: A 511 MET cc_start: 0.8378 (mtm) cc_final: 0.7786 (mmt) REVERT: A 588 VAL cc_start: 0.8331 (p) cc_final: 0.8018 (t) REVERT: A 666 MET cc_start: 0.7593 (mmm) cc_final: 0.7359 (mmm) REVERT: A 680 MET cc_start: 0.7193 (mmt) cc_final: 0.6657 (mmm) REVERT: B 175 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8501 (mp) REVERT: B 300 ASP cc_start: 0.7954 (m-30) cc_final: 0.7632 (m-30) REVERT: B 301 ARG cc_start: 0.8262 (ttm170) cc_final: 0.7823 (ttm170) REVERT: B 389 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.5973 (mptm) REVERT: B 444 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7461 (mtm110) REVERT: B 511 MET cc_start: 0.8372 (mtm) cc_final: 0.7784 (mmt) REVERT: B 588 VAL cc_start: 0.8347 (p) cc_final: 0.8023 (t) REVERT: B 666 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7352 (mmm) REVERT: B 680 MET cc_start: 0.7108 (mmm) cc_final: 0.6892 (mmm) outliers start: 35 outliers final: 16 residues processed: 133 average time/residue: 1.0946 time to fit residues: 157.5686 Evaluate side-chains 126 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 389 LYS 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 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 91 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 528 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.190952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123769 restraints weight = 8746.509| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.71 r_work: 0.2782 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2226 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 : 0.651 7.226 13438 Z= 0.331 Chirality : 0.043 0.222 1550 Planarity : 0.004 0.047 1664 Dihedral : 8.173 139.559 1348 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 3.41 % Allowed : 12.31 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.24), residues: 1212 helix: -0.04 (0.20), residues: 696 sheet: -2.12 (0.50), residues: 86 loop : -1.81 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 572 HIS 0.005 0.001 HIS A 528 PHE 0.018 0.001 PHE B 75 TYR 0.014 0.001 TYR B 630 ARG 0.009 0.001 ARG A 444 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 450) hydrogen bonds : angle 4.15555 ( 1317) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.90016 ( 4) covalent geometry : bond 0.00471 ( 9924) covalent geometry : angle 0.65117 (13434) Misc. bond : bond 0.00067 ( 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 139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 1.150 Fit side-chains REVERT: A 164 LYS cc_start: 0.7882 (mtpp) cc_final: 0.7610 (mmtp) REVERT: A 175 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8488 (mp) REVERT: A 236 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: A 300 ASP cc_start: 0.7982 (m-30) cc_final: 0.7602 (m-30) REVERT: A 301 ARG cc_start: 0.8296 (ttm170) cc_final: 0.8033 (ttm170) REVERT: A 367 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.7081 (pmm) REVERT: A 389 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5669 (mptm) REVERT: A 511 MET cc_start: 0.8360 (mtm) cc_final: 0.7714 (mmt) REVERT: A 588 VAL cc_start: 0.8201 (p) cc_final: 0.7880 (t) REVERT: A 666 MET cc_start: 0.7691 (mmm) cc_final: 0.7440 (mtp) REVERT: A 680 MET cc_start: 0.7120 (mmt) cc_final: 0.6625 (mmm) REVERT: B 175 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8448 (mp) REVERT: B 301 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7971 (ttm170) REVERT: B 389 LYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5706 (mptm) REVERT: B 444 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7494 (mtm110) REVERT: B 511 MET cc_start: 0.8362 (mtm) cc_final: 0.7718 (mmt) REVERT: B 588 VAL cc_start: 0.8229 (p) cc_final: 0.7895 (t) REVERT: B 666 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7402 (mmm) REVERT: B 680 MET cc_start: 0.6983 (mmm) cc_final: 0.6732 (mmm) outliers start: 36 outliers final: 14 residues processed: 125 average time/residue: 1.1581 time to fit residues: 156.2587 Evaluate side-chains 122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 389 LYS 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 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 85 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 0.0170 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.187805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117418 restraints weight = 8777.311| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.63 r_work: 0.2799 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2342 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= 0.172 Angle : 0.628 7.068 13438 Z= 0.319 Chirality : 0.043 0.219 1550 Planarity : 0.004 0.045 1664 Dihedral : 8.007 137.688 1348 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.60 % Allowed : 12.59 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.25), residues: 1212 helix: 0.21 (0.20), residues: 698 sheet: -1.99 (0.52), residues: 86 loop : -1.73 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 572 HIS 0.004 0.001 HIS A 528 PHE 0.016 0.001 PHE A 75 TYR 0.013 0.001 TYR A 630 ARG 0.009 0.000 ARG A 444 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 450) hydrogen bonds : angle 4.03040 ( 1317) SS BOND : bond 0.00165 ( 2) SS BOND : angle 0.82342 ( 4) covalent geometry : bond 0.00418 ( 9924) covalent geometry : angle 0.62814 (13434) Misc. bond : bond 0.00058 ( 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 137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 1.114 Fit side-chains REVERT: A 175 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 196 ARG cc_start: 0.8013 (ptm160) cc_final: 0.6740 (tpt-90) REVERT: A 236 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: A 301 ARG cc_start: 0.8353 (ttm170) cc_final: 0.8086 (ttm170) REVERT: A 367 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7129 (pmm) REVERT: A 389 LYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5639 (mptm) REVERT: A 511 MET cc_start: 0.8293 (mtm) cc_final: 0.7663 (mmt) REVERT: A 588 VAL cc_start: 0.8195 (p) cc_final: 0.7860 (t) REVERT: A 666 MET cc_start: 0.7692 (mmm) cc_final: 0.7445 (mtp) REVERT: A 680 MET cc_start: 0.7192 (mmt) cc_final: 0.6703 (mmm) REVERT: B 175 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8491 (mp) REVERT: B 196 ARG cc_start: 0.8022 (ptm160) cc_final: 0.6754 (tpt-90) REVERT: B 301 ARG cc_start: 0.8263 (ttm170) cc_final: 0.7778 (ttm170) REVERT: B 389 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5748 (mptm) REVERT: B 444 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7504 (mtm110) REVERT: B 511 MET cc_start: 0.8280 (mtm) cc_final: 0.7651 (mmt) REVERT: B 588 VAL cc_start: 0.8234 (p) cc_final: 0.7897 (t) REVERT: B 666 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7412 (mmm) outliers start: 38 outliers final: 18 residues processed: 122 average time/residue: 1.1219 time to fit residues: 148.1565 Evaluate side-chains 123 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 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 389 LYS 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 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 666 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 80 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.187932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117512 restraints weight = 8789.794| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.64 r_work: 0.2829 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2420 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= 0.161 Angle : 0.625 9.458 13438 Z= 0.315 Chirality : 0.042 0.212 1550 Planarity : 0.004 0.046 1664 Dihedral : 7.942 137.444 1348 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 3.31 % Allowed : 13.54 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1212 helix: 0.36 (0.20), residues: 700 sheet: -1.93 (0.53), residues: 86 loop : -1.70 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 572 HIS 0.003 0.001 HIS B 528 PHE 0.016 0.001 PHE B 75 TYR 0.013 0.001 TYR A 630 ARG 0.011 0.001 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 450) hydrogen bonds : angle 3.95496 ( 1317) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.80463 ( 4) covalent geometry : bond 0.00391 ( 9924) covalent geometry : angle 0.62503 (13434) Misc. bond : bond 0.00053 ( 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 137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 1.162 Fit side-chains REVERT: A 175 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8486 (mp) REVERT: A 196 ARG cc_start: 0.8051 (ptm160) cc_final: 0.6808 (tpt-90) REVERT: A 236 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: A 367 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7249 (pmm) REVERT: A 389 LYS cc_start: 0.6181 (OUTLIER) cc_final: 0.5684 (mptm) REVERT: A 511 MET cc_start: 0.8296 (mtm) cc_final: 0.7679 (mmt) REVERT: A 588 VAL cc_start: 0.8194 (p) cc_final: 0.7883 (t) REVERT: A 666 MET cc_start: 0.7781 (mmm) cc_final: 0.7501 (mtp) REVERT: A 680 MET cc_start: 0.7231 (mmt) cc_final: 0.6745 (mmm) REVERT: B 175 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8506 (mp) REVERT: B 196 ARG cc_start: 0.8049 (ptm160) cc_final: 0.6801 (tpt-90) REVERT: B 301 ARG cc_start: 0.8270 (ttm170) cc_final: 0.7811 (ttm170) REVERT: B 389 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.5771 (mptm) REVERT: B 444 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7593 (mtm110) REVERT: B 511 MET cc_start: 0.8288 (mtm) cc_final: 0.7672 (mmt) REVERT: B 588 VAL cc_start: 0.8227 (p) cc_final: 0.7910 (t) REVERT: B 666 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7450 (mmm) outliers start: 35 outliers final: 18 residues processed: 127 average time/residue: 1.2701 time to fit residues: 174.4806 Evaluate side-chains 124 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 389 LYS 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 162 MET 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 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 43 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 112 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.181155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.111625 restraints weight = 8946.428| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.77 r_work: 0.2709 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2482 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= 0.213 Angle : 0.668 8.597 13438 Z= 0.337 Chirality : 0.044 0.213 1550 Planarity : 0.004 0.048 1664 Dihedral : 8.037 136.618 1348 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 3.60 % Allowed : 14.02 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1212 helix: 0.28 (0.20), residues: 700 sheet: -1.91 (0.54), residues: 86 loop : -1.68 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.004 0.001 HIS B 528 PHE 0.018 0.002 PHE A 75 TYR 0.015 0.001 TYR B 630 ARG 0.012 0.001 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 450) hydrogen bonds : angle 4.04621 ( 1317) SS BOND : bond 0.00228 ( 2) SS BOND : angle 0.90220 ( 4) covalent geometry : bond 0.00526 ( 9924) covalent geometry : angle 0.66816 (13434) Misc. bond : bond 0.00075 ( 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 144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 1.321 Fit side-chains REVERT: A 175 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8490 (mp) REVERT: A 236 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: A 301 ARG cc_start: 0.8384 (ttm170) cc_final: 0.7806 (ttm110) REVERT: A 367 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7136 (pmm) REVERT: A 389 LYS cc_start: 0.6154 (OUTLIER) cc_final: 0.5631 (mptm) REVERT: A 511 MET cc_start: 0.8390 (mtm) cc_final: 0.7721 (mmt) REVERT: A 588 VAL cc_start: 0.8223 (p) cc_final: 0.7904 (t) REVERT: A 666 MET cc_start: 0.7852 (mmm) cc_final: 0.7551 (mtp) REVERT: A 680 MET cc_start: 0.7191 (mmt) cc_final: 0.6687 (mmm) REVERT: B 175 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8500 (mp) REVERT: B 301 ARG cc_start: 0.8287 (ttm170) cc_final: 0.7947 (ttm170) REVERT: B 389 LYS cc_start: 0.6265 (OUTLIER) cc_final: 0.5710 (mptm) REVERT: B 444 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7609 (mtm110) REVERT: B 511 MET cc_start: 0.8364 (mtm) cc_final: 0.7703 (mmt) REVERT: B 588 VAL cc_start: 0.8272 (p) cc_final: 0.7938 (t) REVERT: B 666 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7472 (mmm) outliers start: 38 outliers final: 23 residues processed: 134 average time/residue: 1.3456 time to fit residues: 196.2263 Evaluate side-chains 134 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 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 389 LYS 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 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 153 LEU 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 321 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 116 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.187996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116889 restraints weight = 8895.486| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.69 r_work: 0.2799 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9930 Z= 0.131 Angle : 0.605 8.260 13438 Z= 0.305 Chirality : 0.042 0.214 1550 Planarity : 0.004 0.055 1664 Dihedral : 7.837 137.551 1348 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.12 % Allowed : 14.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1212 helix: 0.67 (0.21), residues: 690 sheet: -1.89 (0.53), residues: 86 loop : -1.62 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.003 0.001 HIS A 528 PHE 0.015 0.001 PHE A 75 TYR 0.012 0.001 TYR B 630 ARG 0.013 0.000 ARG A 444 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 450) hydrogen bonds : angle 3.83784 ( 1317) SS BOND : bond 0.00165 ( 2) SS BOND : angle 0.74744 ( 4) covalent geometry : bond 0.00313 ( 9924) covalent geometry : angle 0.60509 (13434) Misc. bond : bond 0.00040 ( 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 135 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.303 Fit side-chains REVERT: A 175 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8394 (mp) REVERT: A 236 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: A 301 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7664 (ttm110) REVERT: A 367 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7219 (pmm) REVERT: A 389 LYS cc_start: 0.6060 (OUTLIER) cc_final: 0.5567 (mptm) REVERT: A 511 MET cc_start: 0.8261 (mtm) cc_final: 0.7588 (mmt) REVERT: A 588 VAL cc_start: 0.8096 (p) cc_final: 0.7766 (t) REVERT: A 645 GLU cc_start: 0.7731 (tp30) cc_final: 0.6678 (pt0) REVERT: A 666 MET cc_start: 0.7803 (mmm) cc_final: 0.7488 (mtp) REVERT: A 680 MET cc_start: 0.7188 (mmt) cc_final: 0.6695 (mmm) REVERT: B 175 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8407 (mp) REVERT: B 236 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: B 301 ARG cc_start: 0.8259 (ttm170) cc_final: 0.8050 (ttm170) REVERT: B 444 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7536 (mtm110) REVERT: B 511 MET cc_start: 0.8255 (mtm) cc_final: 0.7586 (mmt) REVERT: B 588 VAL cc_start: 0.8119 (p) cc_final: 0.7782 (t) REVERT: B 659 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5758 (pp) REVERT: B 666 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7417 (mmm) outliers start: 33 outliers final: 18 residues processed: 126 average time/residue: 1.2910 time to fit residues: 175.8157 Evaluate side-chains 122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 367 MET Chi-restraints excluded: chain A residue 389 LYS 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 175 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 433 LYS 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 659 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 91 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.189246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.118490 restraints weight = 8751.977| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.68 r_work: 0.2821 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9930 Z= 0.117 Angle : 0.593 7.850 13438 Z= 0.298 Chirality : 0.041 0.212 1550 Planarity : 0.004 0.062 1664 Dihedral : 7.694 136.349 1348 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.75 % Allowed : 15.81 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1212 helix: 0.95 (0.21), residues: 688 sheet: -1.73 (0.55), residues: 84 loop : -1.58 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.002 0.001 HIS A 528 PHE 0.013 0.001 PHE A 75 TYR 0.011 0.001 TYR B 630 ARG 0.014 0.001 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 450) hydrogen bonds : angle 3.73607 ( 1317) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.70045 ( 4) covalent geometry : bond 0.00275 ( 9924) covalent geometry : angle 0.59319 (13434) Misc. bond : bond 0.00042 ( 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 135 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 1.126 Fit side-chains REVERT: A 300 ASP cc_start: 0.7925 (m-30) cc_final: 0.7505 (m-30) REVERT: A 301 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7697 (mtm180) REVERT: A 389 LYS cc_start: 0.6205 (OUTLIER) cc_final: 0.5747 (mptm) REVERT: A 511 MET cc_start: 0.8189 (mtm) cc_final: 0.7558 (mmt) REVERT: A 645 GLU cc_start: 0.7696 (tp30) cc_final: 0.6671 (pt0) REVERT: A 666 MET cc_start: 0.7719 (mmm) cc_final: 0.7404 (mtp) REVERT: A 680 MET cc_start: 0.7175 (mmt) cc_final: 0.6698 (mmm) REVERT: B 116 ARG cc_start: 0.7360 (mtp-110) cc_final: 0.6617 (ttm110) REVERT: B 162 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7339 (ttp) REVERT: B 164 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6799 (mmtp) REVERT: B 196 ARG cc_start: 0.7878 (ptm160) cc_final: 0.6640 (tpt-90) REVERT: B 236 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: B 389 LYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5650 (mptm) REVERT: B 444 ARG cc_start: 0.7828 (ttp-170) cc_final: 0.7575 (mtm110) REVERT: B 511 MET cc_start: 0.8225 (mtm) cc_final: 0.7540 (mmt) REVERT: B 666 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7366 (mmm) outliers start: 29 outliers final: 14 residues processed: 122 average time/residue: 1.2091 time to fit residues: 159.4150 Evaluate side-chains 120 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 389 LYS 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 153 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 236 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 66 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 112 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.189447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119435 restraints weight = 8898.832| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.86 r_work: 0.2874 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2719 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= 0.116 Angle : 0.591 7.815 13438 Z= 0.296 Chirality : 0.041 0.211 1550 Planarity : 0.004 0.062 1664 Dihedral : 7.669 136.142 1348 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.27 % Allowed : 16.57 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1212 helix: 1.09 (0.21), residues: 688 sheet: -1.65 (0.55), residues: 84 loop : -1.60 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.002 0.001 HIS A 528 PHE 0.013 0.001 PHE A 75 TYR 0.011 0.001 TYR B 630 ARG 0.014 0.001 ARG A 444 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 450) hydrogen bonds : angle 3.69697 ( 1317) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.69378 ( 4) covalent geometry : bond 0.00273 ( 9924) covalent geometry : angle 0.59060 (13434) Misc. bond : bond 0.00036 ( 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 123 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.249 Fit side-chains REVERT: A 116 ARG cc_start: 0.7400 (mtp-110) cc_final: 0.6623 (ttm110) REVERT: A 196 ARG cc_start: 0.7903 (ptm160) cc_final: 0.6609 (tpt-90) REVERT: A 300 ASP cc_start: 0.7962 (m-30) cc_final: 0.7552 (m-30) REVERT: A 389 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5735 (mptm) REVERT: A 511 MET cc_start: 0.8221 (mtm) cc_final: 0.7556 (mmt) REVERT: A 645 GLU cc_start: 0.7705 (tp30) cc_final: 0.6670 (pt0) REVERT: A 666 MET cc_start: 0.7771 (mmm) cc_final: 0.7399 (mtp) REVERT: A 680 MET cc_start: 0.7221 (mmt) cc_final: 0.6730 (mmm) REVERT: B 116 ARG cc_start: 0.7286 (mtp-110) cc_final: 0.6564 (ttm110) REVERT: B 162 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7439 (ttp) REVERT: B 164 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6780 (mmtp) REVERT: B 171 MET cc_start: 0.8782 (mmm) cc_final: 0.8385 (mmp) REVERT: B 196 ARG cc_start: 0.7867 (ptm160) cc_final: 0.6624 (tpt-90) REVERT: B 300 ASP cc_start: 0.7957 (m-30) cc_final: 0.7556 (m-30) REVERT: B 301 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7615 (ttm110) REVERT: B 389 LYS cc_start: 0.6129 (OUTLIER) cc_final: 0.5664 (mptm) REVERT: B 444 ARG cc_start: 0.7789 (ttp-170) cc_final: 0.7561 (mtm110) REVERT: B 511 MET cc_start: 0.8212 (mtm) cc_final: 0.7549 (mmt) REVERT: B 666 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7313 (mmm) outliers start: 24 outliers final: 14 residues processed: 113 average time/residue: 1.4180 time to fit residues: 172.5883 Evaluate side-chains 113 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 389 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 153 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 164 LYS 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 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 82 optimal weight: 0.9980 chunk 77 optimal weight: 0.0370 chunk 72 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.0030 chunk 86 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 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 = 0.190343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119987 restraints weight = 8822.653| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.69 r_work: 0.2913 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9930 Z= 0.107 Angle : 0.584 7.627 13438 Z= 0.292 Chirality : 0.041 0.211 1550 Planarity : 0.004 0.063 1664 Dihedral : 7.580 135.600 1348 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.18 % Allowed : 17.33 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1212 helix: 1.24 (0.21), residues: 684 sheet: -1.57 (0.56), residues: 84 loop : -1.63 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.002 0.001 HIS A 528 PHE 0.012 0.001 PHE B 75 TYR 0.010 0.001 TYR A 630 ARG 0.014 0.001 ARG A 444 Details of bonding type rmsd hydrogen bonds : bond 0.02999 ( 450) hydrogen bonds : angle 3.67417 ( 1317) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.63710 ( 4) covalent geometry : bond 0.00249 ( 9924) covalent geometry : angle 0.58378 (13434) Misc. bond : bond 0.00035 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7702.26 seconds wall clock time: 136 minutes 6.09 seconds (8166.09 seconds total)