Starting phenix.real_space_refine on Sat Aug 23 17:31:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t56_41043/08_2025/8t56_41043.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t56_41043/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8t56_41043/08_2025/8t56_41043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t56_41043/08_2025/8t56_41043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t56_41043/08_2025/8t56_41043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t56_41043/08_2025/8t56_41043.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 48 5.16 5 C 8956 2.51 5 N 1952 2.21 5 O 2138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13096 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 5005 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 33, 'TRANS': 583} Chain breaks: 5 Chain: "B" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 5005 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 33, 'TRANS': 583} Chain breaks: 5 Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 300 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "D" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "E" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "F" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 216 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "G" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 300 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "H" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "I" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "J" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 216 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "A" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 267 Unusual residues: {'LBN': 1, 'PLM': 10, 'Y01': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 267 Unusual residues: {'LBN': 1, 'PLM': 10, 'Y01': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'CLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'CLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.37, per 1000 atoms: 0.18 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: 1.10 Conformation dependent library (CDL) restraints added in 487.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 2 sheets defined 84.1% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 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: 2.03 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2393 1.32 - 1.45: 4263 1.45 - 1.58: 6544 1.58 - 1.71: 174 1.71 - 1.84: 86 Bond restraints: 13460 Sorted by residual: bond pdb=" O2 LBN B 812 " pdb=" P1 LBN B 812 " ideal model delta sigma weight residual 1.650 1.844 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" O2 LBN A 812 " pdb=" P1 LBN A 812 " ideal model delta sigma weight residual 1.650 1.844 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" C10 CLR D 101 " pdb=" C9 CLR D 101 " ideal model delta sigma weight residual 1.551 1.703 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C10 CLR H 101 " pdb=" C9 CLR H 101 " ideal model delta sigma weight residual 1.551 1.703 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" C14 CLR C 801 " pdb=" C8 CLR C 801 " ideal model delta sigma weight residual 1.519 1.668 -0.149 2.00e-02 2.50e+03 5.53e+01 ... (remaining 13455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 17321 3.56 - 7.12: 723 7.12 - 10.69: 62 10.69 - 14.25: 8 14.25 - 17.81: 2 Bond angle restraints: 18116 Sorted by residual: angle pdb=" N VAL A 612 " pdb=" CA VAL A 612 " pdb=" C VAL A 612 " ideal model delta sigma weight residual 111.62 119.31 -7.69 7.90e-01 1.60e+00 9.47e+01 angle pdb=" N VAL B 612 " pdb=" CA VAL B 612 " pdb=" C VAL B 612 " ideal model delta sigma weight residual 111.62 119.29 -7.67 7.90e-01 1.60e+00 9.44e+01 angle pdb=" C HIS A 229 " pdb=" N PRO A 230 " pdb=" CA PRO A 230 " ideal model delta sigma weight residual 119.56 127.33 -7.77 1.02e+00 9.61e-01 5.80e+01 angle pdb=" C HIS B 229 " pdb=" N PRO B 230 " pdb=" CA PRO B 230 " ideal model delta sigma weight residual 119.56 127.31 -7.75 1.02e+00 9.61e-01 5.77e+01 angle pdb=" C ALA A 409 " pdb=" N PRO A 410 " pdb=" CA PRO A 410 " ideal model delta sigma weight residual 119.56 127.29 -7.73 1.02e+00 9.61e-01 5.75e+01 ... (remaining 18111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 8186 34.93 - 69.85: 178 69.85 - 104.78: 20 104.78 - 139.70: 2 139.70 - 174.63: 4 Dihedral angle restraints: 8390 sinusoidal: 3946 harmonic: 4444 Sorted by residual: dihedral pdb=" O5 LBN B 812 " pdb=" C2 LBN B 812 " pdb=" C3 LBN B 812 " pdb=" O7 LBN B 812 " ideal model delta sinusoidal sigma weight residual 62.67 -111.96 174.63 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN A 812 " pdb=" C2 LBN A 812 " pdb=" C3 LBN A 812 " pdb=" O7 LBN A 812 " ideal model delta sinusoidal sigma weight residual 62.67 -111.93 174.60 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN A 812 " pdb=" O1 LBN A 812 " pdb=" P1 LBN A 812 " pdb=" O3 LBN A 812 " ideal model delta sinusoidal sigma weight residual 275.40 108.33 167.07 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 8387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1433 0.114 - 0.229: 395 0.229 - 0.343: 96 0.343 - 0.457: 12 0.457 - 0.571: 2 Chirality restraints: 1938 Sorted by residual: chirality pdb=" C2 LBN B 812 " pdb=" C1 LBN B 812 " pdb=" C3 LBN B 812 " pdb=" O7 LBN B 812 " both_signs ideal model delta sigma weight residual False -2.36 -2.94 0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" C2 LBN A 812 " pdb=" C1 LBN A 812 " pdb=" C3 LBN A 812 " pdb=" O7 LBN A 812 " both_signs ideal model delta sigma weight residual False -2.36 -2.94 0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" CBB Y01 A 801 " pdb=" CAC Y01 A 801 " pdb=" CAO Y01 A 801 " pdb=" CBE Y01 A 801 " both_signs ideal model delta sigma weight residual False 2.58 2.12 0.45 2.00e-01 2.50e+01 5.13e+00 ... (remaining 1935 not shown) Planarity restraints: 2146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP J 37 " 0.030 2.00e-02 2.50e+03 6.01e-02 3.62e+01 pdb=" C ASP J 37 " -0.104 2.00e-02 2.50e+03 pdb=" O ASP J 37 " 0.037 2.00e-02 2.50e+03 pdb=" OXT ASP J 37 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 37 " -0.030 2.00e-02 2.50e+03 6.01e-02 3.62e+01 pdb=" C ASP F 37 " 0.104 2.00e-02 2.50e+03 pdb=" O ASP F 37 " -0.037 2.00e-02 2.50e+03 pdb=" OXT ASP F 37 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 181 " -0.078 2.00e-02 2.50e+03 4.04e-02 3.26e+01 pdb=" CG TYR A 181 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 181 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 181 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR A 181 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 181 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 181 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 181 " -0.054 2.00e-02 2.50e+03 ... (remaining 2143 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 4737 2.89 - 3.39: 12906 3.39 - 3.89: 21474 3.89 - 4.40: 26400 4.40 - 4.90: 41692 Nonbonded interactions: 107209 Sorted by model distance: nonbonded pdb=" N PHE B 72 " pdb=" N LEU B 73 " model vdw 2.385 2.560 nonbonded pdb=" N PHE A 72 " pdb=" N LEU A 73 " model vdw 2.385 2.560 nonbonded pdb=" OE2 GLU E 22 " pdb=" NZ LYS F 25 " model vdw 2.490 3.120 nonbonded pdb=" OE2 GLU I 22 " pdb=" NZ LYS J 25 " model vdw 2.491 3.120 nonbonded pdb=" O MET B 82 " pdb=" NH2 ARG B 606 " model vdw 2.522 3.120 ... (remaining 107204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.750 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.20), residues: 1458 helix: 0.47 (0.13), residues: 1122 sheet: -0.47 (0.79), residues: 46 loop : 0.83 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.078 0.009 TYR A 181 PHE 0.061 0.005 PHE I 1 TRP 0.037 0.007 TRP B 352 HIS 0.006 0.002 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.02720 (13460) covalent geometry : angle 1.65712 (18116) hydrogen bonds : bond 0.17032 ( 890) hydrogen bonds : angle 6.45373 ( 2616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.297 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: 0.8371 (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: 0.7547 time to fit residues: 183.1593 Evaluate side-chains 150 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3437 r_free = 0.3437 target = 0.110189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.083590 restraints weight = 17659.410| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.64 r_work: 0.2896 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13460 Z= 0.164 Angle : 0.596 6.859 18116 Z= 0.321 Chirality : 0.043 0.143 1938 Planarity : 0.005 0.042 2146 Dihedral : 14.852 174.115 2582 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.75 % Allowed : 6.67 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.21), residues: 1458 helix: 2.06 (0.15), residues: 1118 sheet: -0.86 (0.99), residues: 30 loop : 0.85 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 36 TYR 0.016 0.002 TYR A 261 PHE 0.021 0.002 PHE B 33 TRP 0.026 0.002 TRP A 624 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00358 (13460) covalent geometry : angle 0.59645 (18116) hydrogen bonds : bond 0.06111 ( 890) hydrogen bonds : angle 4.68750 ( 2616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.508 Fit side-chains REVERT: A 311 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: A 389 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.6442 (t80) REVERT: A 536 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6683 (tptt) REVERT: B 254 LYS cc_start: 0.7920 (mttt) cc_final: 0.7320 (mmmt) REVERT: B 389 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.6436 (t80) REVERT: B 536 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6668 (tptt) outliers start: 35 outliers final: 1 residues processed: 170 average time/residue: 0.6788 time to fit residues: 124.5585 Evaluate side-chains 145 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 536 LYS Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain C residue 35 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.113937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.088480 restraints weight = 18058.122| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.64 r_work: 0.2958 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2782 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= 0.123 Angle : 0.505 6.616 18116 Z= 0.263 Chirality : 0.039 0.145 1938 Planarity : 0.004 0.047 2146 Dihedral : 13.568 174.271 2582 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.51 % Allowed : 7.22 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.90 (0.21), residues: 1458 helix: 2.34 (0.15), residues: 1130 sheet: -1.01 (1.00), residues: 30 loop : 0.69 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 36 TYR 0.016 0.001 TYR B 261 PHE 0.017 0.002 PHE A 159 TRP 0.020 0.001 TRP A 624 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00263 (13460) covalent geometry : angle 0.50466 (18116) hydrogen bonds : bond 0.04520 ( 890) hydrogen bonds : angle 4.22559 ( 2616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.567 Fit side-chains REVERT: A 261 TYR cc_start: 0.7481 (t80) cc_final: 0.7248 (t80) REVERT: A 389 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.6387 (t80) REVERT: A 521 MET cc_start: 0.9259 (mtm) cc_final: 0.8960 (mtm) REVERT: A 689 MET cc_start: 0.9258 (tpp) cc_final: 0.9024 (tpt) REVERT: B 35 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8186 (t70) REVERT: B 254 LYS cc_start: 0.7946 (mttt) cc_final: 0.7406 (mmmt) REVERT: B 311 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: B 389 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.6442 (t80) REVERT: B 689 MET cc_start: 0.9254 (tpp) cc_final: 0.9026 (tpt) REVERT: D 34 LYS cc_start: 0.7926 (mtmm) cc_final: 0.7424 (mtmm) REVERT: E 12 TYR cc_start: 0.8984 (t80) cc_final: 0.8751 (t80) REVERT: H 34 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7466 (mtmm) REVERT: I 12 TYR cc_start: 0.8978 (t80) cc_final: 0.8745 (t80) outliers start: 32 outliers final: 1 residues processed: 187 average time/residue: 0.6734 time to fit residues: 136.6418 Evaluate side-chains 152 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 147 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain B residue 35 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 28 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.085698 restraints weight = 17830.904| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.62 r_work: 0.2929 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2957 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= 0.145 Angle : 0.521 7.034 18116 Z= 0.268 Chirality : 0.040 0.138 1938 Planarity : 0.004 0.046 2146 Dihedral : 13.054 163.047 2582 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.51 % Allowed : 9.26 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.22), residues: 1458 helix: 2.35 (0.15), residues: 1130 sheet: -1.34 (0.99), residues: 30 loop : 0.61 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.020 0.002 TYR C 12 PHE 0.021 0.002 PHE B 33 TRP 0.017 0.001 TRP B 624 HIS 0.004 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00346 (13460) covalent geometry : angle 0.52054 (18116) hydrogen bonds : bond 0.04716 ( 890) hydrogen bonds : angle 4.15624 ( 2616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7965 (mttt) cc_final: 0.7388 (mmmt) REVERT: A 311 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: A 389 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.6492 (t80) REVERT: A 521 MET cc_start: 0.9277 (mtm) cc_final: 0.9022 (mtm) REVERT: A 535 LEU cc_start: 0.8543 (mt) cc_final: 0.8333 (mp) REVERT: A 677 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: B 254 LYS cc_start: 0.7980 (mttt) cc_final: 0.7405 (mmmt) REVERT: B 311 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: B 389 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.6534 (t80) REVERT: B 521 MET cc_start: 0.9250 (mtm) cc_final: 0.8989 (mtm) REVERT: B 535 LEU cc_start: 0.8616 (mt) cc_final: 0.8412 (mp) REVERT: B 677 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: D 29 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8105 (mtpp) REVERT: E 13 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8738 (t80) outliers start: 32 outliers final: 6 residues processed: 168 average time/residue: 0.6739 time to fit residues: 123.0133 Evaluate side-chains 164 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 417 ASP 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 D residue 29 LYS Chi-restraints excluded: chain E residue 13 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 116 optimal weight: 0.0980 chunk 107 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.084186 restraints weight = 17866.009| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.60 r_work: 0.2904 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13460 Z= 0.176 Angle : 0.546 7.503 18116 Z= 0.279 Chirality : 0.042 0.154 1938 Planarity : 0.005 0.047 2146 Dihedral : 12.713 144.108 2582 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.98 % Allowed : 9.65 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.76 (0.22), residues: 1458 helix: 2.26 (0.15), residues: 1130 sheet: -1.39 (1.00), residues: 30 loop : 0.58 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 198 TYR 0.022 0.002 TYR G 12 PHE 0.017 0.002 PHE B 33 TRP 0.020 0.001 TRP A 624 HIS 0.009 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00437 (13460) covalent geometry : angle 0.54558 (18116) hydrogen bonds : bond 0.04951 ( 890) hydrogen bonds : angle 4.17467 ( 2616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8091 (mp10) REVERT: A 254 LYS cc_start: 0.7975 (mttt) cc_final: 0.7388 (mmmt) REVERT: A 255 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7597 (mt) REVERT: A 311 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: A 389 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.6488 (t80) REVERT: A 521 MET cc_start: 0.9280 (mtm) cc_final: 0.9074 (mtm) REVERT: B 190 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8085 (mp10) REVERT: B 254 LYS cc_start: 0.7995 (mttt) cc_final: 0.7411 (mmmt) REVERT: B 255 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7599 (mt) REVERT: B 311 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: B 389 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.6481 (t80) REVERT: B 413 LYS cc_start: 0.7465 (tppt) cc_final: 0.7024 (ttmm) REVERT: E 10 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8082 (ttpt) REVERT: I 10 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8073 (ttpt) outliers start: 38 outliers final: 12 residues processed: 168 average time/residue: 0.6861 time to fit residues: 124.8717 Evaluate side-chains 169 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 122 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.111400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.086011 restraints weight = 17653.221| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.60 r_work: 0.2935 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3248 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= 0.126 Angle : 0.499 7.429 18116 Z= 0.254 Chirality : 0.039 0.143 1938 Planarity : 0.004 0.044 2146 Dihedral : 11.764 129.047 2582 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.75 % Allowed : 10.20 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.89 (0.22), residues: 1458 helix: 2.39 (0.15), residues: 1130 sheet: -1.39 (1.00), residues: 30 loop : 0.48 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.020 0.001 TYR A 261 PHE 0.016 0.001 PHE B 33 TRP 0.023 0.001 TRP B 624 HIS 0.008 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00290 (13460) covalent geometry : angle 0.49854 (18116) hydrogen bonds : bond 0.04327 ( 890) hydrogen bonds : angle 4.01129 ( 2616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7964 (mttt) cc_final: 0.7382 (mmmt) REVERT: A 255 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7561 (mt) REVERT: A 311 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 389 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.6488 (t80) REVERT: A 413 LYS cc_start: 0.7433 (tppt) cc_final: 0.7009 (tmtt) REVERT: A 521 MET cc_start: 0.9258 (mtm) cc_final: 0.9017 (mtm) REVERT: B 254 LYS cc_start: 0.7965 (mttt) cc_final: 0.7383 (mmmt) REVERT: B 255 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7564 (mt) REVERT: B 311 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: B 389 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.6479 (t80) REVERT: B 521 MET cc_start: 0.9257 (mtm) cc_final: 0.9000 (mtm) REVERT: E 10 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8074 (ttpt) REVERT: I 10 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8086 (ttpt) outliers start: 35 outliers final: 15 residues processed: 172 average time/residue: 0.7138 time to fit residues: 132.7083 Evaluate side-chains 171 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 417 ASP Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain 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 77 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 118 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.111659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086038 restraints weight = 17761.344| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.61 r_work: 0.2930 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13460 Z= 0.130 Angle : 0.500 7.173 18116 Z= 0.254 Chirality : 0.039 0.145 1938 Planarity : 0.004 0.045 2146 Dihedral : 11.224 118.817 2582 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.51 % Allowed : 9.81 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.94 (0.22), residues: 1458 helix: 2.43 (0.15), residues: 1130 sheet: -1.35 (1.00), residues: 30 loop : 0.47 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 48 TYR 0.021 0.001 TYR A 261 PHE 0.015 0.001 PHE A 159 TRP 0.020 0.001 TRP A 624 HIS 0.010 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00305 (13460) covalent geometry : angle 0.50023 (18116) hydrogen bonds : bond 0.04312 ( 890) hydrogen bonds : angle 3.97461 ( 2616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7945 (mttt) cc_final: 0.7355 (mmmt) REVERT: A 255 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7562 (mt) REVERT: A 311 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: A 389 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.6495 (t80) REVERT: A 521 MET cc_start: 0.9255 (mtm) cc_final: 0.9006 (mtm) REVERT: A 646 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7689 (tt) REVERT: B 254 LYS cc_start: 0.7961 (mttt) cc_final: 0.7387 (mmmt) REVERT: B 255 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7578 (mt) REVERT: B 311 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: B 389 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.6496 (t80) REVERT: B 413 LYS cc_start: 0.7437 (tppt) cc_final: 0.7136 (tmtt) REVERT: B 521 MET cc_start: 0.9255 (mtm) cc_final: 0.9004 (mtm) REVERT: B 646 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7692 (tt) REVERT: E 10 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8089 (ttpt) REVERT: I 10 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8094 (ttpt) outliers start: 32 outliers final: 11 residues processed: 164 average time/residue: 0.6367 time to fit residues: 113.4590 Evaluate side-chains 168 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.108982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.081881 restraints weight = 17616.139| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.65 r_work: 0.2852 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3354 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= 0.142 Angle : 0.514 8.502 18116 Z= 0.261 Chirality : 0.040 0.144 1938 Planarity : 0.004 0.045 2146 Dihedral : 11.087 113.695 2582 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.20 % Allowed : 10.13 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.22), residues: 1458 helix: 2.42 (0.15), residues: 1130 sheet: -1.33 (1.00), residues: 30 loop : 0.49 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 198 TYR 0.023 0.001 TYR A 261 PHE 0.016 0.001 PHE A 159 TRP 0.020 0.001 TRP A 624 HIS 0.009 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00341 (13460) covalent geometry : angle 0.51430 (18116) hydrogen bonds : bond 0.04435 ( 890) hydrogen bonds : angle 4.00318 ( 2616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7902 (mttt) cc_final: 0.7302 (mmmt) REVERT: A 255 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7495 (mt) REVERT: A 311 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: A 389 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.6462 (t80) REVERT: A 521 MET cc_start: 0.9264 (mtm) cc_final: 0.9045 (mtm) REVERT: A 646 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7693 (tt) REVERT: B 190 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8039 (mp10) REVERT: B 254 LYS cc_start: 0.7905 (mttt) cc_final: 0.7331 (mmmt) REVERT: B 255 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7492 (mt) REVERT: B 311 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: B 389 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.6473 (t80) REVERT: B 521 MET cc_start: 0.9247 (mtm) cc_final: 0.9034 (mtm) REVERT: B 646 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7701 (tt) REVERT: E 10 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8055 (ttpt) REVERT: I 10 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8048 (ttpt) outliers start: 28 outliers final: 10 residues processed: 164 average time/residue: 0.5856 time to fit residues: 104.6332 Evaluate side-chains 166 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 311 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 13 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 0.9980 chunk 116 optimal weight: 0.0050 chunk 110 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.110296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.083260 restraints weight = 17669.071| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.66 r_work: 0.2876 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13460 Z= 0.116 Angle : 0.495 8.727 18116 Z= 0.250 Chirality : 0.038 0.136 1938 Planarity : 0.004 0.044 2146 Dihedral : 10.719 109.877 2582 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.88 % Allowed : 10.68 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.08 (0.22), residues: 1458 helix: 2.53 (0.15), residues: 1130 sheet: -1.38 (1.00), residues: 30 loop : 0.54 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 48 TYR 0.025 0.001 TYR A 261 PHE 0.015 0.001 PHE B 159 TRP 0.023 0.001 TRP B 624 HIS 0.010 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00260 (13460) covalent geometry : angle 0.49526 (18116) hydrogen bonds : bond 0.04040 ( 890) hydrogen bonds : angle 3.90656 ( 2616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8542 (p90) cc_final: 0.8246 (p90) REVERT: A 254 LYS cc_start: 0.7895 (mttt) cc_final: 0.7300 (mmmt) REVERT: A 255 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7480 (mt) REVERT: A 311 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: A 389 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.6580 (t80) REVERT: A 416 VAL cc_start: 0.7517 (t) cc_final: 0.7265 (t) REVERT: A 521 MET cc_start: 0.9245 (mtm) cc_final: 0.9003 (mtm) REVERT: A 646 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7682 (tt) REVERT: B 254 LYS cc_start: 0.7908 (mttt) cc_final: 0.7320 (mmmt) REVERT: B 255 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7489 (mt) REVERT: B 311 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 389 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.6574 (t80) REVERT: B 413 LYS cc_start: 0.7590 (tppt) cc_final: 0.7045 (ttmm) REVERT: B 521 MET cc_start: 0.9235 (mtm) cc_final: 0.8982 (mtm) REVERT: B 646 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7695 (tt) REVERT: E 10 LYS cc_start: 0.8493 (tppp) cc_final: 0.8002 (ttpt) REVERT: I 10 LYS cc_start: 0.8508 (tppp) cc_final: 0.8016 (ttpt) outliers start: 24 outliers final: 10 residues processed: 159 average time/residue: 0.6457 time to fit residues: 111.4512 Evaluate side-chains 158 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 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 62 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 0.0670 chunk 106 optimal weight: 0.0970 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.111832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.084860 restraints weight = 17712.725| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.66 r_work: 0.2905 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13460 Z= 0.106 Angle : 0.487 7.726 18116 Z= 0.245 Chirality : 0.038 0.133 1938 Planarity : 0.004 0.043 2146 Dihedral : 10.198 102.139 2582 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.96 % Allowed : 10.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.26 (0.22), residues: 1458 helix: 2.66 (0.15), residues: 1130 sheet: -1.36 (1.02), residues: 30 loop : 0.60 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 48 TYR 0.024 0.001 TYR A 261 PHE 0.015 0.001 PHE B 159 TRP 0.022 0.001 TRP A 624 HIS 0.011 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00232 (13460) covalent geometry : angle 0.48696 (18116) hydrogen bonds : bond 0.03696 ( 890) hydrogen bonds : angle 3.79163 ( 2616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8464 (p90) cc_final: 0.8154 (p90) REVERT: A 254 LYS cc_start: 0.7842 (mttt) cc_final: 0.7264 (mmmt) REVERT: A 311 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: A 389 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.6560 (t80) REVERT: A 416 VAL cc_start: 0.7143 (OUTLIER) cc_final: 0.6847 (t) REVERT: A 521 MET cc_start: 0.9218 (mtm) cc_final: 0.8952 (mtm) REVERT: A 646 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7611 (tt) REVERT: B 254 LYS cc_start: 0.7892 (mttt) cc_final: 0.7305 (mmmt) REVERT: B 311 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: B 389 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.6555 (t80) REVERT: B 416 VAL cc_start: 0.7259 (t) cc_final: 0.6963 (t) REVERT: B 521 MET cc_start: 0.9205 (mtm) cc_final: 0.8989 (mtm) REVERT: B 646 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7644 (tt) REVERT: E 10 LYS cc_start: 0.8470 (tppp) cc_final: 0.7989 (ttpt) REVERT: I 10 LYS cc_start: 0.8468 (tppp) cc_final: 0.7986 (ttpt) outliers start: 25 outliers final: 10 residues processed: 167 average time/residue: 0.6465 time to fit residues: 117.1465 Evaluate side-chains 158 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LYS 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 124 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 0.0020 chunk 7 optimal weight: 0.0870 chunk 42 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.4566 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.111869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.084917 restraints weight = 17685.830| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.66 r_work: 0.2911 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3685 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= 0.105 Angle : 0.486 8.495 18116 Z= 0.244 Chirality : 0.038 0.139 1938 Planarity : 0.004 0.044 2146 Dihedral : 10.038 98.890 2582 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.65 % Allowed : 11.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.32 (0.22), residues: 1458 helix: 2.72 (0.15), residues: 1130 sheet: -1.44 (1.00), residues: 30 loop : 0.56 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 48 TYR 0.008 0.001 TYR A 368 PHE 0.020 0.001 PHE B 33 TRP 0.023 0.001 TRP A 624 HIS 0.010 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00226 (13460) covalent geometry : angle 0.48577 (18116) hydrogen bonds : bond 0.03642 ( 890) hydrogen bonds : angle 3.74562 ( 2616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4412.70 seconds wall clock time: 76 minutes 11.30 seconds (4571.30 seconds total)