Starting phenix.real_space_refine on Fri Jul 3 10:23:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t56_41043/07_2026/8t56_41043.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t56_41043/07_2026/8t56_41043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t56_41043/07_2026/8t56_41043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t56_41043/07_2026/8t56_41043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t56_41043/07_2026/8t56_41043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t56_41043/07_2026/8t56_41043.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8t56_41043/07_2026/8t56_41043.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t56_41043/07_2026/8t56_41043.cif" } resolution = 2.8 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 48 5.16 5 C 8956 2.51 5 N 1952 2.21 5 O 2138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13096 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 5005 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 33, 'TRANS': 583} Chain breaks: 5 Chain: "B" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 5005 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 33, 'TRANS': 583} Chain breaks: 5 Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 300 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "D" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "E" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "F" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 216 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "G" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 300 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "H" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "I" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "J" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 216 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "A" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 267 Unusual residues: {'LBN': 1, 'PLM': 10, 'Y01': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 267 Unusual residues: {'LBN': 1, 'PLM': 10, 'Y01': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'CLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'CLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.20, per 1000 atoms: 0.17 Number of scatterers: 13096 At special positions: 0 Unit cell: (143.17, 114.33, 91.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 2 15.00 O 2138 8.00 N 1952 7.00 C 8956 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: 0.94 Conformation dependent library (CDL) restraints added in 494.7 milliseconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 2 sheets defined 84.1% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 3 through 29 Processing helix chain 'A' and resid 30 through 33 removed outlier: 6.235A pdb=" N PHE A 33 " --> pdb=" O LEU A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 30 through 33' Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 92 through 121 removed outlier: 3.571A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 158 through 194 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 242 through 265 Processing helix chain 'A' and resid 291 through 315 Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.608A pdb=" N VAL A 359 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.554A pdb=" N ALA A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 389 Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 410 through 416 removed outlier: 4.368A pdb=" N PHE A 414 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 438 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 456 through 476 Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.611A pdb=" N SER A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 512 through 524 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 534 through 548 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 559 removed outlier: 3.704A pdb=" N MET A 559 " --> pdb=" O ARG A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 584 Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 590 through 612 removed outlier: 3.552A pdb=" N ILE A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 647 Processing helix chain 'A' and resid 655 through 676 Proline residue: A 662 - end of helix Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 703 through 710 removed outlier: 4.570A pdb=" N ASN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 29 Processing helix chain 'B' and resid 30 through 33 removed outlier: 6.235A pdb=" N PHE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 92 through 121 removed outlier: 3.571A pdb=" N ILE B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 158 through 194 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 242 through 265 Processing helix chain 'B' and resid 291 through 315 Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 355 through 359 removed outlier: 3.609A pdb=" N VAL B 359 " --> pdb=" O PRO B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 366 removed outlier: 3.554A pdb=" N ALA B 365 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 389 Processing helix chain 'B' and resid 389 through 399 Processing helix chain 'B' and resid 401 through 409 Processing helix chain 'B' and resid 410 through 416 removed outlier: 4.367A pdb=" N PHE B 414 " --> pdb=" O PHE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 438 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'B' and resid 456 through 476 Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.612A pdb=" N SER B 480 " --> pdb=" O VAL B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 511 No H-bonds generated for 'chain 'B' and resid 509 through 511' Processing helix chain 'B' and resid 512 through 524 Processing helix chain 'B' and resid 524 through 532 Processing helix chain 'B' and resid 534 through 548 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 559 removed outlier: 3.703A pdb=" N MET B 559 " --> pdb=" O ARG B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 584 Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 590 through 612 removed outlier: 3.551A pdb=" N ILE B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 647 Processing helix chain 'B' and resid 655 through 676 Proline residue: B 662 - end of helix Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 703 through 710 removed outlier: 4.570A pdb=" N ASN B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 34 removed outlier: 5.869A pdb=" N ASP C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) Proline residue: C 19 - end of helix Processing helix chain 'D' and resid 2 through 16 Processing helix chain 'D' and resid 16 through 34 Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 16 through 34 removed outlier: 3.576A pdb=" N ALA E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 37 Proline residue: F 19 - end of helix Processing helix chain 'G' and resid 3 through 34 removed outlier: 5.868A pdb=" N ASP G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) Proline residue: G 19 - end of helix Processing helix chain 'H' and resid 2 through 16 Processing helix chain 'H' and resid 16 through 34 Processing helix chain 'I' and resid 2 through 15 Processing helix chain 'I' and resid 16 through 34 removed outlier: 3.576A pdb=" N ALA I 20 " --> pdb=" O PHE I 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 37 Proline residue: J 19 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.515A pdb=" N ALA A 322 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.514A pdb=" N ALA B 322 " --> pdb=" O VAL B 239 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2616 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: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2393 1.32 - 1.45: 4263 1.45 - 1.58: 6544 1.58 - 1.71: 174 1.71 - 1.84: 86 Bond restraints: 13460 Sorted by residual: bond pdb=" O2 LBN B 812 " pdb=" P1 LBN B 812 " ideal model delta sigma weight residual 1.650 1.844 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" O2 LBN A 812 " pdb=" P1 LBN A 812 " ideal model delta sigma weight residual 1.650 1.844 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" C10 CLR D 101 " pdb=" C9 CLR D 101 " ideal model delta sigma weight residual 1.551 1.703 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C10 CLR H 101 " pdb=" C9 CLR H 101 " ideal model delta sigma weight residual 1.551 1.703 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" C14 CLR C 801 " pdb=" C8 CLR C 801 " ideal model delta sigma weight residual 1.519 1.668 -0.149 2.00e-02 2.50e+03 5.53e+01 ... (remaining 13455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 17321 3.56 - 7.12: 723 7.12 - 10.69: 62 10.69 - 14.25: 8 14.25 - 17.81: 2 Bond angle restraints: 18116 Sorted by residual: angle pdb=" N VAL A 612 " pdb=" CA VAL A 612 " pdb=" C VAL A 612 " ideal model delta sigma weight residual 111.62 119.31 -7.69 7.90e-01 1.60e+00 9.47e+01 angle pdb=" N VAL B 612 " pdb=" CA VAL B 612 " pdb=" C VAL B 612 " ideal model delta sigma weight residual 111.62 119.29 -7.67 7.90e-01 1.60e+00 9.44e+01 angle pdb=" C HIS A 229 " pdb=" N PRO A 230 " pdb=" CA PRO A 230 " ideal model delta sigma weight residual 119.56 127.33 -7.77 1.02e+00 9.61e-01 5.80e+01 angle pdb=" C HIS B 229 " pdb=" N PRO B 230 " pdb=" CA PRO B 230 " ideal model delta sigma weight residual 119.56 127.31 -7.75 1.02e+00 9.61e-01 5.77e+01 angle pdb=" C ALA A 409 " pdb=" N PRO A 410 " pdb=" CA PRO A 410 " ideal model delta sigma weight residual 119.56 127.29 -7.73 1.02e+00 9.61e-01 5.75e+01 ... (remaining 18111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 8186 34.93 - 69.85: 178 69.85 - 104.78: 20 104.78 - 139.70: 2 139.70 - 174.63: 4 Dihedral angle restraints: 8390 sinusoidal: 3946 harmonic: 4444 Sorted by residual: dihedral pdb=" O5 LBN B 812 " pdb=" C2 LBN B 812 " pdb=" C3 LBN B 812 " pdb=" O7 LBN B 812 " ideal model delta sinusoidal sigma weight residual 62.67 -111.96 174.63 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN A 812 " pdb=" C2 LBN A 812 " pdb=" C3 LBN A 812 " pdb=" O7 LBN A 812 " ideal model delta sinusoidal sigma weight residual 62.67 -111.93 174.60 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN A 812 " pdb=" O1 LBN A 812 " pdb=" P1 LBN A 812 " pdb=" O3 LBN A 812 " ideal model delta sinusoidal sigma weight residual 275.40 108.33 167.07 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 8387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1433 0.114 - 0.229: 395 0.229 - 0.343: 96 0.343 - 0.457: 12 0.457 - 0.571: 2 Chirality restraints: 1938 Sorted by residual: chirality pdb=" C2 LBN B 812 " pdb=" C1 LBN B 812 " pdb=" C3 LBN B 812 " pdb=" O7 LBN B 812 " both_signs ideal model delta sigma weight residual False -2.36 -2.94 0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" C2 LBN A 812 " pdb=" C1 LBN A 812 " pdb=" C3 LBN A 812 " pdb=" O7 LBN A 812 " both_signs ideal model delta sigma weight residual False -2.36 -2.94 0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" CBB Y01 A 801 " pdb=" CAC Y01 A 801 " pdb=" CAO Y01 A 801 " pdb=" CBE Y01 A 801 " both_signs ideal model delta sigma weight residual False 2.58 2.12 0.45 2.00e-01 2.50e+01 5.13e+00 ... (remaining 1935 not shown) Planarity restraints: 2146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP J 37 " 0.030 2.00e-02 2.50e+03 6.01e-02 3.62e+01 pdb=" C ASP J 37 " -0.104 2.00e-02 2.50e+03 pdb=" O ASP J 37 " 0.037 2.00e-02 2.50e+03 pdb=" OXT ASP J 37 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 37 " -0.030 2.00e-02 2.50e+03 6.01e-02 3.62e+01 pdb=" C ASP F 37 " 0.104 2.00e-02 2.50e+03 pdb=" O ASP F 37 " -0.037 2.00e-02 2.50e+03 pdb=" OXT ASP F 37 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 181 " -0.078 2.00e-02 2.50e+03 4.04e-02 3.26e+01 pdb=" CG TYR A 181 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 181 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 181 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR A 181 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 181 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 181 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 181 " -0.054 2.00e-02 2.50e+03 ... (remaining 2143 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 4737 2.89 - 3.39: 12906 3.39 - 3.89: 21474 3.89 - 4.40: 26400 4.40 - 4.90: 41692 Nonbonded interactions: 107209 Sorted by model distance: nonbonded pdb=" N PHE B 72 " pdb=" N LEU B 73 " model vdw 2.385 2.560 nonbonded pdb=" N PHE A 72 " pdb=" N LEU A 73 " model vdw 2.385 2.560 nonbonded pdb=" OE2 GLU E 22 " pdb=" NZ LYS F 25 " model vdw 2.490 3.120 nonbonded pdb=" OE2 GLU I 22 " pdb=" NZ LYS J 25 " model vdw 2.491 3.120 nonbonded pdb=" O MET B 82 " pdb=" NH2 ARG B 606 " model vdw 2.522 3.120 ... (remaining 107204 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 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 : 0.027 0.194 13460 Z= 1.390 Angle : 1.657 17.811 18116 Z= 1.056 Chirality : 0.114 0.571 1938 Planarity : 0.009 0.060 2146 Dihedral : 14.219 174.630 5490 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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 are not related in a simple way. whole: 0.58 (0.20), residues: 1458 helix: 0.47 (0.13), residues: 1122 sheet: -0.47 (0.79), residues: 46 loop : 0.83 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.078 0.009 TYR A 181 PHE 0.061 0.005 PHE I 1 TRP 0.037 0.007 TRP B 352 HIS 0.006 0.002 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.02720 / 1.39 (13460) covalent geometry : angle 1.65712 / 1.06 (18116) hydrogen bonds : bond 0.17032 / 10.97 ( 890) hydrogen bonds : angle 6.45373 / 4.66 ( 2616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.458 Fit side-chains REVERT: A 178 MET cc_start: 0.8900 (ttp) cc_final: 0.8623 (ttm) REVERT: A 251 LYS cc_start: 0.8678 (tttt) cc_final: 0.8372 (ttmt) REVERT: A 254 LYS cc_start: 0.8328 (mttt) cc_final: 0.8076 (mmmt) REVERT: A 448 MET cc_start: 0.9063 (mtp) cc_final: 0.8829 (mtm) REVERT: A 534 MET cc_start: 0.8689 (ttp) cc_final: 0.8453 (ttm) REVERT: A 657 PHE cc_start: 0.8069 (m-80) cc_final: 0.7774 (m-80) REVERT: B 178 MET cc_start: 0.8905 (ttp) cc_final: 0.8617 (ttm) REVERT: B 251 LYS cc_start: 0.8681 (tttt) cc_final: 0.8373 (ttmt) REVERT: B 254 LYS cc_start: 0.8352 (mttt) cc_final: 0.8112 (mmmt) REVERT: B 448 MET cc_start: 0.9071 (mtp) cc_final: 0.8846 (mtm) REVERT: B 534 MET cc_start: 0.8711 (ttp) cc_final: 0.8476 (ttm) REVERT: B 657 PHE cc_start: 0.8090 (m-80) cc_final: 0.7745 (m-80) REVERT: E 29 LYS cc_start: 0.8754 (tmmt) cc_final: 0.8539 (tttm) REVERT: I 29 LYS cc_start: 0.8699 (tmmt) cc_final: 0.8471 (tttm) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.5649 time to fit residues: 137.7534 Evaluate side-chains 150 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN A 426 GLN A 475 ASN B 314 ASN B 426 GLN B 475 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.109298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083288 restraints weight = 17720.837| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.62 r_work: 0.2892 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13460 Z= 0.173 Angle : 0.601 6.642 18116 Z= 0.324 Chirality : 0.043 0.146 1938 Planarity : 0.005 0.042 2146 Dihedral : 14.805 174.345 2582 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.67 % Allowed : 6.83 % Favored : 90.50 % 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 are not related in a simple way. whole: 2.64 (0.21), residues: 1458 helix: 2.10 (0.15), residues: 1118 sheet: -0.86 (0.99), residues: 30 loop : 0.88 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 36 TYR 0.015 0.002 TYR A 261 PHE 0.021 0.002 PHE B 33 TRP 0.027 0.002 TRP A 624 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (13460) covalent geometry : angle 0.60087 / 0.32 (18116) hydrogen bonds : bond 0.06204 / 3.92 ( 890) hydrogen bonds : angle 4.68921 / 3.39 ( 2616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.443 Fit side-chains REVERT: A 261 TYR cc_start: 0.7171 (t80) cc_final: 0.6944 (t80) REVERT: A 311 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: A 389 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.6437 (t80) REVERT: B 254 LYS cc_start: 0.7920 (mttt) cc_final: 0.7331 (mmmt) REVERT: B 311 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: B 389 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.6462 (t80) REVERT: B 536 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6606 (tptt) outliers start: 34 outliers final: 3 residues processed: 171 average time/residue: 0.5514 time to fit residues: 102.5056 Evaluate side-chains 144 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 35 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 31 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 HIS A 314 ASN B 162 HIS B 314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.087599 restraints weight = 18062.493| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.64 r_work: 0.2944 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13460 Z= 0.130 Angle : 0.512 6.550 18116 Z= 0.267 Chirality : 0.040 0.148 1938 Planarity : 0.004 0.047 2146 Dihedral : 13.579 174.451 2582 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.51 % Allowed : 7.61 % Favored : 89.87 % 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 are not related in a simple way. whole: 2.87 (0.21), residues: 1458 helix: 2.33 (0.15), residues: 1130 sheet: -1.03 (1.01), residues: 30 loop : 0.66 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 36 TYR 0.016 0.001 TYR B 261 PHE 0.016 0.002 PHE B 159 TRP 0.020 0.001 TRP A 624 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (13460) covalent geometry : angle 0.51243 / 0.27 (18116) hydrogen bonds : bond 0.04620 / 2.91 ( 890) hydrogen bonds : angle 4.24074 / 3.07 ( 2616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.422 Fit side-chains REVERT: A 78 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: A 261 TYR cc_start: 0.7464 (t80) cc_final: 0.7259 (t80) REVERT: A 389 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.6466 (t80) REVERT: A 421 MET cc_start: 0.8417 (tpp) cc_final: 0.8174 (mmm) REVERT: B 254 LYS cc_start: 0.7959 (mttt) cc_final: 0.7421 (mmmt) REVERT: B 389 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.6467 (t80) REVERT: B 521 MET cc_start: 0.9257 (mtm) cc_final: 0.8989 (mtm) REVERT: D 34 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7562 (mtmm) REVERT: E 12 TYR cc_start: 0.8995 (t80) cc_final: 0.8791 (t80) REVERT: I 12 TYR cc_start: 0.8999 (t80) cc_final: 0.8788 (t80) outliers start: 32 outliers final: 1 residues processed: 185 average time/residue: 0.5370 time to fit residues: 107.8219 Evaluate side-chains 152 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 389 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 28 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.086735 restraints weight = 17828.649| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.61 r_work: 0.2946 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13460 Z= 0.131 Angle : 0.505 7.255 18116 Z= 0.260 Chirality : 0.040 0.144 1938 Planarity : 0.004 0.045 2146 Dihedral : 12.977 163.289 2582 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.75 % Allowed : 9.11 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.22), residues: 1458 helix: 2.40 (0.15), residues: 1130 sheet: -1.27 (1.01), residues: 30 loop : 0.59 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 36 TYR 0.018 0.001 TYR C 12 PHE 0.020 0.001 PHE A 33 TRP 0.019 0.001 TRP A 624 HIS 0.007 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13460) covalent geometry : angle 0.50464 / 0.26 (18116) hydrogen bonds : bond 0.04486 / 2.83 ( 890) hydrogen bonds : angle 4.11187 / 2.98 ( 2616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.9006 (ttm-80) cc_final: 0.8654 (ttm-80) REVERT: A 254 LYS cc_start: 0.7956 (mttt) cc_final: 0.7363 (mmmt) REVERT: A 308 GLU cc_start: 0.7833 (tp30) cc_final: 0.7280 (tp30) REVERT: A 311 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: A 389 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.6441 (t80) REVERT: A 521 MET cc_start: 0.9236 (mtm) cc_final: 0.9013 (mtm) REVERT: A 535 LEU cc_start: 0.8584 (mt) cc_final: 0.8383 (mp) REVERT: A 677 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: B 254 LYS cc_start: 0.7977 (mttt) cc_final: 0.7383 (mmmt) REVERT: B 311 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: B 389 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.6452 (t80) REVERT: B 521 MET cc_start: 0.9271 (mtm) cc_final: 0.9040 (mtm) REVERT: B 535 LEU cc_start: 0.8602 (mt) cc_final: 0.8397 (mp) REVERT: B 677 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: H 34 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7346 (mtmm) outliers start: 35 outliers final: 9 residues processed: 178 average time/residue: 0.5062 time to fit residues: 98.4286 Evaluate side-chains 167 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 677 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087080 restraints weight = 17898.541| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.64 r_work: 0.2948 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13460 Z= 0.122 Angle : 0.497 7.301 18116 Z= 0.253 Chirality : 0.039 0.145 1938 Planarity : 0.004 0.044 2146 Dihedral : 12.358 146.797 2582 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 3.06 % Allowed : 9.50 % Favored : 87.44 % 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 are not related in a simple way. whole: 3.03 (0.22), residues: 1458 helix: 2.48 (0.15), residues: 1130 sheet: -1.44 (0.99), residues: 30 loop : 0.58 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 198 TYR 0.019 0.001 TYR A 261 PHE 0.016 0.001 PHE A 33 TRP 0.019 0.001 TRP B 624 HIS 0.008 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (13460) covalent geometry : angle 0.49707 / 0.25 (18116) hydrogen bonds : bond 0.04214 / 2.66 ( 890) hydrogen bonds : angle 4.00410 / 2.90 ( 2616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7946 (mttt) cc_final: 0.7390 (mmmt) REVERT: A 255 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7523 (mt) REVERT: A 261 TYR cc_start: 0.7468 (t80) cc_final: 0.7220 (t80) REVERT: A 311 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: A 389 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.6461 (t80) REVERT: A 521 MET cc_start: 0.9241 (mtm) cc_final: 0.8985 (mtm) REVERT: A 677 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: B 254 LYS cc_start: 0.7981 (mttt) cc_final: 0.7394 (mmmt) REVERT: B 308 GLU cc_start: 0.7858 (tp30) cc_final: 0.7309 (tp30) REVERT: B 311 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: B 389 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.6456 (t80) REVERT: B 413 LYS cc_start: 0.7436 (tppt) cc_final: 0.7028 (tmtt) REVERT: B 521 MET cc_start: 0.9266 (mtm) cc_final: 0.9001 (mtm) REVERT: B 677 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: D 34 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7149 (mtmm) REVERT: E 10 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8057 (ttpt) REVERT: I 10 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8065 (ttpt) outliers start: 39 outliers final: 12 residues processed: 172 average time/residue: 0.5580 time to fit residues: 103.8287 Evaluate side-chains 170 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 13 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 122 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 116 optimal weight: 0.0670 chunk 129 optimal weight: 8.9990 chunk 32 optimal weight: 0.0000 chunk 11 optimal weight: 5.9990 overall best weight: 1.1926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.085565 restraints weight = 17766.226| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.62 r_work: 0.2902 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13460 Z= 0.145 Angle : 0.518 7.376 18116 Z= 0.263 Chirality : 0.040 0.149 1938 Planarity : 0.004 0.045 2146 Dihedral : 11.928 129.163 2582 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 3.45 % Allowed : 9.42 % Favored : 87.13 % 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 are not related in a simple way. whole: 2.97 (0.22), residues: 1458 helix: 2.44 (0.15), residues: 1130 sheet: -1.43 (0.99), residues: 30 loop : 0.54 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 36 TYR 0.018 0.001 TYR C 12 PHE 0.016 0.001 PHE B 159 TRP 0.018 0.001 TRP A 624 HIS 0.009 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (13460) covalent geometry : angle 0.51790 / 0.26 (18116) hydrogen bonds : bond 0.04533 / 2.86 ( 890) hydrogen bonds : angle 4.02878 / 2.93 ( 2616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8085 (mp10) REVERT: A 254 LYS cc_start: 0.7986 (mttt) cc_final: 0.7414 (mmmt) REVERT: A 255 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7572 (mt) REVERT: A 311 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: A 389 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.6529 (t80) REVERT: A 413 LYS cc_start: 0.7433 (tppt) cc_final: 0.7140 (tmtt) REVERT: A 521 MET cc_start: 0.9246 (mtm) cc_final: 0.9030 (mtm) REVERT: B 190 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: B 254 LYS cc_start: 0.7978 (mttt) cc_final: 0.7400 (mmmt) REVERT: B 255 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7587 (mt) REVERT: B 308 GLU cc_start: 0.7875 (tp30) cc_final: 0.7309 (tp30) REVERT: B 311 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: B 389 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.6522 (t80) REVERT: B 521 MET cc_start: 0.9287 (mtm) cc_final: 0.9026 (mtm) REVERT: E 10 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8079 (ttpt) REVERT: I 10 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8089 (ttpt) outliers start: 44 outliers final: 12 residues processed: 173 average time/residue: 0.5386 time to fit residues: 101.4738 Evaluate side-chains 175 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 13 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 95 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.110676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.083584 restraints weight = 17671.464| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.66 r_work: 0.2883 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13460 Z= 0.115 Angle : 0.486 7.400 18116 Z= 0.247 Chirality : 0.039 0.139 1938 Planarity : 0.004 0.042 2146 Dihedral : 11.157 119.561 2582 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.35 % Allowed : 10.28 % Favored : 87.36 % 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 are not related in a simple way. whole: 3.05 (0.22), residues: 1458 helix: 2.52 (0.15), residues: 1130 sheet: -1.40 (1.00), residues: 30 loop : 0.47 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 36 TYR 0.021 0.001 TYR A 261 PHE 0.015 0.001 PHE B 159 TRP 0.022 0.001 TRP B 624 HIS 0.009 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (13460) covalent geometry : angle 0.48562 / 0.25 (18116) hydrogen bonds : bond 0.04028 / 2.54 ( 890) hydrogen bonds : angle 3.91129 / 2.84 ( 2616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.440 Fit side-chains REVERT: A 254 LYS cc_start: 0.7924 (mttt) cc_final: 0.7334 (mmmt) REVERT: A 255 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7485 (mt) REVERT: A 311 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: A 389 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.6345 (t80) REVERT: A 521 MET cc_start: 0.9219 (mtm) cc_final: 0.8963 (mtm) REVERT: B 254 LYS cc_start: 0.7901 (mttt) cc_final: 0.7312 (mmmt) REVERT: B 255 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7457 (mt) REVERT: B 311 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: B 389 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.6338 (t80) REVERT: B 521 MET cc_start: 0.9251 (mtm) cc_final: 0.9020 (mtm) REVERT: D 34 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7086 (mtmm) REVERT: E 10 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8037 (ttpt) REVERT: H 34 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7292 (mtmm) REVERT: I 10 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8056 (ttpt) outliers start: 30 outliers final: 10 residues processed: 164 average time/residue: 0.5675 time to fit residues: 100.8691 Evaluate side-chains 165 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 13 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS B 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.109997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.082827 restraints weight = 17619.404| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.66 r_work: 0.2872 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13460 Z= 0.124 Angle : 0.498 8.259 18116 Z= 0.252 Chirality : 0.039 0.140 1938 Planarity : 0.004 0.044 2146 Dihedral : 10.931 114.043 2582 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.12 % Allowed : 10.75 % Favored : 87.13 % 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 are not related in a simple way. whole: 3.07 (0.22), residues: 1458 helix: 2.53 (0.15), residues: 1130 sheet: -1.37 (0.99), residues: 30 loop : 0.50 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 198 TYR 0.024 0.001 TYR A 261 PHE 0.015 0.001 PHE B 159 TRP 0.019 0.001 TRP B 624 HIS 0.009 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (13460) covalent geometry : angle 0.49830 / 0.25 (18116) hydrogen bonds : bond 0.04120 / 2.60 ( 890) hydrogen bonds : angle 3.92280 / 2.85 ( 2616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7917 (mttt) cc_final: 0.7330 (mmmt) REVERT: A 255 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7467 (mt) REVERT: A 311 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: A 389 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.6546 (t80) REVERT: A 521 MET cc_start: 0.9230 (mtm) cc_final: 0.9028 (mtm) REVERT: A 646 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7667 (tt) REVERT: B 254 LYS cc_start: 0.7901 (mttt) cc_final: 0.7322 (mmmt) REVERT: B 311 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: B 389 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.6551 (t80) REVERT: B 413 LYS cc_start: 0.7568 (tmtt) cc_final: 0.7004 (tppt) REVERT: B 521 MET cc_start: 0.9258 (mtm) cc_final: 0.9007 (mtm) REVERT: B 646 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7626 (tt) REVERT: E 10 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8037 (ttpt) REVERT: H 34 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7285 (mtmm) REVERT: I 10 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8037 (ttpt) outliers start: 27 outliers final: 11 residues processed: 159 average time/residue: 0.5580 time to fit residues: 96.4788 Evaluate side-chains 165 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 643 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 13 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS B 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.083060 restraints weight = 17701.130| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.66 r_work: 0.2878 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13460 Z= 0.119 Angle : 0.493 8.083 18116 Z= 0.249 Chirality : 0.039 0.136 1938 Planarity : 0.004 0.044 2146 Dihedral : 10.605 107.243 2582 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.28 % Allowed : 11.38 % Favored : 86.34 % 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 are not related in a simple way. whole: 3.17 (0.22), residues: 1458 helix: 2.59 (0.15), residues: 1130 sheet: -1.39 (0.99), residues: 30 loop : 0.58 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 198 TYR 0.026 0.001 TYR A 261 PHE 0.021 0.001 PHE B 33 TRP 0.020 0.001 TRP B 624 HIS 0.009 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13460) covalent geometry : angle 0.49267 / 0.25 (18116) hydrogen bonds : bond 0.04024 / 2.54 ( 890) hydrogen bonds : angle 3.87221 / 2.82 ( 2616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: A 254 LYS cc_start: 0.7891 (mttt) cc_final: 0.7290 (mmmt) REVERT: A 255 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7460 (mt) REVERT: A 311 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: A 389 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.6586 (t80) REVERT: A 646 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7595 (tt) REVERT: B 190 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: B 254 LYS cc_start: 0.7899 (mttt) cc_final: 0.7327 (mmmt) REVERT: B 311 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: B 389 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.6583 (t80) REVERT: B 413 LYS cc_start: 0.7608 (tmtt) cc_final: 0.6996 (tppt) REVERT: B 416 VAL cc_start: 0.7403 (t) cc_final: 0.7065 (t) REVERT: B 521 MET cc_start: 0.9257 (mtm) cc_final: 0.9009 (mtm) REVERT: B 646 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7634 (tt) REVERT: E 10 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7983 (ttpt) REVERT: H 34 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7266 (mtmm) REVERT: I 10 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8048 (ttpt) outliers start: 29 outliers final: 10 residues processed: 159 average time/residue: 0.5315 time to fit residues: 91.9845 Evaluate side-chains 164 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 13 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 106 optimal weight: 0.0170 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS B 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.083791 restraints weight = 17731.186| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.66 r_work: 0.2887 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13460 Z= 0.115 Angle : 0.489 7.638 18116 Z= 0.247 Chirality : 0.038 0.133 1938 Planarity : 0.004 0.044 2146 Dihedral : 10.320 103.155 2582 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.96 % Allowed : 11.62 % Favored : 86.42 % 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 are not related in a simple way. whole: 3.26 (0.22), residues: 1458 helix: 2.66 (0.15), residues: 1130 sheet: -1.38 (1.00), residues: 30 loop : 0.63 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 198 TYR 0.027 0.001 TYR A 261 PHE 0.019 0.001 PHE B 33 TRP 0.020 0.001 TRP A 624 HIS 0.011 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (13460) covalent geometry : angle 0.48937 / 0.25 (18116) hydrogen bonds : bond 0.03911 / 2.47 ( 890) hydrogen bonds : angle 3.82024 / 2.78 ( 2616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7888 (mttt) cc_final: 0.7293 (mmmt) REVERT: A 255 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7456 (mt) REVERT: A 311 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: A 389 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.6537 (t80) REVERT: A 416 VAL cc_start: 0.7156 (OUTLIER) cc_final: 0.6867 (t) REVERT: A 646 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7602 (tt) REVERT: B 254 LYS cc_start: 0.7900 (mttt) cc_final: 0.7317 (mmmt) REVERT: B 311 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: B 389 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.6543 (t80) REVERT: B 413 LYS cc_start: 0.7655 (tmtt) cc_final: 0.7071 (tppt) REVERT: B 416 VAL cc_start: 0.7230 (OUTLIER) cc_final: 0.6863 (t) REVERT: B 521 MET cc_start: 0.9246 (mtm) cc_final: 0.9005 (mtm) REVERT: E 10 LYS cc_start: 0.8477 (tppp) cc_final: 0.7996 (ttpt) REVERT: H 34 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7158 (mtmm) REVERT: I 10 LYS cc_start: 0.8479 (tppp) cc_final: 0.7998 (ttpt) outliers start: 25 outliers final: 9 residues processed: 158 average time/residue: 0.5561 time to fit residues: 95.7234 Evaluate side-chains 159 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 13 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS B 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.081055 restraints weight = 17750.579| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.65 r_work: 0.2838 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13460 Z= 0.168 Angle : 0.540 7.554 18116 Z= 0.272 Chirality : 0.041 0.139 1938 Planarity : 0.004 0.046 2146 Dihedral : 10.847 106.480 2582 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.43 % Allowed : 11.70 % Favored : 85.87 % 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 are not related in a simple way. whole: 3.10 (0.22), residues: 1458 helix: 2.52 (0.15), residues: 1130 sheet: -1.33 (1.00), residues: 30 loop : 0.63 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.027 0.001 TYR A 261 PHE 0.019 0.002 PHE B 33 TRP 0.016 0.001 TRP B 624 HIS 0.010 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (13460) covalent geometry : angle 0.53962 / 0.27 (18116) hydrogen bonds : bond 0.04653 / 2.94 ( 890) hydrogen bonds : angle 4.00191 / 2.91 ( 2616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.06 seconds wall clock time: 62 minutes 22.59 seconds (3742.59 seconds total)