Starting phenix.real_space_refine on Thu Jul 31 16:47:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t56_41043/07_2025/8t56_41043.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t56_41043/07_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_41043/07_2025/8t56_41043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t56_41043/07_2025/8t56_41043.map" model { file = "/net/cci-nas-00/data/ceres_data/8t56_41043/07_2025/8t56_41043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t56_41043/07_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.77, per 1000 atoms: 0.59 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: 3.47 Conformation dependent library (CDL) restraints added in 1.5 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: 1.32 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: 3.75 Time building geometry restraints manager: 4.01 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.810 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- 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 : 1.405 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: 1.4465 time to fit residues: 352.9159 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 : 1.411 ------------------------------------------------------------------------------- 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 = 0.112606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087137 restraints weight = 17853.528| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.62 r_work: 0.2955 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 6.902 18116 Z= 0.321 Chirality : 0.043 0.143 1938 Planarity : 0.005 0.044 2146 Dihedral : 14.729 174.666 2582 Min Nonbonded Distance : 2.625 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 0.05909 ( 890) hydrogen bonds : angle 4.67173 ( 2616) covalent geometry : bond 0.00346 (13460) covalent geometry : angle 0.59925 (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 : 1.289 Fit side-chains REVERT: A 261 TYR cc_start: 0.7259 (t80) cc_final: 0.7049 (t80) REVERT: A 389 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.6505 (t80) REVERT: B 254 LYS cc_start: 0.7969 (mttt) cc_final: 0.7408 (mmmt) REVERT: B 389 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.6500 (t80) REVERT: B 536 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6696 (tptt) REVERT: H 29 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8106 (mtpp) outliers start: 34 outliers final: 2 residues processed: 170 average time/residue: 1.3641 time to fit residues: 252.1977 Evaluate side-chains 140 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 71 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 57 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.114184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.088733 restraints weight = 18012.685| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.64 r_work: 0.2963 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13460 Z= 0.123 Angle : 0.505 7.199 18116 Z= 0.263 Chirality : 0.039 0.144 1938 Planarity : 0.004 0.047 2146 Dihedral : 13.507 173.883 2582 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.94 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: 2.98 (0.21), residues: 1458 helix: 2.39 (0.15), residues: 1130 sheet: -1.02 (1.00), residues: 30 loop : 0.77 (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 0.014 0.001 TYR I 12 ARG 0.004 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 890) hydrogen bonds : angle 4.21379 ( 2616) covalent geometry : bond 0.00262 (13460) covalent geometry : angle 0.50473 (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 202 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 1.330 Fit side-chains REVERT: A 78 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: A 261 TYR cc_start: 0.7414 (t80) cc_final: 0.7167 (t80) REVERT: A 311 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: A 389 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.6421 (t80) REVERT: A 446 MET cc_start: 0.8959 (tpt) cc_final: 0.8420 (tpt) REVERT: A 521 MET cc_start: 0.9252 (mtm) cc_final: 0.8950 (mtm) REVERT: A 689 MET cc_start: 0.9257 (tpp) cc_final: 0.9015 (tpt) REVERT: B 36 ARG cc_start: 0.9115 (ttm-80) cc_final: 0.8877 (ttm-80) REVERT: B 254 LYS cc_start: 0.7927 (mttt) cc_final: 0.7381 (mmmt) REVERT: B 261 TYR cc_start: 0.7463 (t80) cc_final: 0.7236 (t80) REVERT: B 311 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: B 389 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.6439 (t80) REVERT: B 689 MET cc_start: 0.9258 (tpp) cc_final: 0.9022 (tpt) REVERT: E 12 TYR cc_start: 0.8970 (t80) cc_final: 0.8745 (t80) REVERT: H 29 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8027 (mtpp) REVERT: H 34 LYS cc_start: 0.7952 (mtmm) cc_final: 0.7435 (mtmm) REVERT: I 12 TYR cc_start: 0.8975 (t80) cc_final: 0.8751 (t80) outliers start: 31 outliers final: 4 residues processed: 182 average time/residue: 1.3494 time to fit residues: 267.2884 Evaluate side-chains 156 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 129 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 109 optimal weight: 0.0970 chunk 134 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.111574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.085769 restraints weight = 17680.786| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.64 r_work: 0.2928 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13460 Z= 0.150 Angle : 0.524 7.342 18116 Z= 0.269 Chirality : 0.041 0.153 1938 Planarity : 0.004 0.047 2146 Dihedral : 13.055 163.165 2582 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.51 % Allowed : 9.11 % Favored : 88.38 % 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: 2.93 (0.21), residues: 1458 helix: 2.36 (0.15), residues: 1130 sheet: -1.36 (0.99), residues: 30 loop : 0.75 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 624 HIS 0.007 0.001 HIS B 293 PHE 0.021 0.002 PHE B 33 TYR 0.020 0.002 TYR C 12 ARG 0.003 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 890) hydrogen bonds : angle 4.15899 ( 2616) covalent geometry : bond 0.00362 (13460) covalent geometry : angle 0.52424 (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 186 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7947 (mttt) cc_final: 0.7378 (mmmt) REVERT: A 255 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7546 (mt) REVERT: A 389 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.6477 (t80) REVERT: A 521 MET cc_start: 0.9274 (mtm) cc_final: 0.9020 (mtm) REVERT: B 254 LYS cc_start: 0.7994 (mttt) cc_final: 0.7440 (mmmt) REVERT: B 261 TYR cc_start: 0.7521 (t80) cc_final: 0.7296 (t80) REVERT: B 311 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: B 389 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.6461 (t80) REVERT: D 29 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8079 (mtpp) REVERT: E 13 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8718 (t80) REVERT: H 29 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8048 (mtpp) outliers start: 32 outliers final: 6 residues processed: 170 average time/residue: 1.3770 time to fit residues: 254.3023 Evaluate side-chains 160 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU 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 646 LEU 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 646 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain E residue 13 PHE 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: 0.0870 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.112733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087054 restraints weight = 17772.014| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.63 r_work: 0.2953 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3144 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= 0.120 Angle : 0.492 7.438 18116 Z= 0.251 Chirality : 0.039 0.153 1938 Planarity : 0.004 0.045 2146 Dihedral : 12.419 149.474 2582 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.43 % Allowed : 10.28 % 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: 3.02 (0.22), residues: 1458 helix: 2.45 (0.15), residues: 1130 sheet: -1.36 (1.00), residues: 30 loop : 0.67 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 624 HIS 0.008 0.001 HIS A 293 PHE 0.016 0.001 PHE B 33 TYR 0.017 0.001 TYR A 261 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 890) hydrogen bonds : angle 4.01660 ( 2616) covalent geometry : bond 0.00269 (13460) covalent geometry : angle 0.49241 (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: 31 poor density : 157 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7973 (mttt) cc_final: 0.7385 (mmmt) REVERT: A 255 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7529 (mt) REVERT: A 311 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: A 389 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.6434 (t80) REVERT: A 416 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7218 (t) REVERT: A 521 MET cc_start: 0.9255 (mtm) cc_final: 0.9020 (mtm) REVERT: A 677 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: B 254 LYS cc_start: 0.8028 (mttt) cc_final: 0.7451 (mmmt) REVERT: B 308 GLU cc_start: 0.7848 (tp30) cc_final: 0.7303 (tp30) REVERT: B 311 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: B 389 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.6428 (t80) REVERT: B 413 LYS cc_start: 0.7439 (tppt) cc_final: 0.7008 (ttmm) REVERT: B 677 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: D 34 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7345 (mtmm) REVERT: H 29 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.8024 (mtpp) REVERT: I 10 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8086 (ttpt) outliers start: 31 outliers final: 9 residues processed: 173 average time/residue: 1.3384 time to fit residues: 251.8150 Evaluate side-chains 164 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 587 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain H residue 29 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 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: 0.8980 chunk 123 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.109012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.083484 restraints weight = 18032.681| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.60 r_work: 0.2893 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13460 Z= 0.196 Angle : 0.566 7.508 18116 Z= 0.287 Chirality : 0.043 0.160 1938 Planarity : 0.005 0.045 2146 Dihedral : 12.348 131.457 2582 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 3.53 % Allowed : 9.65 % Favored : 86.81 % 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: 2.79 (0.22), residues: 1458 helix: 2.27 (0.15), residues: 1130 sheet: -1.40 (0.99), residues: 30 loop : 0.66 (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 0.019 0.002 PHE G 13 TYR 0.022 0.002 TYR A 468 ARG 0.005 0.001 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.05143 ( 890) hydrogen bonds : angle 4.18821 ( 2616) covalent geometry : bond 0.00491 (13460) covalent geometry : angle 0.56590 (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 196 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8084 (mp10) REVERT: A 254 LYS cc_start: 0.7940 (mttt) cc_final: 0.7361 (mmmt) REVERT: A 255 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7575 (mt) REVERT: A 311 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: A 389 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.6533 (t80) REVERT: A 521 MET cc_start: 0.9269 (mtm) cc_final: 0.9020 (mtm) REVERT: B 190 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: B 254 LYS cc_start: 0.8018 (mttt) cc_final: 0.7473 (mmmt) REVERT: B 255 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7631 (mt) REVERT: B 308 GLU cc_start: 0.7869 (tp30) cc_final: 0.7299 (tp30) REVERT: B 311 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: B 389 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.6526 (t80) REVERT: E 10 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8104 (ttpt) REVERT: I 10 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8081 (ttpt) outliers start: 45 outliers final: 17 residues processed: 168 average time/residue: 1.3978 time to fit residues: 255.4090 Evaluate side-chains 175 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLN 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 643 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 222 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 128 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 15 optimal weight: 0.0040 chunk 115 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 76 optimal weight: 0.1980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.112888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.087286 restraints weight = 17797.678| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.62 r_work: 0.2950 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13460 Z= 0.114 Angle : 0.491 7.481 18116 Z= 0.250 Chirality : 0.038 0.143 1938 Planarity : 0.004 0.043 2146 Dihedral : 11.342 121.135 2582 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.04 % Allowed : 11.38 % 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: 3.02 (0.22), residues: 1458 helix: 2.47 (0.15), residues: 1130 sheet: -1.48 (0.98), residues: 30 loop : 0.58 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 624 HIS 0.009 0.001 HIS B 293 PHE 0.015 0.001 PHE B 33 TYR 0.020 0.001 TYR A 261 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 890) hydrogen bonds : angle 3.95244 ( 2616) covalent geometry : bond 0.00248 (13460) covalent geometry : angle 0.49121 (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 176 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7953 (mttt) cc_final: 0.7360 (mmmt) REVERT: A 311 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: A 389 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.6424 (t80) REVERT: A 416 VAL cc_start: 0.7326 (OUTLIER) cc_final: 0.6991 (t) REVERT: A 521 MET cc_start: 0.9244 (mtm) cc_final: 0.9022 (mtm) REVERT: B 254 LYS cc_start: 0.8027 (mttt) cc_final: 0.7446 (mmmt) REVERT: B 255 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7587 (mt) REVERT: B 308 GLU cc_start: 0.7850 (tp30) cc_final: 0.7351 (tp30) REVERT: B 311 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: B 389 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.6426 (t80) REVERT: B 413 LYS cc_start: 0.7475 (tppt) cc_final: 0.7160 (tmtt) REVERT: B 646 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7634 (tp) REVERT: E 10 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8111 (ttpt) REVERT: I 10 LYS cc_start: 0.8615 (tppp) cc_final: 0.8111 (ttpt) outliers start: 26 outliers final: 9 residues processed: 160 average time/residue: 1.3672 time to fit residues: 237.4448 Evaluate side-chains 163 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 417 ASP 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 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: 0.9990 chunk 6 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 65 optimal weight: 0.0170 chunk 95 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.110915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.083828 restraints weight = 17787.412| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.67 r_work: 0.2887 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13460 Z= 0.113 Angle : 0.485 7.695 18116 Z= 0.246 Chirality : 0.038 0.145 1938 Planarity : 0.004 0.044 2146 Dihedral : 10.768 111.100 2582 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.04 % Allowed : 10.99 % 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: 3.13 (0.22), residues: 1458 helix: 2.56 (0.15), residues: 1130 sheet: -1.36 (1.00), residues: 30 loop : 0.58 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 624 HIS 0.010 0.001 HIS A 293 PHE 0.015 0.001 PHE B 159 TYR 0.022 0.001 TYR B 261 ARG 0.005 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 890) hydrogen bonds : angle 3.87470 ( 2616) covalent geometry : bond 0.00249 (13460) covalent geometry : angle 0.48489 (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 179 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7432 (mt) REVERT: A 311 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: A 389 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.6479 (t80) REVERT: A 416 VAL cc_start: 0.7144 (OUTLIER) cc_final: 0.6845 (t) REVERT: A 521 MET cc_start: 0.9236 (mtm) cc_final: 0.9007 (mtm) REVERT: B 254 LYS cc_start: 0.7949 (mttt) cc_final: 0.7361 (mmmt) REVERT: B 255 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7507 (mt) REVERT: B 308 GLU cc_start: 0.7850 (tp30) cc_final: 0.7343 (tp30) REVERT: B 311 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: B 389 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.6530 (t80) REVERT: B 413 LYS cc_start: 0.7520 (tppt) cc_final: 0.7277 (tmtt) REVERT: B 646 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7605 (tp) REVERT: E 10 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8053 (ttpt) REVERT: I 10 LYS cc_start: 0.8552 (tppp) cc_final: 0.8059 (ttpt) outliers start: 26 outliers final: 7 residues processed: 167 average time/residue: 1.3871 time to fit residues: 251.6672 Evaluate side-chains 160 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 643 MET 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 646 LEU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 13 PHE 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: 0.0170 chunk 118 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 114 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 102 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 overall best weight: 0.2018 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.113473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.086542 restraints weight = 17617.864| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.66 r_work: 0.2934 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13460 Z= 0.100 Angle : 0.476 8.159 18116 Z= 0.239 Chirality : 0.037 0.137 1938 Planarity : 0.004 0.042 2146 Dihedral : 10.221 103.600 2582 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.73 % Allowed : 11.77 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.22), residues: 1458 helix: 2.69 (0.15), residues: 1128 sheet: -1.46 (0.99), residues: 30 loop : 0.62 (0.35), residues: 300 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 0.014 0.001 PHE B 159 TYR 0.025 0.001 TYR B 261 ARG 0.004 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 890) hydrogen bonds : angle 3.75360 ( 2616) covalent geometry : bond 0.00203 (13460) covalent geometry : angle 0.47635 (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 172 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7394 (mt) REVERT: A 311 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: A 389 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.6542 (t80) REVERT: A 416 VAL cc_start: 0.6970 (OUTLIER) cc_final: 0.6680 (t) REVERT: A 446 MET cc_start: 0.8908 (tpt) cc_final: 0.8399 (tpt) REVERT: A 521 MET cc_start: 0.9185 (mtm) cc_final: 0.8962 (mtm) REVERT: B 254 LYS cc_start: 0.7907 (mttt) cc_final: 0.7314 (mmmt) REVERT: B 255 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7486 (mt) REVERT: B 311 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: B 389 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.6527 (t80) REVERT: B 446 MET cc_start: 0.8957 (tpt) cc_final: 0.8690 (tpp) REVERT: B 521 MET cc_start: 0.9173 (mtm) cc_final: 0.8936 (mtm) REVERT: B 646 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7615 (tt) REVERT: E 10 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8049 (ttpt) REVERT: I 10 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8040 (ttpt) outliers start: 22 outliers final: 9 residues processed: 159 average time/residue: 1.3086 time to fit residues: 226.7806 Evaluate side-chains 159 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 643 MET 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 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 48 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3452 r_free = 0.3452 target = 0.111198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.084083 restraints weight = 17703.922| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.66 r_work: 0.2892 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13460 Z= 0.121 Angle : 0.501 8.670 18116 Z= 0.252 Chirality : 0.039 0.138 1938 Planarity : 0.004 0.045 2146 Dihedral : 10.249 102.003 2582 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.57 % Allowed : 12.32 % Favored : 86.11 % 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: 3.24 (0.22), residues: 1458 helix: 2.65 (0.15), residues: 1130 sheet: -1.40 (0.99), residues: 30 loop : 0.56 (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 0.022 0.001 PHE B 33 TYR 0.028 0.001 TYR B 261 ARG 0.005 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 890) hydrogen bonds : angle 3.80495 ( 2616) covalent geometry : bond 0.00280 (13460) covalent geometry : angle 0.50127 (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 163 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7441 (mt) REVERT: A 311 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: A 389 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.6591 (t80) REVERT: A 416 VAL cc_start: 0.7007 (OUTLIER) cc_final: 0.6727 (t) REVERT: A 521 MET cc_start: 0.9233 (mtm) cc_final: 0.9016 (mtm) REVERT: B 254 LYS cc_start: 0.7940 (mttt) cc_final: 0.7344 (mmmt) REVERT: B 255 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7506 (mt) REVERT: B 311 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: B 389 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.6590 (t80) REVERT: B 416 VAL cc_start: 0.7325 (t) cc_final: 0.7033 (t) REVERT: E 10 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8058 (ttpt) REVERT: I 10 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8047 (ttpt) outliers start: 20 outliers final: 7 residues processed: 151 average time/residue: 1.3280 time to fit residues: 218.4931 Evaluate side-chains 158 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 643 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 112 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.110908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.083792 restraints weight = 17822.490| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.66 r_work: 0.2886 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3598 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= 0.120 Angle : 0.503 8.121 18116 Z= 0.252 Chirality : 0.039 0.135 1938 Planarity : 0.004 0.044 2146 Dihedral : 10.261 101.465 2582 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.49 % Allowed : 12.56 % Favored : 85.95 % 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: 3.24 (0.22), residues: 1458 helix: 2.64 (0.15), residues: 1130 sheet: -1.42 (0.99), residues: 30 loop : 0.58 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 624 HIS 0.010 0.001 HIS A 293 PHE 0.022 0.001 PHE B 33 TYR 0.028 0.001 TYR B 261 ARG 0.005 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 890) hydrogen bonds : angle 3.81671 ( 2616) covalent geometry : bond 0.00276 (13460) covalent geometry : angle 0.50298 (18116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8888.75 seconds wall clock time: 151 minutes 54.26 seconds (9114.26 seconds total)