Starting phenix.real_space_refine on Wed Sep 17 20:45:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9azl_44015/09_2025/9azl_44015.cif Found real_map, /net/cci-nas-00/data/ceres_data/9azl_44015/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9azl_44015/09_2025/9azl_44015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9azl_44015/09_2025/9azl_44015.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9azl_44015/09_2025/9azl_44015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9azl_44015/09_2025/9azl_44015.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.00, per 1000 atoms: 0.27 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: 1.00 Conformation dependent library (CDL) restraints added in 582.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.44 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: 1.89 Time building geometry restraints manager: 1.33 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 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: 3.040 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.420 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (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 ARG 0.012 0.000 ARG B 122 TYR 0.015 0.001 TYR B 179 PHE 0.029 0.001 PHE B 615 TRP 0.004 0.001 TRP A 718 HIS 0.015 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00318 (11429) covalent geometry : angle 0.59889 (15411) hydrogen bonds : bond 0.13595 ( 710) hydrogen bonds : angle 5.03432 ( 2085) *********************** 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 : 0.480 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: 0.5985 time to fit residues: 90.9589 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 : 0.398 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 534 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.162195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109566 restraints weight = 13148.692| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.15 r_work: 0.3127 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11429 Z= 0.133 Angle : 0.521 6.764 15411 Z= 0.268 Chirality : 0.040 0.152 1815 Planarity : 0.003 0.042 1903 Dihedral : 7.930 136.490 1597 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.13 % Allowed : 11.78 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.23), residues: 1424 helix: 2.32 (0.18), residues: 852 sheet: -0.17 (0.40), residues: 160 loop : -1.05 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 458 TYR 0.014 0.001 TYR B 179 PHE 0.012 0.001 PHE A 270 TRP 0.007 0.001 TRP B 132 HIS 0.004 0.001 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.00307 (11429) covalent geometry : angle 0.52104 (15411) hydrogen bonds : bond 0.04491 ( 710) hydrogen bonds : angle 4.07595 ( 2085) *********************** 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 164 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.501 Fit side-chains REVERT: A 51 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7095 (mm-40) REVERT: A 64 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8081 (pp30) REVERT: A 498 ARG cc_start: 0.7109 (mtp85) cc_final: 0.6835 (mmt-90) REVERT: A 640 LYS cc_start: 0.7516 (tppt) cc_final: 0.7094 (tmmt) REVERT: A 680 ARG cc_start: 0.7366 (tpt-90) cc_final: 0.7157 (tpt-90) REVERT: A 681 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6760 (tp) REVERT: B 78 ASP cc_start: 0.7880 (m-30) cc_final: 0.7626 (m-30) REVERT: B 155 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8000 (mmm) REVERT: B 498 ARG cc_start: 0.7458 (mmt180) cc_final: 0.7249 (mmt180) REVERT: B 578 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6756 (mt-10) REVERT: B 629 GLN cc_start: 0.7353 (tt0) cc_final: 0.7132 (tt0) REVERT: B 640 LYS cc_start: 0.7480 (tmmt) cc_final: 0.7259 (tmmt) REVERT: B 677 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7660 (mt) outliers start: 26 outliers final: 5 residues processed: 149 average time/residue: 0.5694 time to fit residues: 92.4727 Evaluate side-chains 128 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 672 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 590 ASP 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 101 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 77 optimal weight: 0.0570 overall best weight: 1.3904 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.162643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109503 restraints weight = 13315.127| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.18 r_work: 0.3105 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11429 Z= 0.146 Angle : 0.526 10.075 15411 Z= 0.267 Chirality : 0.041 0.147 1815 Planarity : 0.003 0.034 1903 Dihedral : 7.570 131.857 1586 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.95 % Allowed : 12.44 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.23), residues: 1424 helix: 2.30 (0.18), residues: 852 sheet: -0.20 (0.40), residues: 160 loop : -1.04 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 122 TYR 0.016 0.001 TYR B 179 PHE 0.011 0.001 PHE A 270 TRP 0.007 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00349 (11429) covalent geometry : angle 0.52556 (15411) hydrogen bonds : bond 0.04643 ( 710) hydrogen bonds : angle 3.99865 ( 2085) *********************** 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 160 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.480 Fit side-chains REVERT: A 51 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7085 (mm-40) REVERT: A 64 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8116 (pp30) REVERT: A 498 ARG cc_start: 0.7071 (mtp85) cc_final: 0.6745 (mmt-90) REVERT: A 629 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: A 640 LYS cc_start: 0.7625 (tppt) cc_final: 0.7280 (tmmt) REVERT: A 681 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6703 (tp) REVERT: B 78 ASP cc_start: 0.7808 (m-30) cc_final: 0.7528 (m-30) REVERT: B 155 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7952 (mmm) REVERT: B 384 LYS cc_start: 0.7124 (mttt) cc_final: 0.6553 (mptt) REVERT: B 498 ARG cc_start: 0.7499 (mmt180) cc_final: 0.7274 (mmt180) REVERT: B 499 LYS cc_start: 0.8404 (tmtt) cc_final: 0.8111 (tmtm) REVERT: B 578 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6775 (mt-10) REVERT: B 640 LYS cc_start: 0.7702 (tmmt) cc_final: 0.7356 (tmmt) REVERT: B 677 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7628 (mt) REVERT: B 700 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8045 (mt-10) outliers start: 36 outliers final: 13 residues processed: 143 average time/residue: 0.6012 time to fit residues: 93.3368 Evaluate side-chains 136 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 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 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 89 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN B 629 GLN B 660 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.115390 restraints weight = 13564.451| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.89 r_work: 0.3098 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1163 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= 0.170 Angle : 0.539 6.774 15411 Z= 0.276 Chirality : 0.041 0.143 1815 Planarity : 0.003 0.027 1903 Dihedral : 7.610 134.701 1586 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.62 % Allowed : 13.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.23), residues: 1424 helix: 2.21 (0.18), residues: 856 sheet: -0.33 (0.41), residues: 154 loop : -1.03 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 122 TYR 0.016 0.001 TYR B 179 PHE 0.011 0.002 PHE A 270 TRP 0.007 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00413 (11429) covalent geometry : angle 0.53877 (15411) hydrogen bonds : bond 0.04840 ( 710) hydrogen bonds : angle 4.03507 ( 2085) *********************** 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 152 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.467 Fit side-chains REVERT: A 51 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7405 (mm-40) REVERT: A 580 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8618 (mp) REVERT: A 681 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7352 (tp) REVERT: B 44 GLU cc_start: 0.6977 (mp0) cc_final: 0.6673 (mp0) REVERT: B 384 LYS cc_start: 0.8030 (mttt) cc_final: 0.7693 (mptt) REVERT: B 578 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7415 (mt-10) REVERT: B 677 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8370 (mt) outliers start: 32 outliers final: 14 residues processed: 138 average time/residue: 0.6019 time to fit residues: 90.1080 Evaluate side-chains 129 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 250 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 580 LEU 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 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 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 32 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 13 optimal weight: 0.0070 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN B 629 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118393 restraints weight = 13372.314| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.83 r_work: 0.3145 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1181 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= 0.121 Angle : 0.520 10.807 15411 Z= 0.263 Chirality : 0.040 0.139 1815 Planarity : 0.003 0.032 1903 Dihedral : 7.443 135.262 1586 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.05 % Allowed : 14.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.23), residues: 1424 helix: 2.42 (0.18), residues: 856 sheet: -0.26 (0.42), residues: 154 loop : -1.03 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 122 TYR 0.015 0.001 TYR B 179 PHE 0.009 0.001 PHE A 615 TRP 0.006 0.001 TRP B 132 HIS 0.003 0.001 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.00276 (11429) covalent geometry : angle 0.52008 (15411) hydrogen bonds : bond 0.04201 ( 710) hydrogen bonds : angle 3.84533 ( 2085) *********************** 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 162 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.460 Fit side-chains REVERT: A 51 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7373 (mm-40) REVERT: A 580 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8593 (mp) REVERT: A 681 LEU cc_start: 0.7578 (mt) cc_final: 0.7301 (tp) REVERT: B 155 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8721 (mmm) REVERT: B 578 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7325 (mt-10) REVERT: B 629 GLN cc_start: 0.8003 (tt0) cc_final: 0.7759 (tt0) REVERT: B 677 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8333 (mt) outliers start: 25 outliers final: 9 residues processed: 149 average time/residue: 0.5456 time to fit residues: 88.8031 Evaluate side-chains 129 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.158519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109331 restraints weight = 13423.175| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.01 r_work: 0.3086 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11429 Z= 0.200 Angle : 0.570 7.583 15411 Z= 0.291 Chirality : 0.042 0.147 1815 Planarity : 0.003 0.032 1903 Dihedral : 7.839 145.544 1586 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.45 % Allowed : 15.38 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.23), residues: 1424 helix: 2.16 (0.18), residues: 854 sheet: -0.31 (0.42), residues: 154 loop : -1.04 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 122 TYR 0.017 0.001 TYR B 434 PHE 0.012 0.002 PHE A 615 TRP 0.009 0.001 TRP A 132 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00496 (11429) covalent geometry : angle 0.57026 (15411) hydrogen bonds : bond 0.05159 ( 710) hydrogen bonds : angle 4.09878 ( 2085) *********************** 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 146 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.368 Fit side-chains REVERT: A 51 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7338 (mm-40) REVERT: A 681 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7238 (tp) REVERT: B 578 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7182 (mt-10) REVERT: B 629 GLN cc_start: 0.7905 (tt0) cc_final: 0.7683 (tt0) REVERT: B 677 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8297 (mt) outliers start: 30 outliers final: 14 residues processed: 134 average time/residue: 0.5415 time to fit residues: 79.0486 Evaluate side-chains 130 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 250 VAL Chi-restraints excluded: chain A residue 396 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 86 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 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 660 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113077 restraints weight = 13525.366| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.04 r_work: 0.3138 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11429 Z= 0.121 Angle : 0.526 9.478 15411 Z= 0.265 Chirality : 0.040 0.139 1815 Planarity : 0.003 0.035 1903 Dihedral : 7.571 143.156 1586 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.80 % Allowed : 16.28 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.23), residues: 1424 helix: 2.38 (0.18), residues: 856 sheet: -0.25 (0.42), residues: 154 loop : -1.03 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 122 TYR 0.015 0.001 TYR B 179 PHE 0.012 0.001 PHE A 615 TRP 0.005 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00276 (11429) covalent geometry : angle 0.52578 (15411) hydrogen bonds : bond 0.04230 ( 710) hydrogen bonds : angle 3.85681 ( 2085) *********************** 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 149 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.374 Fit side-chains REVERT: A 51 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7293 (mm-40) REVERT: A 629 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: A 640 LYS cc_start: 0.7669 (tppt) cc_final: 0.7434 (tmmt) REVERT: A 681 LEU cc_start: 0.7525 (mt) cc_final: 0.7193 (tp) REVERT: B 155 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8594 (mmm) REVERT: B 499 LYS cc_start: 0.8613 (tmtt) cc_final: 0.8384 (tmtm) REVERT: B 578 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7173 (mt-10) REVERT: B 629 GLN cc_start: 0.7861 (tt0) cc_final: 0.7660 (tt0) REVERT: B 677 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8240 (mt) outliers start: 22 outliers final: 12 residues processed: 142 average time/residue: 0.5424 time to fit residues: 84.2221 Evaluate side-chains 134 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 396 THR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 672 VAL 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 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 34 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 60 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 629 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.163621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117661 restraints weight = 13377.619| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.84 r_work: 0.3162 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11429 Z= 0.110 Angle : 0.512 7.326 15411 Z= 0.259 Chirality : 0.040 0.148 1815 Planarity : 0.003 0.039 1903 Dihedral : 7.323 136.670 1586 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.47 % Allowed : 17.10 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.23), residues: 1424 helix: 2.55 (0.18), residues: 854 sheet: -0.24 (0.41), residues: 158 loop : -1.00 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 122 TYR 0.015 0.001 TYR B 179 PHE 0.027 0.001 PHE B 615 TRP 0.006 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00243 (11429) covalent geometry : angle 0.51233 (15411) hydrogen bonds : bond 0.03935 ( 710) hydrogen bonds : angle 3.74564 ( 2085) *********************** 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 148 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.380 Fit side-chains REVERT: A 51 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7289 (mm-40) REVERT: A 84 ARG cc_start: 0.6966 (mmm-85) cc_final: 0.6406 (tpt-90) REVERT: A 533 MET cc_start: 0.8351 (ttp) cc_final: 0.8102 (tpp) REVERT: A 629 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: B 155 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8659 (mmm) REVERT: B 499 LYS cc_start: 0.8625 (tmtt) cc_final: 0.8408 (tmtm) REVERT: B 578 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7213 (mt-10) REVERT: B 629 GLN cc_start: 0.7958 (tt0) cc_final: 0.7729 (tt0) outliers start: 18 outliers final: 6 residues processed: 138 average time/residue: 0.5329 time to fit residues: 80.3868 Evaluate side-chains 128 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 629 GLN Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 661 ILE 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 19 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.164088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118007 restraints weight = 13252.113| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.84 r_work: 0.3171 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1441 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= 0.114 Angle : 0.537 9.035 15411 Z= 0.269 Chirality : 0.040 0.139 1815 Planarity : 0.003 0.038 1903 Dihedral : 7.242 133.945 1585 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.72 % Allowed : 16.94 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.23), residues: 1424 helix: 2.57 (0.18), residues: 854 sheet: -0.23 (0.41), residues: 158 loop : -0.97 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 122 TYR 0.015 0.001 TYR A 32 PHE 0.027 0.001 PHE B 615 TRP 0.006 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00256 (11429) covalent geometry : angle 0.53731 (15411) hydrogen bonds : bond 0.03994 ( 710) hydrogen bonds : angle 3.74705 ( 2085) *********************** 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 145 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.487 Fit side-chains REVERT: A 51 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7255 (mm-40) REVERT: A 84 ARG cc_start: 0.6875 (mmm-85) cc_final: 0.6499 (tpt-90) REVERT: A 533 MET cc_start: 0.8329 (ttp) cc_final: 0.8102 (tpp) REVERT: A 629 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: A 640 LYS cc_start: 0.7599 (tmmt) cc_final: 0.7283 (tppt) REVERT: B 155 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8649 (mmm) REVERT: B 578 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7186 (mt-10) REVERT: B 629 GLN cc_start: 0.7917 (tt0) cc_final: 0.7668 (tt0) REVERT: B 677 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8263 (mt) outliers start: 21 outliers final: 9 residues processed: 133 average time/residue: 0.5211 time to fit residues: 75.7295 Evaluate side-chains 132 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 629 GLN 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 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 7 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117028 restraints weight = 13401.387| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.03 r_work: 0.3087 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11429 Z= 0.187 Angle : 0.604 9.438 15411 Z= 0.302 Chirality : 0.042 0.150 1815 Planarity : 0.003 0.053 1903 Dihedral : 7.615 140.974 1585 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.47 % Allowed : 17.27 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.23), residues: 1424 helix: 2.21 (0.18), residues: 856 sheet: -0.28 (0.42), residues: 154 loop : -1.01 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 122 TYR 0.016 0.002 TYR B 434 PHE 0.028 0.002 PHE B 615 TRP 0.010 0.001 TRP A 132 HIS 0.005 0.001 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.00461 (11429) covalent geometry : angle 0.60423 (15411) hydrogen bonds : bond 0.05037 ( 710) hydrogen bonds : angle 4.04390 ( 2085) ********************** 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 137 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.443 Fit side-chains REVERT: A 51 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7325 (mm-40) REVERT: A 84 ARG cc_start: 0.6997 (mmm-85) cc_final: 0.6520 (tpt-90) REVERT: A 568 ASP cc_start: 0.8277 (m-30) cc_final: 0.7927 (p0) REVERT: A 640 LYS cc_start: 0.7823 (tmmt) cc_final: 0.7601 (tppt) REVERT: B 578 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7295 (mt-10) REVERT: B 629 GLN cc_start: 0.8014 (tt0) cc_final: 0.7805 (tt0) REVERT: B 677 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8427 (mt) outliers start: 18 outliers final: 10 residues processed: 128 average time/residue: 0.5404 time to fit residues: 75.1568 Evaluate side-chains 128 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 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 6 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 0.0050 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.164103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118754 restraints weight = 13432.334| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.96 r_work: 0.3137 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 11429 Z= 0.111 Angle : 0.551 10.597 15411 Z= 0.274 Chirality : 0.040 0.140 1815 Planarity : 0.003 0.059 1903 Dihedral : 7.321 135.720 1585 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.23 % Allowed : 17.59 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.23), residues: 1424 helix: 2.54 (0.18), residues: 854 sheet: -0.25 (0.41), residues: 158 loop : -1.02 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 122 TYR 0.017 0.001 TYR A 32 PHE 0.028 0.001 PHE B 615 TRP 0.004 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00244 (11429) covalent geometry : angle 0.55110 (15411) hydrogen bonds : bond 0.03982 ( 710) hydrogen bonds : angle 3.79663 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4024.77 seconds wall clock time: 69 minutes 31.44 seconds (4171.44 seconds total)