Starting phenix.real_space_refine on Sun Dec 29 16:40:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpb_43406/12_2024/8vpb_43406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpb_43406/12_2024/8vpb_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_43406/12_2024/8vpb_43406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpb_43406/12_2024/8vpb_43406.map" model { file = "/net/cci-nas-00/data/ceres_data/8vpb_43406/12_2024/8vpb_43406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpb_43406/12_2024/8vpb_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.86, per 1000 atoms: 0.72 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: 2.88 Conformation dependent library (CDL) restraints added in 1.6 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: 1.29 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: 3.88 Time building geometry restraints manager: 3.30 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: 0.00 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.990 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- 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= 0.149 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 *********************** 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 : 1.227 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: 0.2053 time to fit residues: 47.9095 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 : 1.306 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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= 0.167 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 *********************** 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 : 1.129 Fit side-chains REVERT: A 100 PHE cc_start: 0.6778 (m-80) cc_final: 0.6537 (m-80) REVERT: A 434 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.5666 (t80) REVERT: A 648 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5886 (tm-30) REVERT: B 152 GLN cc_start: 0.8104 (tt0) cc_final: 0.7671 (tm-30) REVERT: B 265 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7883 (tt0) REVERT: B 598 MET cc_start: 0.7911 (tpp) cc_final: 0.7594 (tpp) REVERT: B 691 TYR cc_start: 0.7121 (m-80) cc_final: 0.6880 (m-80) outliers start: 39 outliers final: 19 residues processed: 186 average time/residue: 0.1951 time to fit residues: 54.8547 Evaluate side-chains 173 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 69 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 135 optimal weight: 0.0020 chunk 111 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11098 Z= 0.153 Angle : 0.515 10.869 14968 Z= 0.259 Chirality : 0.040 0.168 1774 Planarity : 0.003 0.039 1846 Dihedral : 4.357 29.147 1498 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.02 % Allowed : 21.73 % Favored : 75.25 % 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: 1.18 (0.23), residues: 1382 helix: 1.78 (0.18), residues: 850 sheet: 0.50 (0.46), residues: 124 loop : -1.28 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 718 HIS 0.006 0.001 HIS A 60 PHE 0.008 0.001 PHE A 194 TYR 0.011 0.001 TYR A 225 ARG 0.001 0.000 ARG B 269 *********************** 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 196 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.5701 (t80) REVERT: A 648 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6465 (tm-30) REVERT: B 152 GLN cc_start: 0.8073 (tt0) cc_final: 0.7670 (tm-30) REVERT: B 265 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7868 (tt0) REVERT: B 691 TYR cc_start: 0.7053 (m-80) cc_final: 0.6803 (m-80) REVERT: B 717 MET cc_start: 0.8461 (mmm) cc_final: 0.7456 (ttm) outliers start: 36 outliers final: 21 residues processed: 181 average time/residue: 0.1893 time to fit residues: 52.5901 Evaluate side-chains 176 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 337 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 389 TYR 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 250 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 327 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 13 optimal weight: 0.0570 chunk 59 optimal weight: 0.0070 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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** B 660 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11098 Z= 0.136 Angle : 0.511 12.163 14968 Z= 0.254 Chirality : 0.039 0.162 1774 Planarity : 0.003 0.039 1846 Dihedral : 4.249 28.852 1498 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.27 % Allowed : 21.22 % Favored : 75.50 % 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: 1.26 (0.23), residues: 1382 helix: 1.87 (0.18), residues: 850 sheet: 0.58 (0.47), residues: 128 loop : -1.35 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 132 HIS 0.006 0.001 HIS A 60 PHE 0.014 0.001 PHE A 100 TYR 0.011 0.001 TYR A 225 ARG 0.001 0.000 ARG B 109 *********************** 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 201 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 598 MET cc_start: 0.7946 (tpt) cc_final: 0.7710 (tpt) REVERT: A 648 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6394 (tm-30) REVERT: B 152 GLN cc_start: 0.8056 (tt0) cc_final: 0.7654 (tm-30) REVERT: B 265 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7841 (tt0) REVERT: B 598 MET cc_start: 0.7809 (tpp) cc_final: 0.7566 (tpp) outliers start: 39 outliers final: 26 residues processed: 185 average time/residue: 0.1883 time to fit residues: 52.6196 Evaluate side-chains 182 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 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 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 187 SER 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 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 75 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 629 GLN B 534 ASN B 652 ASN B 659 ASN B 660 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11098 Z= 0.346 Angle : 0.619 12.853 14968 Z= 0.313 Chirality : 0.043 0.159 1774 Planarity : 0.003 0.037 1846 Dihedral : 4.638 31.413 1498 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.36 % Allowed : 21.22 % Favored : 74.41 % 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: 0.81 (0.23), residues: 1382 helix: 1.46 (0.18), residues: 852 sheet: 0.38 (0.47), residues: 124 loop : -1.40 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 132 HIS 0.007 0.001 HIS A 60 PHE 0.020 0.002 PHE A 194 TYR 0.017 0.002 TYR B 225 ARG 0.002 0.000 ARG B 269 *********************** 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 203 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 1.186 Fit side-chains REVERT: A 434 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.6008 (t80) REVERT: A 598 MET cc_start: 0.8014 (tpt) cc_final: 0.7744 (tpt) REVERT: B 434 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.5920 (t80) REVERT: B 691 TYR cc_start: 0.7141 (m-80) cc_final: 0.6867 (m-80) outliers start: 52 outliers final: 38 residues processed: 185 average time/residue: 0.1892 time to fit residues: 53.3441 Evaluate side-chains 184 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 37 MET 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 379 MET 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 553 ILE Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 646 LEU 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 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 345 THR 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 591 GLU Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 681 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 128 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** B 534 ASN B 660 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1518 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= 0.179 Angle : 0.546 12.972 14968 Z= 0.272 Chirality : 0.040 0.159 1774 Planarity : 0.003 0.037 1846 Dihedral : 4.499 29.290 1498 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.86 % Allowed : 22.23 % 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: 1.01 (0.23), residues: 1382 helix: 1.61 (0.18), residues: 864 sheet: 0.40 (0.47), residues: 128 loop : -1.38 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 132 HIS 0.008 0.001 HIS A 60 PHE 0.013 0.001 PHE A 100 TYR 0.012 0.001 TYR A 225 ARG 0.001 0.000 ARG B 109 *********************** 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 199 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7216 (t) REVERT: A 434 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.5758 (t80) REVERT: A 598 MET cc_start: 0.8019 (tpt) cc_final: 0.7660 (tpt) REVERT: A 648 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6518 (tt0) REVERT: B 434 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.5808 (t80) REVERT: B 691 TYR cc_start: 0.7100 (m-80) cc_final: 0.6781 (m-80) REVERT: B 717 MET cc_start: 0.8436 (mmm) cc_final: 0.7461 (ttm) outliers start: 46 outliers final: 35 residues processed: 184 average time/residue: 0.1905 time to fit residues: 53.4975 Evaluate side-chains 182 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 58 LEU 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 352 VAL Chi-restraints excluded: chain A residue 379 MET 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 612 TYR 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 187 SER Chi-restraints excluded: chain B residue 215 VAL 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 327 ASN 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 15 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 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 A 629 GLN B 152 GLN B 600 ASN B 659 ASN B 660 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1551 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= 0.172 Angle : 0.546 13.438 14968 Z= 0.271 Chirality : 0.040 0.157 1774 Planarity : 0.003 0.037 1846 Dihedral : 4.405 29.101 1498 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.86 % Allowed : 22.57 % Favored : 73.57 % 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: 1.10 (0.23), residues: 1382 helix: 1.69 (0.18), residues: 862 sheet: 0.42 (0.47), residues: 128 loop : -1.35 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 132 HIS 0.009 0.001 HIS A 60 PHE 0.025 0.001 PHE B 564 TYR 0.012 0.001 TYR A 225 ARG 0.006 0.000 ARG B 630 *********************** 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 196 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.7571 (OUTLIER) cc_final: 0.6821 (t) REVERT: A 387 MET cc_start: 0.8031 (tpp) cc_final: 0.7608 (tpt) REVERT: A 434 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.5672 (t80) REVERT: A 598 MET cc_start: 0.8063 (tpt) cc_final: 0.7673 (tpt) REVERT: A 648 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6382 (tt0) REVERT: B 265 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7801 (tt0) REVERT: B 434 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.5771 (t80) REVERT: B 598 MET cc_start: 0.7835 (tpp) cc_final: 0.7629 (tpp) REVERT: B 691 TYR cc_start: 0.7033 (m-80) cc_final: 0.6773 (m-80) REVERT: B 717 MET cc_start: 0.8408 (mmm) cc_final: 0.7463 (ttm) outliers start: 46 outliers final: 36 residues processed: 181 average time/residue: 0.1848 time to fit residues: 51.9010 Evaluate side-chains 185 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 58 LEU 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 379 MET 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 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 215 VAL 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 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 53 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 0.0670 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 629 GLN ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN B 652 ASN B 659 ASN B 660 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1608 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= 0.166 Angle : 0.561 13.674 14968 Z= 0.275 Chirality : 0.040 0.156 1774 Planarity : 0.003 0.037 1846 Dihedral : 4.364 29.010 1498 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.78 % Allowed : 22.99 % Favored : 73.24 % 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: 1.12 (0.23), residues: 1382 helix: 1.71 (0.18), residues: 862 sheet: 0.43 (0.47), residues: 128 loop : -1.33 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 132 HIS 0.010 0.001 HIS A 60 PHE 0.022 0.001 PHE B 564 TYR 0.012 0.001 TYR A 225 ARG 0.005 0.000 ARG B 630 *********************** 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: 45 poor density : 150 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6762 (t) REVERT: A 387 MET cc_start: 0.8033 (tpp) cc_final: 0.7618 (tpt) REVERT: A 434 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.5661 (t80) REVERT: A 568 ASP cc_start: 0.8411 (p0) cc_final: 0.8188 (p0) REVERT: A 598 MET cc_start: 0.8053 (tpt) cc_final: 0.7655 (tpt) REVERT: A 648 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6628 (tt0) REVERT: B 434 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.5802 (t80) REVERT: B 598 MET cc_start: 0.7783 (tpp) cc_final: 0.7539 (tpp) REVERT: B 691 TYR cc_start: 0.7019 (m-80) cc_final: 0.6795 (m-80) outliers start: 45 outliers final: 38 residues processed: 177 average time/residue: 0.1848 time to fit residues: 50.5743 Evaluate side-chains 191 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 58 LEU 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 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 514 THR 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 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 316 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN B 660 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11098 Z= 0.248 Angle : 0.599 13.897 14968 Z= 0.296 Chirality : 0.042 0.152 1774 Planarity : 0.003 0.038 1846 Dihedral : 4.486 29.195 1498 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.78 % Allowed : 23.07 % Favored : 73.15 % 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: 1.56 (0.18), residues: 862 sheet: 0.34 (0.47), residues: 128 loop : -1.34 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 132 HIS 0.011 0.001 HIS A 60 PHE 0.020 0.001 PHE A 570 TYR 0.014 0.001 TYR B 225 ARG 0.005 0.000 ARG B 630 *********************** 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 193 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 1.246 Fit side-chains REVERT: A 171 CYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7214 (t) REVERT: A 434 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.5777 (t80) REVERT: A 568 ASP cc_start: 0.8403 (p0) cc_final: 0.8181 (p0) REVERT: A 598 MET cc_start: 0.8074 (tpt) cc_final: 0.7660 (tpt) REVERT: A 648 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6536 (tt0) REVERT: B 434 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.5875 (t80) REVERT: B 598 MET cc_start: 0.7824 (tpp) cc_final: 0.7592 (tpp) REVERT: B 691 TYR cc_start: 0.7059 (m-80) cc_final: 0.6797 (m-80) outliers start: 45 outliers final: 39 residues processed: 178 average time/residue: 0.1792 time to fit residues: 49.5400 Evaluate side-chains 186 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 58 LEU 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 379 MET 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 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 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 187 SER Chi-restraints excluded: chain B residue 215 VAL 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 443 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11098 Z= 0.292 Angle : 0.628 14.525 14968 Z= 0.312 Chirality : 0.042 0.158 1774 Planarity : 0.003 0.037 1846 Dihedral : 4.640 29.422 1498 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.78 % Allowed : 23.24 % Favored : 72.99 % 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: 0.78 (0.23), residues: 1382 helix: 1.40 (0.18), residues: 862 sheet: 0.23 (0.47), residues: 128 loop : -1.33 (0.31), residues: 392 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 0.017 0.002 PHE B 564 TYR 0.016 0.001 TYR A 714 ARG 0.003 0.000 ARG B 630 ********************** 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 190 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 1.207 Fit side-chains REVERT: A 171 CYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7201 (t) REVERT: A 434 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.5853 (t80) REVERT: A 598 MET cc_start: 0.8108 (tpt) cc_final: 0.7596 (tpt) REVERT: B 434 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.5897 (t80) REVERT: B 598 MET cc_start: 0.7877 (tpp) cc_final: 0.7625 (tpp) REVERT: B 691 TYR cc_start: 0.7168 (m-80) cc_final: 0.6868 (m-80) outliers start: 45 outliers final: 40 residues processed: 177 average time/residue: 0.1848 time to fit residues: 50.0737 Evaluate side-chains 183 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 58 LEU 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 379 MET 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 187 SER Chi-restraints excluded: chain B residue 215 VAL 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 443 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 30.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN B 579 ASN ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4293 r_free = 0.4293 target = 0.186242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.123430 restraints weight = 14694.268| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.73 r_work: 0.3451 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1730 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= 0.172 Angle : 0.579 14.709 14968 Z= 0.284 Chirality : 0.041 0.169 1774 Planarity : 0.003 0.038 1846 Dihedral : 4.454 29.109 1498 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.36 % Allowed : 23.91 % Favored : 72.73 % 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: 1.01 (0.23), residues: 1382 helix: 1.61 (0.18), residues: 862 sheet: 0.42 (0.47), residues: 126 loop : -1.36 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 132 HIS 0.012 0.001 HIS A 60 PHE 0.018 0.001 PHE B 564 TYR 0.012 0.001 TYR A 225 ARG 0.003 0.000 ARG B 630 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.81 seconds wall clock time: 45 minutes 33.88 seconds (2733.88 seconds total)