Starting phenix.real_space_refine on Tue Jun 10 02:24:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9azl_44015/06_2025/9azl_44015.cif Found real_map, /net/cci-nas-00/data/ceres_data/9azl_44015/06_2025/9azl_44015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9azl_44015/06_2025/9azl_44015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9azl_44015/06_2025/9azl_44015.map" model { file = "/net/cci-nas-00/data/ceres_data/9azl_44015/06_2025/9azl_44015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9azl_44015/06_2025/9azl_44015.cif" } resolution = 2.99 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= 0.018 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 5 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 7274 2.51 5 N 1833 2.21 5 O 2082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11252 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5572 Classifications: {'peptide': 714} Link IDs: {'PTRANS': 13, 'TRANS': 700} Chain: "B" Number of atoms: 5572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5572 Classifications: {'peptide': 714} Link IDs: {'PTRANS': 13, 'TRANS': 700} 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: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'ADP': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.33, per 1000 atoms: 0.65 Number of scatterers: 11252 At special positions: 0 Unit cell: (87.345, 110.637, 135.223, 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 5 15.00 Mg 2 11.99 O 2082 8.00 N 1833 7.00 C 7274 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: 2.81 Conformation dependent library (CDL) restraints added in 1.5 seconds 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 65.3% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.779A pdb=" N LEU A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 81' Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.746A 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 165 through 187 Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.514A 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: 4.030A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 268 Processing helix chain 'A' and resid 268 through 281 removed outlier: 3.928A pdb=" N ASP A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 305 removed outlier: 3.587A pdb=" N LEU A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 354 removed outlier: 4.665A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 417 removed outlier: 3.707A pdb=" N GLU A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 464 removed outlier: 4.220A pdb=" N ALA A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Proline residue: A 438 - end of helix removed outlier: 4.454A pdb=" N GLN A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Proline residue: A 447 - end of helix removed outlier: 4.286A pdb=" N ILE A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 463 " --> pdb=" O LEU A 459 " (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 Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.514A pdb=" N MET A 598 " --> pdb=" O LYS A 594 " (cutoff:3.500A) removed outlier: 3.590A 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 616 through 621 removed outlier: 3.702A pdb=" N GLY A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 639 Processing helix chain 'A' and resid 654 through 667 Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 703 through 710 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 54 through 65 Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.577A pdb=" N LEU B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 75 through 81' Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 125 through 131 Processing helix chain 'B' and resid 153 through 159 Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 165 through 187 Processing helix chain 'B' and resid 188 through 196 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: 3.855A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 268 Processing helix chain 'B' and resid 268 through 281 removed outlier: 3.558A pdb=" N ASP B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 305 removed outlier: 3.942A pdb=" N ILE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 354 removed outlier: 4.659A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 363 through 418 Processing helix chain 'B' and resid 421 through 464 removed outlier: 4.311A pdb=" N ALA B 433 " --> pdb=" O ASN B 429 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Proline residue: B 438 - end of helix removed outlier: 4.442A pdb=" N GLN B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 4.361A pdb=" N ILE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 removed outlier: 3.679A pdb=" N LEU B 528 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) 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: 3.569A 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 616 through 621 removed outlier: 3.713A pdb=" N GLY B 620 " --> pdb=" O LEU B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 639 Processing helix chain 'B' and resid 654 through 666 Processing helix chain 'B' and resid 680 through 684 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 Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 73 removed outlier: 6.571A pdb=" N THR A 133 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE A 92 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLY A 135 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN A 90 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 87 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 112 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILE A 106 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 502 through 509 removed outlier: 6.709A pdb=" N LYS A 503 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP A 492 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 505 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 490 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 562 through 565 removed outlier: 6.374A pdb=" N ALA A 563 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP A 647 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 565 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU A 644 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE A 677 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 646 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 689 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU A 692 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 73 removed outlier: 7.004A pdb=" N THR B 133 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE B 92 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLY B 135 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN B 90 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 112 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE B 106 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 502 through 509 removed outlier: 6.679A pdb=" N LYS B 503 " --> pdb=" O ASP B 492 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 492 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE B 505 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN B 490 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 562 through 565 removed outlier: 6.388A pdb=" N ALA B 563 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASP B 647 " --> pdb=" O ALA B 563 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 565 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 644 " --> pdb=" O ILE B 675 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE B 677 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 646 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY B 519 " --> pdb=" O ALA B 678 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N THR B 514 " --> pdb=" O LYS B 689 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N TYR B 691 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 516 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU B 693 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL B 518 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU B 700 " --> pdb=" O LEU B 692 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 2085 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: 3.75 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1838 1.31 - 1.43: 2719 1.43 - 1.56: 6766 1.56 - 1.68: 10 1.68 - 1.81: 96 Bond restraints: 11429 Sorted by residual: bond pdb=" C31 POV B 803 " pdb=" O31 POV B 803 " ideal model delta sigma weight residual 1.327 1.409 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C21 POV B 803 " pdb=" O21 POV B 803 " ideal model delta sigma weight residual 1.330 1.403 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" N POV B 803 " pdb=" C12 POV B 803 " ideal model delta sigma weight residual 1.508 1.446 0.062 2.00e-02 2.50e+03 9.70e+00 bond pdb=" N POV B 803 " pdb=" C14 POV B 803 " ideal model delta sigma weight residual 1.490 1.430 0.060 2.00e-02 2.50e+03 9.08e+00 bond pdb=" N POV B 803 " pdb=" C15 POV B 803 " ideal model delta sigma weight residual 1.491 1.436 0.055 2.00e-02 2.50e+03 7.48e+00 ... (remaining 11424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 15265 2.49 - 4.98: 113 4.98 - 7.47: 23 7.47 - 9.96: 8 9.96 - 12.45: 2 Bond angle restraints: 15411 Sorted by residual: angle pdb=" CA LYS B 640 " pdb=" CB LYS B 640 " pdb=" CG LYS B 640 " ideal model delta sigma weight residual 114.10 122.53 -8.43 2.00e+00 2.50e-01 1.78e+01 angle pdb=" O11 POV B 803 " pdb=" P POV B 803 " pdb=" O12 POV B 803 " ideal model delta sigma weight residual 97.67 110.12 -12.45 3.00e+00 1.11e-01 1.72e+01 angle pdb=" CA LYS A 640 " pdb=" CB LYS A 640 " pdb=" CG LYS A 640 " ideal model delta sigma weight residual 114.10 121.80 -7.70 2.00e+00 2.50e-01 1.48e+01 angle pdb=" O13 POV B 803 " pdb=" P POV B 803 " pdb=" O14 POV B 803 " ideal model delta sigma weight residual 121.11 109.60 11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CA ILE B 684 " pdb=" CB ILE B 684 " pdb=" CG1 ILE B 684 " ideal model delta sigma weight residual 110.40 116.91 -6.51 1.70e+00 3.46e-01 1.47e+01 ... (remaining 15406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.24: 6470 25.24 - 50.48: 377 50.48 - 75.72: 56 75.72 - 100.96: 7 100.96 - 126.20: 1 Dihedral angle restraints: 6911 sinusoidal: 2783 harmonic: 4128 Sorted by residual: dihedral pdb=" CA ARG A 96 " pdb=" C ARG A 96 " pdb=" N LEU A 97 " pdb=" CA LEU A 97 " ideal model delta harmonic sigma weight residual -180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" C3 POV B 803 " pdb=" C31 POV B 803 " pdb=" O31 POV B 803 " pdb=" C32 POV B 803 " ideal model delta sinusoidal sigma weight residual 172.61 -61.19 -126.20 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" CA PRO B 609 " pdb=" C PRO B 609 " pdb=" N LEU B 610 " pdb=" CA LEU B 610 " ideal model delta harmonic sigma weight residual -180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 6908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1175 0.030 - 0.059: 393 0.059 - 0.088: 152 0.088 - 0.118: 76 0.118 - 0.147: 19 Chirality restraints: 1815 Sorted by residual: chirality pdb=" CB ILE B 684 " pdb=" CA ILE B 684 " pdb=" CG1 ILE B 684 " pdb=" CG2 ILE B 684 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ASP B 94 " pdb=" N ASP B 94 " pdb=" C ASP B 94 " pdb=" CB ASP B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE A 543 " pdb=" N ILE A 543 " pdb=" C ILE A 543 " pdb=" CB ILE A 543 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 1812 not shown) Planarity restraints: 1903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 608 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO B 609 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 609 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 609 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 640 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C LYS B 640 " -0.041 2.00e-02 2.50e+03 pdb=" O LYS B 640 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO B 641 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 684 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C ILE B 684 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE B 684 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 685 " 0.013 2.00e-02 2.50e+03 ... (remaining 1900 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 90 2.59 - 3.17: 9560 3.17 - 3.75: 17162 3.75 - 4.32: 23603 4.32 - 4.90: 40725 Nonbonded interactions: 91140 Sorted by model distance: nonbonded pdb=" O3B ADP A 801 " pdb="MG MG A 802 " model vdw 2.016 2.170 nonbonded pdb=" O3B ADP B 801 " pdb="MG MG B 802 " model vdw 2.063 2.170 nonbonded pdb=" OE1 GLN B 567 " pdb="MG MG B 802 " model vdw 2.073 2.170 nonbonded pdb=" NE2 GLN A 567 " pdb="MG MG A 802 " model vdw 2.091 2.250 nonbonded pdb=" O PRO B 609 " pdb=" OG1 THR B 614 " model vdw 2.238 3.040 ... (remaining 91135 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' and (resid 9 through 722 or resid 801 through 802)) } 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: 2.170 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.730 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:10.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.003 0.082 11429 Z= 0.152 Angle : 0.599 12.452 15411 Z= 0.295 Chirality : 0.040 0.147 1815 Planarity : 0.003 0.067 1903 Dihedral : 15.612 126.204 4259 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.39 % Allowed : 12.11 % Favored : 86.50 % 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: 1.55 (0.23), residues: 1424 helix: 2.17 (0.18), residues: 852 sheet: -0.20 (0.40), residues: 152 loop : -0.89 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 718 HIS 0.015 0.001 HIS A 679 PHE 0.029 0.001 PHE B 615 TYR 0.015 0.001 TYR B 179 ARG 0.012 0.000 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.13595 ( 710) hydrogen bonds : angle 5.03432 ( 2085) covalent geometry : bond 0.00318 (11429) covalent geometry : angle 0.59889 (15411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.305 Fit side-chains REVERT: A 619 SER cc_start: 0.8459 (m) cc_final: 0.8205 (t) REVERT: A 640 LYS cc_start: 0.7529 (tppt) cc_final: 0.7171 (tmmt) REVERT: B 629 GLN cc_start: 0.7320 (tt0) cc_final: 0.6877 (tt0) outliers start: 17 outliers final: 10 residues processed: 140 average time/residue: 1.1496 time to fit residues: 175.8458 Evaluate side-chains 127 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 661 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 629 GLN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.165099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112318 restraints weight = 13153.445| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.16 r_work: 0.3161 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11429 Z= 0.116 Angle : 0.507 6.768 15411 Z= 0.260 Chirality : 0.040 0.151 1815 Planarity : 0.003 0.043 1903 Dihedral : 7.825 134.429 1597 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.96 % Allowed : 12.03 % Favored : 86.01 % 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: 1.76 (0.23), residues: 1424 helix: 2.42 (0.18), residues: 852 sheet: -0.15 (0.40), residues: 160 loop : -1.02 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.005 0.001 HIS B 660 PHE 0.011 0.001 PHE A 270 TYR 0.014 0.001 TYR B 179 ARG 0.004 0.000 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 710) hydrogen bonds : angle 4.00134 ( 2085) covalent geometry : bond 0.00255 (11429) covalent geometry : angle 0.50678 (15411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.512 Fit side-chains REVERT: A 51 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7082 (mm-40) REVERT: A 64 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8031 (pp30) REVERT: A 498 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6815 (mmt-90) REVERT: A 548 HIS cc_start: 0.6675 (m90) cc_final: 0.6051 (m90) REVERT: A 629 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: A 640 LYS cc_start: 0.7494 (tppt) cc_final: 0.7036 (tmmt) REVERT: A 681 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6769 (tp) REVERT: B 78 ASP cc_start: 0.7873 (m-30) cc_final: 0.7628 (m-30) REVERT: B 155 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7933 (mmm) REVERT: B 578 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6733 (mt-10) REVERT: B 629 GLN cc_start: 0.7338 (tt0) cc_final: 0.7110 (tt0) REVERT: B 640 LYS cc_start: 0.7473 (tmmt) cc_final: 0.7249 (tmmt) REVERT: B 677 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7592 (mt) outliers start: 24 outliers final: 3 residues processed: 154 average time/residue: 1.4940 time to fit residues: 252.2040 Evaluate side-chains 130 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 677 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 57 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 629 GLN B 534 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.164479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111354 restraints weight = 13289.994| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.18 r_work: 0.3134 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11429 Z= 0.126 Angle : 0.510 10.060 15411 Z= 0.257 Chirality : 0.040 0.148 1815 Planarity : 0.003 0.032 1903 Dihedral : 7.448 131.577 1585 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.45 % Allowed : 12.85 % Favored : 84.70 % 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: 1.78 (0.23), residues: 1424 helix: 2.44 (0.18), residues: 852 sheet: -0.14 (0.41), residues: 160 loop : -1.02 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 PHE 0.010 0.001 PHE A 270 TYR 0.015 0.001 TYR B 179 ARG 0.007 0.000 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 710) hydrogen bonds : angle 3.90850 ( 2085) covalent geometry : bond 0.00291 (11429) covalent geometry : angle 0.50956 (15411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.723 Fit side-chains REVERT: A 51 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7091 (mm-40) REVERT: A 64 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7954 (pp30) REVERT: A 498 ARG cc_start: 0.7052 (mtp85) cc_final: 0.6781 (mmt-90) REVERT: A 629 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: A 640 LYS cc_start: 0.7562 (tppt) cc_final: 0.7190 (tmmt) REVERT: A 681 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6740 (tp) REVERT: B 44 GLU cc_start: 0.6147 (mp0) cc_final: 0.5944 (mp0) REVERT: B 78 ASP cc_start: 0.7805 (m-30) cc_final: 0.7545 (m-30) REVERT: B 155 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7929 (mmm) REVERT: B 578 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6766 (mt-10) REVERT: B 640 LYS cc_start: 0.7588 (tmmt) cc_final: 0.7290 (tmmt) REVERT: B 677 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7600 (mt) outliers start: 30 outliers final: 13 residues processed: 141 average time/residue: 1.2003 time to fit residues: 185.3007 Evaluate side-chains 140 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 589 MET Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 698 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 128 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 602 HIS B 629 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112912 restraints weight = 13327.487| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.84 r_work: 0.3076 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11429 Z= 0.226 Angle : 0.589 7.701 15411 Z= 0.301 Chirality : 0.043 0.151 1815 Planarity : 0.003 0.033 1903 Dihedral : 7.740 135.019 1585 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.19 % Allowed : 13.01 % Favored : 83.80 % 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: 1.33 (0.23), residues: 1424 helix: 2.03 (0.18), residues: 856 sheet: -0.38 (0.41), residues: 154 loop : -1.08 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 PHE 0.014 0.002 PHE A 270 TYR 0.018 0.002 TYR B 434 ARG 0.007 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.05434 ( 710) hydrogen bonds : angle 4.20502 ( 2085) covalent geometry : bond 0.00561 (11429) covalent geometry : angle 0.58933 (15411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 1.239 Fit side-chains REVERT: A 51 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7427 (mm-40) REVERT: A 629 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: A 681 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7410 (tp) REVERT: B 384 LYS cc_start: 0.8063 (mttt) cc_final: 0.7738 (mptt) REVERT: B 578 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7443 (mt-10) REVERT: B 629 GLN cc_start: 0.8074 (tt0) cc_final: 0.7868 (tt0) REVERT: B 677 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8458 (mt) outliers start: 39 outliers final: 15 residues processed: 142 average time/residue: 1.1893 time to fit residues: 183.7225 Evaluate side-chains 129 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 698 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 62 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114793 restraints weight = 13281.632| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.75 r_work: 0.3100 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11429 Z= 0.173 Angle : 0.565 10.176 15411 Z= 0.287 Chirality : 0.041 0.140 1815 Planarity : 0.003 0.029 1903 Dihedral : 7.752 140.955 1585 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.86 % Allowed : 14.08 % Favored : 83.06 % 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: 1.40 (0.23), residues: 1424 helix: 2.11 (0.18), residues: 856 sheet: -0.34 (0.41), residues: 154 loop : -1.12 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 PHE 0.011 0.002 PHE A 145 TYR 0.016 0.001 TYR B 179 ARG 0.009 0.000 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04939 ( 710) hydrogen bonds : angle 4.08709 ( 2085) covalent geometry : bond 0.00422 (11429) covalent geometry : angle 0.56477 (15411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.404 Fit side-chains REVERT: A 51 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7412 (mm-40) REVERT: A 629 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: A 640 LYS cc_start: 0.7664 (tmmt) cc_final: 0.7393 (tppt) REVERT: A 681 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7350 (tp) REVERT: B 384 LYS cc_start: 0.8014 (mttt) cc_final: 0.7625 (mptt) REVERT: B 578 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7325 (mt-10) REVERT: B 677 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8388 (mt) outliers start: 35 outliers final: 16 residues processed: 141 average time/residue: 1.1649 time to fit residues: 179.4630 Evaluate side-chains 134 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 698 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 126 optimal weight: 0.0370 chunk 98 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 84 optimal weight: 0.0050 overall best weight: 0.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN B 249 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 = 0.3915 r_free = 0.3915 target = 0.166489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120608 restraints weight = 13478.780| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.84 r_work: 0.3187 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11429 Z= 0.103 Angle : 0.509 10.449 15411 Z= 0.256 Chirality : 0.039 0.140 1815 Planarity : 0.003 0.036 1903 Dihedral : 7.383 136.161 1585 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.80 % Allowed : 15.22 % Favored : 82.98 % 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: 1.80 (0.23), residues: 1424 helix: 2.50 (0.18), residues: 854 sheet: -0.21 (0.41), residues: 158 loop : -1.09 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 PHE 0.009 0.001 PHE A 257 TYR 0.014 0.001 TYR B 179 ARG 0.010 0.000 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 710) hydrogen bonds : angle 3.72683 ( 2085) covalent geometry : bond 0.00214 (11429) covalent geometry : angle 0.50888 (15411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.415 Fit side-chains REVERT: A 51 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7336 (mm-40) REVERT: A 84 ARG cc_start: 0.7127 (mmm-85) cc_final: 0.6537 (tpt-90) REVERT: A 681 LEU cc_start: 0.7486 (mt) cc_final: 0.7210 (tp) REVERT: B 155 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8646 (mmm) REVERT: B 578 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7209 (mt-10) REVERT: B 629 GLN cc_start: 0.7951 (tt0) cc_final: 0.7667 (tt0) outliers start: 22 outliers final: 9 residues processed: 148 average time/residue: 1.0900 time to fit residues: 176.9758 Evaluate side-chains 127 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 698 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 89 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN B 652 ASN ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115275 restraints weight = 13562.266| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.87 r_work: 0.3160 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11429 Z= 0.119 Angle : 0.526 7.961 15411 Z= 0.263 Chirality : 0.040 0.139 1815 Planarity : 0.003 0.035 1903 Dihedral : 7.377 134.694 1585 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.96 % Allowed : 15.79 % Favored : 82.24 % 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: 1.83 (0.23), residues: 1424 helix: 2.51 (0.18), residues: 854 sheet: -0.19 (0.42), residues: 158 loop : -1.07 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 PHE 0.011 0.001 PHE A 615 TYR 0.015 0.001 TYR B 179 ARG 0.009 0.000 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 710) hydrogen bonds : angle 3.75752 ( 2085) covalent geometry : bond 0.00272 (11429) covalent geometry : angle 0.52567 (15411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.269 Fit side-chains REVERT: A 51 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7286 (mm-40) REVERT: A 580 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8495 (mp) REVERT: A 629 GLN cc_start: 0.8087 (tt0) cc_final: 0.7693 (tt0) REVERT: A 640 LYS cc_start: 0.7518 (tmmt) cc_final: 0.7217 (tppt) REVERT: A 681 LEU cc_start: 0.7441 (mt) cc_final: 0.7129 (tp) REVERT: B 44 GLU cc_start: 0.6691 (mp0) cc_final: 0.6469 (mp0) REVERT: B 155 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8607 (mmm) REVERT: B 499 LYS cc_start: 0.8603 (tmtt) cc_final: 0.8377 (tmtm) REVERT: B 578 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7156 (mt-10) REVERT: B 629 GLN cc_start: 0.7887 (tt0) cc_final: 0.7629 (tt0) REVERT: B 677 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8099 (mt) outliers start: 24 outliers final: 10 residues processed: 140 average time/residue: 1.2506 time to fit residues: 191.4796 Evaluate side-chains 128 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 698 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.163614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116257 restraints weight = 13429.304| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.90 r_work: 0.3176 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11429 Z= 0.115 Angle : 0.531 10.259 15411 Z= 0.266 Chirality : 0.040 0.139 1815 Planarity : 0.003 0.038 1903 Dihedral : 7.286 132.473 1585 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.72 % Allowed : 16.20 % Favored : 82.08 % 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: 1.88 (0.23), residues: 1424 helix: 2.55 (0.18), residues: 854 sheet: -0.20 (0.42), residues: 158 loop : -1.02 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 PHE 0.014 0.001 PHE A 615 TYR 0.015 0.001 TYR B 179 ARG 0.011 0.000 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 710) hydrogen bonds : angle 3.73040 ( 2085) covalent geometry : bond 0.00259 (11429) covalent geometry : angle 0.53098 (15411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.194 Fit side-chains REVERT: A 41 LYS cc_start: 0.7613 (mttp) cc_final: 0.7262 (ttpt) REVERT: A 51 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7242 (mm-40) REVERT: A 84 ARG cc_start: 0.7066 (mmm-85) cc_final: 0.6529 (tpt-90) REVERT: A 629 GLN cc_start: 0.8079 (tt0) cc_final: 0.7669 (tt0) REVERT: A 640 LYS cc_start: 0.7552 (tmmt) cc_final: 0.7334 (tppt) REVERT: B 155 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8544 (mmm) REVERT: B 499 LYS cc_start: 0.8585 (tmtt) cc_final: 0.8344 (tmtm) REVERT: B 578 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7103 (mt-10) REVERT: B 629 GLN cc_start: 0.7827 (tt0) cc_final: 0.7595 (tt0) outliers start: 21 outliers final: 10 residues processed: 135 average time/residue: 1.1163 time to fit residues: 164.6609 Evaluate side-chains 130 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 698 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 120 optimal weight: 0.1980 chunk 135 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 114 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 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 = 0.3927 r_free = 0.3927 target = 0.167397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117702 restraints weight = 13427.426| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.14 r_work: 0.3206 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11429 Z= 0.104 Angle : 0.523 9.658 15411 Z= 0.260 Chirality : 0.040 0.141 1815 Planarity : 0.003 0.038 1903 Dihedral : 7.098 126.645 1585 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.55 % Allowed : 16.45 % Favored : 82.00 % 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: 2.02 (0.24), residues: 1424 helix: 2.65 (0.18), residues: 854 sheet: -0.17 (0.41), residues: 160 loop : -0.95 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 132 HIS 0.003 0.001 HIS B 207 PHE 0.029 0.001 PHE B 615 TYR 0.014 0.001 TYR B 179 ARG 0.011 0.000 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 710) hydrogen bonds : angle 3.64498 ( 2085) covalent geometry : bond 0.00226 (11429) covalent geometry : angle 0.52286 (15411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.364 Fit side-chains REVERT: A 41 LYS cc_start: 0.7241 (mttp) cc_final: 0.6880 (ttpt) REVERT: A 51 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7109 (mm-40) REVERT: A 84 ARG cc_start: 0.6882 (mmm-85) cc_final: 0.6331 (tpt-90) REVERT: A 629 GLN cc_start: 0.7859 (tt0) cc_final: 0.7441 (tt0) REVERT: A 640 LYS cc_start: 0.7553 (tmmt) cc_final: 0.7349 (tppt) REVERT: B 155 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8258 (mmm) REVERT: B 499 LYS cc_start: 0.8524 (tmtt) cc_final: 0.8250 (tmtm) REVERT: B 578 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6913 (mt-10) REVERT: B 629 GLN cc_start: 0.7615 (tt0) cc_final: 0.7370 (tt0) outliers start: 19 outliers final: 9 residues processed: 138 average time/residue: 1.1726 time to fit residues: 178.2633 Evaluate side-chains 131 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 698 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 20 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 chunk 128 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.164046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115077 restraints weight = 13279.003| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.03 r_work: 0.3158 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11429 Z= 0.139 Angle : 0.569 9.781 15411 Z= 0.282 Chirality : 0.041 0.139 1815 Planarity : 0.003 0.058 1903 Dihedral : 7.213 129.084 1584 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.39 % Allowed : 16.94 % Favored : 81.67 % 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: 1.83 (0.23), residues: 1424 helix: 2.49 (0.18), residues: 852 sheet: -0.26 (0.42), residues: 158 loop : -0.97 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 132 HIS 0.004 0.001 HIS B 660 PHE 0.028 0.002 PHE B 615 TYR 0.015 0.001 TYR B 179 ARG 0.014 0.000 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 710) hydrogen bonds : angle 3.82251 ( 2085) covalent geometry : bond 0.00330 (11429) covalent geometry : angle 0.56896 (15411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.382 Fit side-chains REVERT: A 51 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7162 (mm-40) REVERT: A 84 ARG cc_start: 0.6987 (mmm-85) cc_final: 0.6434 (tpt-90) REVERT: A 154 MET cc_start: 0.8212 (mtp) cc_final: 0.7994 (mmm) REVERT: A 533 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7725 (tpp) REVERT: A 629 GLN cc_start: 0.7868 (tt0) cc_final: 0.7452 (tt0) REVERT: B 499 LYS cc_start: 0.8540 (tmtt) cc_final: 0.8258 (tmtm) REVERT: B 578 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6947 (mt-10) REVERT: B 629 GLN cc_start: 0.7659 (tt0) cc_final: 0.7429 (tt0) REVERT: B 677 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7949 (mt) outliers start: 17 outliers final: 11 residues processed: 128 average time/residue: 1.1430 time to fit residues: 159.7758 Evaluate side-chains 132 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 698 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 63 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111770 restraints weight = 13383.564| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.95 r_work: 0.3105 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11429 Z= 0.186 Angle : 0.606 11.632 15411 Z= 0.302 Chirality : 0.042 0.136 1815 Planarity : 0.003 0.025 1903 Dihedral : 7.534 139.386 1584 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.31 % Allowed : 17.18 % Favored : 81.51 % 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: 1.55 (0.23), residues: 1424 helix: 2.22 (0.18), residues: 854 sheet: -0.32 (0.42), residues: 154 loop : -0.99 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.005 0.001 HIS B 660 PHE 0.027 0.002 PHE B 615 TYR 0.016 0.001 TYR B 434 ARG 0.005 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.05003 ( 710) hydrogen bonds : angle 4.01464 ( 2085) covalent geometry : bond 0.00458 (11429) covalent geometry : angle 0.60622 (15411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8416.18 seconds wall clock time: 147 minutes 58.81 seconds (8878.81 seconds total)