Starting phenix.real_space_refine on Thu May 15 21:58:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t56_41043/05_2025/8t56_41043.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t56_41043/05_2025/8t56_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t56_41043/05_2025/8t56_41043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t56_41043/05_2025/8t56_41043.map" model { file = "/net/cci-nas-00/data/ceres_data/8t56_41043/05_2025/8t56_41043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t56_41043/05_2025/8t56_41043.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.10, per 1000 atoms: 0.54 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: 3.07 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.31 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: 4.21 Time building geometry restraints manager: 3.58 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.470 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.550 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (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 TRP 0.037 0.007 TRP B 352 HIS 0.006 0.002 HIS A 236 PHE 0.061 0.005 PHE I 1 TYR 0.078 0.009 TYR A 181 ARG 0.008 0.001 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.17032 ( 890) hydrogen bonds : angle 6.45373 ( 2616) covalent geometry : bond 0.02720 (13460) covalent geometry : angle 1.65712 (18116) *********************** 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 : 1.444 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: 0.8680 (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: 1.3880 time to fit residues: 338.4129 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 : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3488 r_free = 0.3488 target = 0.112614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087096 restraints weight = 17848.918| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.63 r_work: 0.2936 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2150 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= 0.160 Angle : 0.599 6.896 18116 Z= 0.321 Chirality : 0.043 0.144 1938 Planarity : 0.005 0.044 2146 Dihedral : 14.729 174.673 2582 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.67 % Allowed : 6.67 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.21), residues: 1458 helix: 2.11 (0.15), residues: 1118 sheet: -0.87 (0.99), residues: 30 loop : 0.87 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 624 HIS 0.005 0.001 HIS A 379 PHE 0.022 0.002 PHE B 33 TYR 0.016 0.002 TYR A 261 ARG 0.007 0.001 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.05911 ( 890) hydrogen bonds : angle 4.67162 ( 2616) covalent geometry : bond 0.00346 (13460) covalent geometry : angle 0.59895 (18116) *********************** 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 : 1.317 Fit side-chains REVERT: A 261 TYR cc_start: 0.7239 (t80) cc_final: 0.7028 (t80) REVERT: A 311 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: A 389 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.6498 (t80) REVERT: B 254 LYS cc_start: 0.7960 (mttt) cc_final: 0.7398 (mmmt) REVERT: B 389 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.6492 (t80) REVERT: B 536 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.6688 (tptt) REVERT: H 29 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8097 (mtpp) outliers start: 34 outliers final: 2 residues processed: 170 average time/residue: 1.3069 time to fit residues: 241.3414 Evaluate side-chains 142 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 389 PHE Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain H residue 29 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 0.0870 chunk 135 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3505 r_free = 0.3505 target = 0.113880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.088390 restraints weight = 17992.698| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.64 r_work: 0.2958 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2833 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= 0.127 Angle : 0.509 7.080 18116 Z= 0.265 Chirality : 0.040 0.145 1938 Planarity : 0.004 0.047 2146 Dihedral : 13.431 172.729 2582 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.43 % Allowed : 7.61 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.21), residues: 1458 helix: 2.38 (0.15), residues: 1130 sheet: -1.04 (1.00), residues: 30 loop : 0.76 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 624 HIS 0.005 0.001 HIS A 293 PHE 0.016 0.002 PHE B 159 TYR 0.015 0.001 TYR B 261 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 890) hydrogen bonds : angle 4.20306 ( 2616) covalent geometry : bond 0.00276 (13460) covalent geometry : angle 0.50898 (18116) *********************** 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 203 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.332 Fit side-chains REVERT: A 78 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: A 261 TYR cc_start: 0.7451 (t80) cc_final: 0.7196 (t80) REVERT: A 389 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.6443 (t80) REVERT: A 446 MET cc_start: 0.8967 (tpt) cc_final: 0.8718 (tpp) REVERT: A 521 MET cc_start: 0.9243 (mtm) cc_final: 0.8988 (mtm) REVERT: B 36 ARG cc_start: 0.9119 (ttm-80) cc_final: 0.8881 (ttm-80) REVERT: B 254 LYS cc_start: 0.7921 (mttt) cc_final: 0.7397 (mmmt) REVERT: B 261 TYR cc_start: 0.7476 (t80) cc_final: 0.7225 (t80) REVERT: B 311 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: B 389 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.6434 (t80) REVERT: E 12 TYR cc_start: 0.8963 (t80) cc_final: 0.8748 (t80) REVERT: H 29 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.8013 (mtpp) REVERT: H 34 LYS cc_start: 0.7944 (mtmm) cc_final: 0.7426 (mtmm) REVERT: I 12 TYR cc_start: 0.8977 (t80) cc_final: 0.8764 (t80) outliers start: 31 outliers final: 3 residues processed: 182 average time/residue: 1.2752 time to fit residues: 252.5616 Evaluate side-chains 151 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 417 ASP 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 H residue 29 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 3 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 109 optimal weight: 0.2980 chunk 134 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.087354 restraints weight = 17693.813| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.63 r_work: 0.2958 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3025 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= 0.126 Angle : 0.502 7.477 18116 Z= 0.256 Chirality : 0.039 0.144 1938 Planarity : 0.004 0.046 2146 Dihedral : 12.889 163.138 2582 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.59 % Allowed : 9.42 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.22), residues: 1458 helix: 2.45 (0.15), residues: 1130 sheet: -1.37 (0.96), residues: 30 loop : 0.75 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.007 0.001 HIS B 293 PHE 0.021 0.001 PHE B 33 TYR 0.021 0.001 TYR C 12 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 890) hydrogen bonds : angle 4.07732 ( 2616) covalent geometry : bond 0.00286 (13460) covalent geometry : angle 0.50169 (18116) *********************** 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 188 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.9013 (ttm-80) cc_final: 0.8705 (ttm-80) REVERT: A 254 LYS cc_start: 0.7984 (mttt) cc_final: 0.7410 (mmmt) REVERT: A 255 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7564 (mt) REVERT: A 311 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: A 389 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.6436 (t80) REVERT: A 521 MET cc_start: 0.9268 (mtm) cc_final: 0.9031 (mtm) REVERT: A 535 LEU cc_start: 0.8572 (mt) cc_final: 0.8367 (mp) REVERT: A 677 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: B 36 ARG cc_start: 0.9119 (ttm-80) cc_final: 0.8856 (ttm-80) REVERT: B 254 LYS cc_start: 0.8020 (mttt) cc_final: 0.7429 (mmmt) REVERT: B 311 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: B 389 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.6431 (t80) REVERT: B 535 LEU cc_start: 0.8575 (mt) cc_final: 0.8358 (mp) REVERT: B 677 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: D 34 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7266 (mtmm) REVERT: H 29 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.8023 (mtpp) outliers start: 33 outliers final: 5 residues processed: 170 average time/residue: 1.2971 time to fit residues: 239.6526 Evaluate side-chains 159 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU 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 416 VAL Chi-restraints excluded: chain A residue 417 ASP 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 677 GLU Chi-restraints excluded: chain H residue 29 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 87 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3495 r_free = 0.3495 target = 0.113150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.087759 restraints weight = 17735.701| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.63 r_work: 0.2963 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13460 Z= 0.117 Angle : 0.490 7.102 18116 Z= 0.249 Chirality : 0.039 0.153 1938 Planarity : 0.004 0.045 2146 Dihedral : 12.215 146.870 2582 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.67 % Allowed : 10.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.22), residues: 1458 helix: 2.54 (0.15), residues: 1130 sheet: -1.38 (0.98), residues: 30 loop : 0.73 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 624 HIS 0.008 0.001 HIS A 293 PHE 0.017 0.001 PHE B 33 TYR 0.020 0.001 TYR B 261 ARG 0.003 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 890) hydrogen bonds : angle 3.96836 ( 2616) covalent geometry : bond 0.00264 (13460) covalent geometry : angle 0.48972 (18116) *********************** 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 188 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7944 (mttt) cc_final: 0.7350 (mmmt) REVERT: A 255 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7488 (mt) REVERT: A 311 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: A 389 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.6469 (t80) REVERT: A 521 MET cc_start: 0.9247 (mtm) cc_final: 0.8956 (mtm) REVERT: A 677 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: B 254 LYS cc_start: 0.7982 (mttt) cc_final: 0.7402 (mmmt) REVERT: B 311 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: B 389 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.6435 (t80) REVERT: B 413 LYS cc_start: 0.7498 (tppt) cc_final: 0.7116 (tmtt) REVERT: B 677 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: E 10 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8056 (ttpt) REVERT: I 10 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8059 (ttpt) outliers start: 34 outliers final: 10 residues processed: 170 average time/residue: 1.3154 time to fit residues: 243.0625 Evaluate side-chains 166 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 416 VAL 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 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 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 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 0 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3450 r_free = 0.3450 target = 0.110051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.084494 restraints weight = 18034.605| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.61 r_work: 0.2902 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3184 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= 0.173 Angle : 0.544 7.356 18116 Z= 0.275 Chirality : 0.042 0.152 1938 Planarity : 0.005 0.045 2146 Dihedral : 12.157 129.781 2582 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 3.30 % Allowed : 10.05 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.22), residues: 1458 helix: 2.40 (0.15), residues: 1130 sheet: -1.43 (0.99), residues: 30 loop : 0.65 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 624 HIS 0.009 0.001 HIS A 293 PHE 0.016 0.002 PHE B 225 TYR 0.020 0.002 TYR A 261 ARG 0.005 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04850 ( 890) hydrogen bonds : angle 4.10907 ( 2616) covalent geometry : bond 0.00426 (13460) covalent geometry : angle 0.54426 (18116) *********************** 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 191 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8068 (mp10) REVERT: A 254 LYS cc_start: 0.7957 (mttt) cc_final: 0.7376 (mmmt) REVERT: A 255 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7550 (mt) REVERT: A 311 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: A 389 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.6525 (t80) REVERT: A 521 MET cc_start: 0.9275 (mtm) cc_final: 0.9033 (mtm) REVERT: B 190 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: B 254 LYS cc_start: 0.7990 (mttt) cc_final: 0.7412 (mmmt) REVERT: B 255 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7582 (mt) REVERT: B 311 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: B 389 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.6519 (t80) REVERT: E 10 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8067 (ttpt) REVERT: I 10 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8079 (ttpt) outliers start: 42 outliers final: 13 residues processed: 163 average time/residue: 1.2841 time to fit residues: 228.3328 Evaluate side-chains 168 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 416 VAL 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 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 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 128 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 125 optimal weight: 0.0970 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 98 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3495 r_free = 0.3495 target = 0.113288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087548 restraints weight = 17816.279| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.62 r_work: 0.2961 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13460 Z= 0.113 Angle : 0.483 7.264 18116 Z= 0.245 Chirality : 0.038 0.141 1938 Planarity : 0.004 0.043 2146 Dihedral : 11.203 119.378 2582 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.96 % Allowed : 11.46 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.22), residues: 1458 helix: 2.57 (0.15), residues: 1130 sheet: -1.45 (0.99), residues: 30 loop : 0.58 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 624 HIS 0.009 0.001 HIS A 293 PHE 0.015 0.001 PHE B 159 TYR 0.020 0.001 TYR A 261 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 890) hydrogen bonds : angle 3.90123 ( 2616) covalent geometry : bond 0.00246 (13460) covalent geometry : angle 0.48290 (18116) *********************** 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 177 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7987 (mttt) cc_final: 0.7406 (mmmt) REVERT: A 311 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: A 389 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.6425 (t80) REVERT: A 416 VAL cc_start: 0.7269 (OUTLIER) cc_final: 0.6933 (t) REVERT: A 521 MET cc_start: 0.9242 (mtm) cc_final: 0.9019 (mtm) REVERT: A 646 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7615 (tt) REVERT: B 254 LYS cc_start: 0.7997 (mttt) cc_final: 0.7418 (mmmt) REVERT: B 255 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7572 (mt) REVERT: B 311 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: B 389 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.6416 (t80) REVERT: B 413 LYS cc_start: 0.7476 (tppt) cc_final: 0.7158 (tmtt) REVERT: B 646 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7633 (tt) REVERT: E 10 LYS cc_start: 0.8612 (tppp) cc_final: 0.8110 (ttpt) REVERT: I 10 LYS cc_start: 0.8629 (tppp) cc_final: 0.8127 (ttpt) outliers start: 25 outliers final: 9 residues processed: 163 average time/residue: 1.2558 time to fit residues: 223.5559 Evaluate side-chains 162 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 9 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain I residue 9 VAL 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 133 optimal weight: 6.9990 chunk 6 optimal weight: 0.0570 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3427 r_free = 0.3427 target = 0.109546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.082384 restraints weight = 17823.512| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.66 r_work: 0.2860 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3366 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= 0.142 Angle : 0.512 8.031 18116 Z= 0.259 Chirality : 0.040 0.146 1938 Planarity : 0.004 0.045 2146 Dihedral : 11.088 114.257 2582 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.35 % Allowed : 10.36 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.22), residues: 1458 helix: 2.52 (0.15), residues: 1130 sheet: -1.38 (0.98), residues: 30 loop : 0.56 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 624 HIS 0.009 0.001 HIS B 293 PHE 0.016 0.001 PHE B 159 TYR 0.024 0.001 TYR A 261 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 890) hydrogen bonds : angle 3.95735 ( 2616) covalent geometry : bond 0.00340 (13460) covalent geometry : angle 0.51185 (18116) *********************** 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 176 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7882 (mttt) cc_final: 0.7287 (mmmt) REVERT: A 255 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7474 (mt) REVERT: A 311 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: A 389 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.6438 (t80) REVERT: A 416 VAL cc_start: 0.7226 (OUTLIER) cc_final: 0.6930 (t) REVERT: A 521 MET cc_start: 0.9254 (mtm) cc_final: 0.9034 (mtm) REVERT: A 646 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7640 (tt) REVERT: B 254 LYS cc_start: 0.7924 (mttt) cc_final: 0.7340 (mmmt) REVERT: B 255 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7495 (mt) REVERT: B 311 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: B 389 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.6425 (t80) REVERT: B 646 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7655 (tt) REVERT: E 10 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8056 (ttpt) REVERT: I 10 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8052 (ttpt) outliers start: 30 outliers final: 11 residues processed: 161 average time/residue: 1.3094 time to fit residues: 229.3947 Evaluate side-chains 166 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 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 643 MET 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 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 133 optimal weight: 0.9990 chunk 118 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3445 r_free = 0.3445 target = 0.110850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.083739 restraints weight = 17650.302| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.66 r_work: 0.2889 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13460 Z= 0.111 Angle : 0.489 8.526 18116 Z= 0.247 Chirality : 0.038 0.138 1938 Planarity : 0.004 0.043 2146 Dihedral : 10.674 108.850 2582 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.12 % Allowed : 10.91 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.22), residues: 1458 helix: 2.61 (0.15), residues: 1130 sheet: -1.42 (0.98), residues: 30 loop : 0.57 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 624 HIS 0.010 0.001 HIS B 293 PHE 0.015 0.001 PHE B 159 TYR 0.025 0.001 TYR B 261 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 890) hydrogen bonds : angle 3.86715 ( 2616) covalent geometry : bond 0.00244 (13460) covalent geometry : angle 0.48944 (18116) *********************** 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 170 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7907 (mttt) cc_final: 0.7318 (mmmt) REVERT: A 255 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7447 (mt) REVERT: A 311 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: A 389 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.6517 (t80) REVERT: A 416 VAL cc_start: 0.7156 (OUTLIER) cc_final: 0.6843 (t) REVERT: A 521 MET cc_start: 0.9232 (mtm) cc_final: 0.8992 (mtm) REVERT: A 646 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7587 (tt) REVERT: B 254 LYS cc_start: 0.7921 (mttt) cc_final: 0.7329 (mmmt) REVERT: B 311 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: B 389 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.6513 (t80) REVERT: B 559 MET cc_start: 0.7899 (ttp) cc_final: 0.7641 (ptt) REVERT: B 646 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7589 (tt) REVERT: E 10 LYS cc_start: 0.8554 (tppp) cc_final: 0.8065 (ttpt) REVERT: I 10 LYS cc_start: 0.8556 (tppp) cc_final: 0.8064 (ttpt) outliers start: 27 outliers final: 10 residues processed: 156 average time/residue: 1.2686 time to fit residues: 215.4188 Evaluate side-chains 160 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 587 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 13 PHE 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 48 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 84 optimal weight: 0.2980 chunk 133 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3445 r_free = 0.3445 target = 0.110789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.083644 restraints weight = 17683.397| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.66 r_work: 0.2884 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3516 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= 0.117 Angle : 0.497 7.848 18116 Z= 0.250 Chirality : 0.038 0.137 1938 Planarity : 0.004 0.044 2146 Dihedral : 10.483 105.185 2582 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.81 % Allowed : 11.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.22), residues: 1458 helix: 2.62 (0.15), residues: 1130 sheet: -1.36 (0.99), residues: 30 loop : 0.59 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 624 HIS 0.009 0.001 HIS B 293 PHE 0.021 0.001 PHE B 33 TYR 0.026 0.001 TYR B 261 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 890) hydrogen bonds : angle 3.84936 ( 2616) covalent geometry : bond 0.00264 (13460) covalent geometry : angle 0.49727 (18116) ********************** 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 169 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7867 (mttt) cc_final: 0.7270 (mmmt) REVERT: A 255 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7453 (mt) REVERT: A 311 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: A 389 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.6597 (t80) REVERT: A 416 VAL cc_start: 0.7070 (OUTLIER) cc_final: 0.6762 (t) REVERT: A 521 MET cc_start: 0.9235 (mtm) cc_final: 0.8981 (mtm) REVERT: A 646 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7593 (tt) REVERT: B 254 LYS cc_start: 0.7905 (mttt) cc_final: 0.7323 (mmmt) REVERT: B 311 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: B 389 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.6596 (t80) REVERT: B 559 MET cc_start: 0.8041 (ttp) cc_final: 0.7744 (ptt) REVERT: E 10 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8051 (ttpt) REVERT: I 10 LYS cc_start: 0.8535 (tppp) cc_final: 0.8051 (ttpt) outliers start: 23 outliers final: 10 residues processed: 157 average time/residue: 1.3352 time to fit residues: 227.7291 Evaluate side-chains 157 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU 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 646 LEU Chi-restraints excluded: chain B residue 222 GLU 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 E residue 9 VAL Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 13 PHE 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 54 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3427 r_free = 0.3427 target = 0.109425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.082171 restraints weight = 17821.791| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.66 r_work: 0.2857 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3477 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= 0.143 Angle : 0.530 9.857 18116 Z= 0.266 Chirality : 0.040 0.155 1938 Planarity : 0.004 0.045 2146 Dihedral : 10.677 105.377 2582 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.20 % Allowed : 11.54 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.22), residues: 1458 helix: 2.57 (0.15), residues: 1130 sheet: -1.36 (0.99), residues: 30 loop : 0.60 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 624 HIS 0.011 0.001 HIS A 293 PHE 0.022 0.001 PHE B 33 TYR 0.028 0.001 TYR B 261 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 890) hydrogen bonds : angle 3.93290 ( 2616) covalent geometry : bond 0.00341 (13460) covalent geometry : angle 0.52975 (18116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8401.46 seconds wall clock time: 145 minutes 14.51 seconds (8714.51 seconds total)