Starting phenix.real_space_refine on Tue Jul 29 02:58:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpb_43406/07_2025/8vpb_43406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpb_43406/07_2025/8vpb_43406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vpb_43406/07_2025/8vpb_43406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpb_43406/07_2025/8vpb_43406.map" model { file = "/net/cci-nas-00/data/ceres_data/8vpb_43406/07_2025/8vpb_43406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpb_43406/07_2025/8vpb_43406.cif" } resolution = 3.23 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 7064 2.51 5 N 1784 2.21 5 O 2018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10928 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5436 Classifications: {'peptide': 697} Link IDs: {'PTRANS': 13, 'TRANS': 683} Chain breaks: 2 Chain: "B" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5436 Classifications: {'peptide': 697} Link IDs: {'PTRANS': 13, 'TRANS': 683} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.80, per 1000 atoms: 0.71 Number of scatterers: 10928 At special positions: 0 Unit cell: (94.462, 111.284, 135.87, 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) S 56 16.00 P 4 15.00 Mg 2 11.99 O 2018 8.00 N 1784 7.00 C 7064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2588 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 65.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 38 through 47 removed outlier: 3.523A pdb=" N GLY A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 75 through 81 Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.552A pdb=" N LYS A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 166 through 187 removed outlier: 3.749A pdb=" N LEU A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.666A pdb=" N ASP A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 203 through 251 Processing helix chain 'A' and resid 254 through 259 removed outlier: 4.155A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 259' Processing helix chain 'A' and resid 262 through 305 removed outlier: 4.954A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 353 removed outlier: 3.584A pdb=" N PHE A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.788A pdb=" N ILE A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 417 removed outlier: 3.569A pdb=" N THR A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 443 removed outlier: 3.945A pdb=" N LEU A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Proline residue: A 438 - end of helix Processing helix chain 'A' and resid 445 through 464 removed outlier: 3.608A pdb=" N GLN A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N THR A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.538A pdb=" N LEU A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.582A pdb=" N ILE A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 581 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.502A pdb=" N ILE A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 608 Processing helix chain 'A' and resid 626 through 639 Processing helix chain 'A' and resid 654 through 667 removed outlier: 3.520A pdb=" N GLY A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 removed outlier: 3.646A pdb=" N ILE A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 710 removed outlier: 3.678A pdb=" N ALA A 709 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.967A pdb=" N ILE B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 82 removed outlier: 3.760A pdb=" N LEU B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 167 through 188 removed outlier: 3.617A pdb=" N ALA B 175 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.671A pdb=" N ASP B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 203 through 251 Processing helix chain 'B' and resid 254 through 259 removed outlier: 3.969A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 305 removed outlier: 4.887A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 354 Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 354 through 360 removed outlier: 3.548A pdb=" N ILE B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 417 removed outlier: 3.663A pdb=" N THR B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 444 removed outlier: 4.131A pdb=" N LEU B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Proline residue: B 438 - end of helix Processing helix chain 'B' and resid 445 through 464 removed outlier: 4.267A pdb=" N ILE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 removed outlier: 3.587A pdb=" N ARG B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 533 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 575 through 581 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.887A pdb=" N ILE B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 608 Processing helix chain 'B' and resid 626 through 639 Processing helix chain 'B' and resid 649 through 653 removed outlier: 3.590A pdb=" N ASN B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 703 through 710 Processing helix chain 'B' and resid 712 through 722 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 7.426A pdb=" N LYS A 36 " --> pdb=" O TYR A 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 73 removed outlier: 5.973A pdb=" N GLY A 135 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 90 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A 112 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE A 106 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 111 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 123 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509 Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 494 removed outlier: 6.603A pdb=" N PHE A 493 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 562 through 565 removed outlier: 6.150A pdb=" N ALA A 563 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ASP A 647 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 565 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU A 644 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE A 677 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 646 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 519 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 692 " --> pdb=" O GLU A 700 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLU A 700 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 removed outlier: 7.143A pdb=" N LYS B 36 " --> pdb=" O TYR B 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 73 removed outlier: 5.446A pdb=" N GLY B 135 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA B 87 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL B 102 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR B 112 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE B 106 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 500 through 509 removed outlier: 6.980A pdb=" N VAL B 501 " --> pdb=" O ARG B 494 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ARG B 494 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS B 503 " --> pdb=" O ASP B 492 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP B 492 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 505 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN B 490 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 562 through 565 removed outlier: 6.434A pdb=" N ALA B 563 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ASP B 647 " --> pdb=" O ALA B 563 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 565 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B 644 " --> pdb=" O ILE B 675 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE B 677 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 646 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 516 " --> pdb=" O LYS B 689 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU B 700 " --> pdb=" O LEU B 692 " (cutoff:3.500A) 685 hydrogen bonds defined for protein. 2010 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: 3.91 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3198 1.34 - 1.46: 1505 1.46 - 1.57: 6293 1.57 - 1.69: 6 1.69 - 1.81: 96 Bond restraints: 11098 Sorted by residual: bond pdb=" CA SER A 566 " pdb=" C SER A 566 " ideal model delta sigma weight residual 1.528 1.476 0.052 1.37e-02 5.33e+03 1.41e+01 bond pdb=" CA ASP A 568 " pdb=" C ASP A 568 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.34e-02 5.57e+03 5.42e+00 bond pdb=" CA LEU A 610 " pdb=" C LEU A 610 " ideal model delta sigma weight residual 1.532 1.510 0.022 1.12e-02 7.97e+03 3.88e+00 bond pdb=" C ASP A 568 " pdb=" O ASP A 568 " ideal model delta sigma weight residual 1.235 1.217 0.019 1.26e-02 6.30e+03 2.21e+00 bond pdb=" C LEU A 608 " pdb=" N PRO A 609 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.33e-02 5.65e+03 2.00e+00 ... (remaining 11093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 14646 1.44 - 2.87: 226 2.87 - 4.31: 59 4.31 - 5.75: 30 5.75 - 7.19: 7 Bond angle restraints: 14968 Sorted by residual: angle pdb=" N SER A 566 " pdb=" CA SER A 566 " pdb=" C SER A 566 " ideal model delta sigma weight residual 110.53 115.21 -4.68 1.29e+00 6.01e-01 1.32e+01 angle pdb=" N VAL A 569 " pdb=" CA VAL A 569 " pdb=" C VAL A 569 " ideal model delta sigma weight residual 109.51 113.99 -4.48 1.43e+00 4.89e-01 9.80e+00 angle pdb=" CA GLU B 245 " pdb=" CB GLU B 245 " pdb=" CG GLU B 245 " ideal model delta sigma weight residual 114.10 119.97 -5.87 2.00e+00 2.50e-01 8.61e+00 angle pdb=" C LEU A 610 " pdb=" CA LEU A 610 " pdb=" CB LEU A 610 " ideal model delta sigma weight residual 116.34 112.37 3.97 1.40e+00 5.10e-01 8.06e+00 angle pdb=" CA TYR A 714 " pdb=" CB TYR A 714 " pdb=" CG TYR A 714 " ideal model delta sigma weight residual 113.90 118.95 -5.05 1.80e+00 3.09e-01 7.87e+00 ... (remaining 14963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5800 17.86 - 35.72: 729 35.72 - 53.57: 134 53.57 - 71.43: 31 71.43 - 89.29: 4 Dihedral angle restraints: 6698 sinusoidal: 2674 harmonic: 4024 Sorted by residual: dihedral pdb=" CA SER A 360 " pdb=" C SER A 360 " pdb=" N PHE A 361 " pdb=" CA PHE A 361 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA VAL B 685 " pdb=" C VAL B 685 " pdb=" N ASN B 686 " pdb=" CA ASN B 686 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA SER A 421 " pdb=" C SER A 421 " pdb=" N GLY A 422 " pdb=" CA GLY A 422 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 6695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1313 0.039 - 0.077: 333 0.077 - 0.116: 108 0.116 - 0.155: 18 0.155 - 0.193: 2 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CB ILE B 92 " pdb=" CA ILE B 92 " pdb=" CG1 ILE B 92 " pdb=" CG2 ILE B 92 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CG LEU A 637 " pdb=" CB LEU A 637 " pdb=" CD1 LEU A 637 " pdb=" CD2 LEU A 637 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE B 543 " pdb=" N ILE B 543 " pdb=" C ILE B 543 " pdb=" CB ILE B 543 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1771 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 565 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C VAL A 565 " -0.066 2.00e-02 2.50e+03 pdb=" O VAL A 565 " 0.025 2.00e-02 2.50e+03 pdb=" N SER A 566 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 608 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO A 609 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 609 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 609 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 20 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.45e+00 pdb=" CG ASP A 20 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP A 20 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 20 " -0.010 2.00e-02 2.50e+03 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 100 2.61 - 3.18: 9622 3.18 - 3.76: 17000 3.76 - 4.33: 21946 4.33 - 4.90: 37200 Nonbonded interactions: 85868 Sorted by model distance: nonbonded pdb=" OG1 THR A 526 " pdb="MG MG A 802 " model vdw 2.041 2.170 nonbonded pdb=" OG1 THR B 526 " pdb="MG MG B 802 " model vdw 2.063 2.170 nonbonded pdb=" O3B ADP B 801 " pdb="MG MG B 802 " model vdw 2.121 2.170 nonbonded pdb=" O1B ADP A 801 " pdb="MG MG A 802 " model vdw 2.170 2.170 nonbonded pdb=" NZ LYS A 525 " pdb="MG MG A 802 " model vdw 2.185 2.250 ... (remaining 85863 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.100 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 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 : 0.002 0.052 11098 Z= 0.127 Angle : 0.535 7.187 14968 Z= 0.276 Chirality : 0.040 0.193 1774 Planarity : 0.003 0.041 1846 Dihedral : 15.784 89.288 4110 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.17 % Allowed : 22.15 % Favored : 77.68 % 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: 0.83 (0.23), residues: 1382 helix: 1.60 (0.19), residues: 810 sheet: 0.09 (0.44), residues: 142 loop : -1.33 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.009 0.001 HIS A 60 PHE 0.011 0.001 PHE B 535 TYR 0.011 0.001 TYR A 225 ARG 0.001 0.000 ARG B 630 Details of bonding type rmsd hydrogen bonds : bond 0.15063 ( 685) hydrogen bonds : angle 5.58312 ( 2010) covalent geometry : bond 0.00235 (11098) covalent geometry : angle 0.53522 (14968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 1.118 Fit side-chains REVERT: B 691 TYR cc_start: 0.7333 (m-80) cc_final: 0.6816 (m-80) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 0.2021 time to fit residues: 47.5291 Evaluate side-chains 144 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A 704 HIS B 660 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.187382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124516 restraints weight = 14728.954| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.75 r_work: 0.3468 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11098 Z= 0.122 Angle : 0.524 8.457 14968 Z= 0.266 Chirality : 0.040 0.159 1774 Planarity : 0.003 0.043 1846 Dihedral : 4.409 29.777 1498 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.27 % Allowed : 20.05 % Favored : 76.68 % 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: 1.05 (0.23), residues: 1382 helix: 1.70 (0.18), residues: 848 sheet: 0.40 (0.46), residues: 124 loop : -1.36 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 718 HIS 0.006 0.001 HIS A 60 PHE 0.011 0.001 PHE A 194 TYR 0.014 0.001 TYR B 32 ARG 0.002 0.000 ARG B 269 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 685) hydrogen bonds : angle 4.33840 ( 2010) covalent geometry : bond 0.00260 (11098) covalent geometry : angle 0.52402 (14968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.093 Fit side-chains REVERT: A 100 PHE cc_start: 0.6484 (m-80) cc_final: 0.6238 (m-80) REVERT: A 434 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.5508 (t80) REVERT: A 648 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5856 (tm-30) REVERT: B 152 GLN cc_start: 0.7983 (tt0) cc_final: 0.7493 (tm-30) REVERT: B 265 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7905 (tt0) REVERT: B 588 ASP cc_start: 0.8148 (t0) cc_final: 0.7936 (t0) REVERT: B 598 MET cc_start: 0.7924 (tpp) cc_final: 0.7660 (tpp) REVERT: B 691 TYR cc_start: 0.7045 (m-80) cc_final: 0.6789 (m-80) outliers start: 39 outliers final: 19 residues processed: 186 average time/residue: 0.1823 time to fit residues: 51.4988 Evaluate side-chains 174 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 10 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 629 GLN A 652 ASN B 660 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.186088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.122895 restraints weight = 14880.253| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.73 r_work: 0.3444 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11098 Z= 0.134 Angle : 0.531 10.827 14968 Z= 0.267 Chirality : 0.040 0.166 1774 Planarity : 0.003 0.039 1846 Dihedral : 4.432 29.323 1498 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.69 % Allowed : 21.22 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.07 (0.23), residues: 1382 helix: 1.69 (0.18), residues: 852 sheet: 0.45 (0.47), residues: 124 loop : -1.33 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 718 HIS 0.005 0.001 HIS A 60 PHE 0.011 0.001 PHE A 194 TYR 0.012 0.001 TYR B 225 ARG 0.001 0.000 ARG B 269 Details of bonding type rmsd hydrogen bonds : bond 0.04906 ( 685) hydrogen bonds : angle 4.29031 ( 2010) covalent geometry : bond 0.00297 (11098) covalent geometry : angle 0.53059 (14968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.6621 (m-80) cc_final: 0.6385 (m-80) REVERT: A 434 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.5642 (t80) REVERT: A 648 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: B 152 GLN cc_start: 0.7989 (tt0) cc_final: 0.7502 (tm-30) REVERT: B 265 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7917 (tt0) REVERT: B 691 TYR cc_start: 0.7045 (m-80) cc_final: 0.6742 (m-80) REVERT: B 717 MET cc_start: 0.8500 (mmm) cc_final: 0.7472 (ttm) outliers start: 44 outliers final: 27 residues processed: 184 average time/residue: 0.1853 time to fit residues: 51.6222 Evaluate side-chains 178 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 135 optimal weight: 0.0370 chunk 6 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 128 optimal weight: 0.0170 chunk 52 optimal weight: 0.9980 overall best weight: 1.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN B 659 ASN B 660 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.183727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119696 restraints weight = 14696.677| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.72 r_work: 0.3404 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11098 Z= 0.167 Angle : 0.561 11.918 14968 Z= 0.283 Chirality : 0.041 0.160 1774 Planarity : 0.003 0.037 1846 Dihedral : 4.539 30.708 1498 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.61 % Allowed : 20.47 % Favored : 74.92 % 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: 0.96 (0.23), residues: 1382 helix: 1.59 (0.18), residues: 850 sheet: 0.40 (0.47), residues: 124 loop : -1.31 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 132 HIS 0.006 0.001 HIS A 60 PHE 0.014 0.001 PHE A 194 TYR 0.014 0.001 TYR B 225 ARG 0.002 0.000 ARG B 269 Details of bonding type rmsd hydrogen bonds : bond 0.05237 ( 685) hydrogen bonds : angle 4.38112 ( 2010) covalent geometry : bond 0.00389 (11098) covalent geometry : angle 0.56104 (14968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: A 434 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.5645 (t80) REVERT: A 629 GLN cc_start: 0.8742 (pt0) cc_final: 0.8392 (mt0) REVERT: A 648 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6051 (tm-30) REVERT: B 434 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.5805 (t80) REVERT: B 598 MET cc_start: 0.7907 (tpp) cc_final: 0.7673 (tpp) REVERT: B 691 TYR cc_start: 0.7067 (m-80) cc_final: 0.6747 (m-80) outliers start: 55 outliers final: 35 residues processed: 194 average time/residue: 0.1886 time to fit residues: 56.1064 Evaluate side-chains 183 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 80 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 629 GLN B 152 GLN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.186173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123103 restraints weight = 14640.902| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.71 r_work: 0.3446 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11098 Z= 0.121 Angle : 0.534 13.269 14968 Z= 0.266 Chirality : 0.040 0.159 1774 Planarity : 0.003 0.038 1846 Dihedral : 4.436 29.241 1498 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.52 % Allowed : 21.81 % Favored : 74.66 % 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: 1.06 (0.23), residues: 1382 helix: 1.65 (0.18), residues: 862 sheet: 0.41 (0.47), residues: 128 loop : -1.36 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 132 HIS 0.007 0.001 HIS A 60 PHE 0.008 0.001 PHE A 428 TYR 0.012 0.001 TYR A 225 ARG 0.001 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 685) hydrogen bonds : angle 4.22663 ( 2010) covalent geometry : bond 0.00257 (11098) covalent geometry : angle 0.53353 (14968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6894 (t) REVERT: A 434 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.5639 (t80) REVERT: A 598 MET cc_start: 0.7883 (tpt) cc_final: 0.7633 (tpt) REVERT: A 648 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6166 (tm-30) REVERT: B 265 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7896 (tt0) REVERT: B 434 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.5805 (t80) REVERT: B 630 ARG cc_start: 0.8471 (ptp-110) cc_final: 0.8213 (ptp-110) REVERT: B 691 TYR cc_start: 0.7045 (m-80) cc_final: 0.6758 (m-80) outliers start: 42 outliers final: 30 residues processed: 183 average time/residue: 0.1817 time to fit residues: 51.2518 Evaluate side-chains 182 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 133 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN B 660 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.187758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126663 restraints weight = 14773.497| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.95 r_work: 0.3461 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11098 Z= 0.114 Angle : 0.529 13.525 14968 Z= 0.263 Chirality : 0.040 0.157 1774 Planarity : 0.003 0.038 1846 Dihedral : 4.324 28.948 1498 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.52 % Allowed : 22.57 % Favored : 73.91 % 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: 1.17 (0.23), residues: 1382 helix: 1.76 (0.18), residues: 860 sheet: 0.46 (0.47), residues: 128 loop : -1.34 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 132 HIS 0.007 0.001 HIS A 60 PHE 0.011 0.001 PHE A 570 TYR 0.012 0.001 TYR A 225 ARG 0.001 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 685) hydrogen bonds : angle 4.12066 ( 2010) covalent geometry : bond 0.00235 (11098) covalent geometry : angle 0.52925 (14968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6568 (t) REVERT: A 387 MET cc_start: 0.7641 (tpp) cc_final: 0.7237 (tpt) REVERT: A 434 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.5441 (t80) REVERT: A 598 MET cc_start: 0.7883 (tpt) cc_final: 0.7571 (tpt) REVERT: A 629 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: A 648 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6341 (tt0) REVERT: B 265 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7712 (tt0) REVERT: B 434 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.5551 (t80) REVERT: B 598 MET cc_start: 0.7846 (tpp) cc_final: 0.7634 (tpp) REVERT: B 717 MET cc_start: 0.8486 (mmm) cc_final: 0.7451 (ttm) outliers start: 42 outliers final: 32 residues processed: 184 average time/residue: 0.1839 time to fit residues: 52.1191 Evaluate side-chains 185 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS B 660 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.187422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124981 restraints weight = 14895.657| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.76 r_work: 0.3475 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11098 Z= 0.116 Angle : 0.533 13.513 14968 Z= 0.265 Chirality : 0.040 0.162 1774 Planarity : 0.003 0.038 1846 Dihedral : 4.296 28.905 1498 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.94 % Allowed : 22.99 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.23 (0.23), residues: 1382 helix: 1.80 (0.18), residues: 860 sheet: 0.49 (0.47), residues: 128 loop : -1.32 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 132 HIS 0.009 0.001 HIS A 60 PHE 0.008 0.001 PHE A 570 TYR 0.012 0.001 TYR A 225 ARG 0.001 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 685) hydrogen bonds : angle 4.08788 ( 2010) covalent geometry : bond 0.00246 (11098) covalent geometry : angle 0.53297 (14968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6632 (t) REVERT: A 387 MET cc_start: 0.7798 (tpp) cc_final: 0.7408 (tpt) REVERT: A 434 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.5535 (t80) REVERT: A 598 MET cc_start: 0.7893 (tpt) cc_final: 0.7596 (tpt) REVERT: B 265 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7701 (tt0) REVERT: B 434 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.5674 (t80) REVERT: B 598 MET cc_start: 0.7842 (tpp) cc_final: 0.7621 (tpp) REVERT: B 630 ARG cc_start: 0.8494 (ptp-110) cc_final: 0.8278 (ptp-110) REVERT: B 691 TYR cc_start: 0.6995 (m-80) cc_final: 0.6698 (m-80) outliers start: 47 outliers final: 37 residues processed: 185 average time/residue: 0.1967 time to fit residues: 55.1022 Evaluate side-chains 191 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 52 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN B 659 ASN B 660 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.186277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123517 restraints weight = 14740.471| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.73 r_work: 0.3458 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11098 Z= 0.127 Angle : 0.547 13.563 14968 Z= 0.272 Chirality : 0.040 0.157 1774 Planarity : 0.003 0.037 1846 Dihedral : 4.323 28.967 1498 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.36 % Allowed : 23.74 % Favored : 72.90 % 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: 1.17 (0.23), residues: 1382 helix: 1.75 (0.18), residues: 862 sheet: 0.43 (0.47), residues: 128 loop : -1.31 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 132 HIS 0.009 0.001 HIS A 60 PHE 0.008 0.001 PHE B 435 TYR 0.012 0.001 TYR A 225 ARG 0.002 0.000 ARG B 680 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 685) hydrogen bonds : angle 4.11958 ( 2010) covalent geometry : bond 0.00277 (11098) covalent geometry : angle 0.54694 (14968) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 2.891 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.7412 (OUTLIER) cc_final: 0.6707 (t) REVERT: A 387 MET cc_start: 0.7806 (tpp) cc_final: 0.7414 (tpt) REVERT: A 434 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.5561 (t80) REVERT: A 598 MET cc_start: 0.7943 (tpt) cc_final: 0.7625 (tpt) REVERT: B 434 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.5665 (t80) REVERT: B 598 MET cc_start: 0.7841 (tpp) cc_final: 0.7618 (tpp) REVERT: B 691 TYR cc_start: 0.7031 (m-80) cc_final: 0.6743 (m-80) outliers start: 40 outliers final: 36 residues processed: 182 average time/residue: 0.2204 time to fit residues: 62.2189 Evaluate side-chains 189 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 113 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 100 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 659 ASN B 660 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.186535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.123868 restraints weight = 14943.529| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.75 r_work: 0.3458 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11098 Z= 0.125 Angle : 0.554 14.044 14968 Z= 0.276 Chirality : 0.041 0.195 1774 Planarity : 0.003 0.038 1846 Dihedral : 4.338 28.929 1498 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.78 % Allowed : 23.57 % Favored : 72.65 % 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: 1.17 (0.23), residues: 1382 helix: 1.75 (0.18), residues: 860 sheet: 0.47 (0.47), residues: 128 loop : -1.32 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 132 HIS 0.012 0.001 HIS A 60 PHE 0.008 0.001 PHE B 217 TYR 0.012 0.001 TYR A 225 ARG 0.004 0.000 ARG B 630 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 685) hydrogen bonds : angle 4.15262 ( 2010) covalent geometry : bond 0.00273 (11098) covalent geometry : angle 0.55429 (14968) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6724 (t) REVERT: A 387 MET cc_start: 0.7890 (tpp) cc_final: 0.7496 (tpt) REVERT: A 434 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.5656 (t80) REVERT: A 598 MET cc_start: 0.7927 (tpt) cc_final: 0.7596 (tpt) REVERT: B 265 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7738 (tt0) REVERT: B 434 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.5748 (t80) REVERT: B 598 MET cc_start: 0.7871 (tpp) cc_final: 0.7641 (tpp) REVERT: B 691 TYR cc_start: 0.6999 (m-80) cc_final: 0.6714 (m-80) outliers start: 45 outliers final: 38 residues processed: 178 average time/residue: 0.1807 time to fit residues: 49.6805 Evaluate side-chains 187 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 59 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 65 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN B 629 GLN B 652 ASN B 659 ASN B 660 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.186155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123531 restraints weight = 14772.518| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.73 r_work: 0.3453 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11098 Z= 0.128 Angle : 0.558 13.949 14968 Z= 0.277 Chirality : 0.041 0.161 1774 Planarity : 0.003 0.038 1846 Dihedral : 4.341 28.917 1498 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.69 % Allowed : 23.66 % Favored : 72.65 % 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: 1.16 (0.23), residues: 1382 helix: 1.74 (0.18), residues: 860 sheet: 0.46 (0.48), residues: 128 loop : -1.32 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 132 HIS 0.012 0.001 HIS A 60 PHE 0.008 0.001 PHE B 217 TYR 0.015 0.001 TYR A 714 ARG 0.006 0.000 ARG B 630 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 685) hydrogen bonds : angle 4.15548 ( 2010) covalent geometry : bond 0.00280 (11098) covalent geometry : angle 0.55760 (14968) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6777 (t) REVERT: A 387 MET cc_start: 0.7897 (tpp) cc_final: 0.7502 (tpt) REVERT: A 434 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.5650 (t80) REVERT: A 598 MET cc_start: 0.7935 (tpt) cc_final: 0.7591 (tpt) REVERT: B 434 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.5739 (t80) REVERT: B 691 TYR cc_start: 0.6988 (m-80) cc_final: 0.6713 (m-80) REVERT: B 717 MET cc_start: 0.8424 (mmm) cc_final: 0.7399 (ttm) outliers start: 44 outliers final: 40 residues processed: 178 average time/residue: 0.1808 time to fit residues: 50.0380 Evaluate side-chains 188 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 101 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 125 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN B 534 ASN B 659 ASN B 660 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.179496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114557 restraints weight = 14861.826| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.70 r_work: 0.3336 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 11098 Z= 0.274 Angle : 0.705 13.846 14968 Z= 0.359 Chirality : 0.045 0.159 1774 Planarity : 0.004 0.036 1846 Dihedral : 4.877 33.214 1498 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.94 % Allowed : 23.74 % Favored : 72.32 % 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: 0.43 (0.23), residues: 1382 helix: 1.12 (0.17), residues: 860 sheet: 0.11 (0.47), residues: 128 loop : -1.48 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 409 HIS 0.013 0.002 HIS A 60 PHE 0.022 0.002 PHE A 194 TYR 0.020 0.002 TYR B 225 ARG 0.005 0.000 ARG B 630 Details of bonding type rmsd hydrogen bonds : bond 0.06184 ( 685) hydrogen bonds : angle 4.72776 ( 2010) covalent geometry : bond 0.00655 (11098) covalent geometry : angle 0.70540 (14968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7455.21 seconds wall clock time: 129 minutes 7.88 seconds (7747.88 seconds total)