Starting phenix.real_space_refine on Sun Nov 17 12:00:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t56_41043/11_2024/8t56_41043.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t56_41043/11_2024/8t56_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t56_41043/11_2024/8t56_41043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t56_41043/11_2024/8t56_41043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t56_41043/11_2024/8t56_41043.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t56_41043/11_2024/8t56_41043.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 48 5.16 5 C 8956 2.51 5 N 1952 2.21 5 O 2138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.45, per 1000 atoms: 0.57 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: 3.65 Conformation dependent library (CDL) restraints added in 1.4 seconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 2 sheets defined 84.1% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 3 through 29 Processing helix chain 'A' and resid 30 through 33 removed outlier: 6.235A pdb=" N PHE A 33 " --> pdb=" O LEU A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 30 through 33' Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 92 through 121 removed outlier: 3.571A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 158 through 194 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 242 through 265 Processing helix chain 'A' and resid 291 through 315 Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.608A pdb=" N VAL A 359 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.554A pdb=" N ALA A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 389 Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 410 through 416 removed outlier: 4.368A pdb=" N PHE A 414 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 438 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 456 through 476 Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.611A pdb=" N SER A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 512 through 524 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 534 through 548 Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 554 through 559 removed outlier: 3.704A pdb=" N MET A 559 " --> pdb=" O ARG A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 584 Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 590 through 612 removed outlier: 3.552A pdb=" N ILE A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 647 Processing helix chain 'A' and resid 655 through 676 Proline residue: A 662 - end of helix Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 703 through 710 removed outlier: 4.570A pdb=" N ASN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 29 Processing helix chain 'B' and resid 30 through 33 removed outlier: 6.235A pdb=" N PHE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 92 through 121 removed outlier: 3.571A pdb=" N ILE B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 158 through 194 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 242 through 265 Processing helix chain 'B' and resid 291 through 315 Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 355 through 359 removed outlier: 3.609A pdb=" N VAL B 359 " --> pdb=" O PRO B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 366 removed outlier: 3.554A pdb=" N ALA B 365 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 389 Processing helix chain 'B' and resid 389 through 399 Processing helix chain 'B' and resid 401 through 409 Processing helix chain 'B' and resid 410 through 416 removed outlier: 4.367A pdb=" N PHE B 414 " --> pdb=" O PHE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 438 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'B' and resid 456 through 476 Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.612A pdb=" N SER B 480 " --> pdb=" O VAL B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 511 No H-bonds generated for 'chain 'B' and resid 509 through 511' Processing helix chain 'B' and resid 512 through 524 Processing helix chain 'B' and resid 524 through 532 Processing helix chain 'B' and resid 534 through 548 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 554 through 559 removed outlier: 3.703A pdb=" N MET B 559 " --> pdb=" O ARG B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 584 Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 590 through 612 removed outlier: 3.551A pdb=" N ILE B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 647 Processing helix chain 'B' and resid 655 through 676 Proline residue: B 662 - end of helix Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 703 through 710 removed outlier: 4.570A pdb=" N ASN B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 34 removed outlier: 5.869A pdb=" N ASP C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) Proline residue: C 19 - end of helix Processing helix chain 'D' and resid 2 through 16 Processing helix chain 'D' and resid 16 through 34 Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 16 through 34 removed outlier: 3.576A pdb=" N ALA E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 37 Proline residue: F 19 - end of helix Processing helix chain 'G' and resid 3 through 34 removed outlier: 5.868A pdb=" N ASP G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) Proline residue: G 19 - end of helix Processing helix chain 'H' and resid 2 through 16 Processing helix chain 'H' and resid 16 through 34 Processing helix chain 'I' and resid 2 through 15 Processing helix chain 'I' and resid 16 through 34 removed outlier: 3.576A pdb=" N ALA I 20 " --> pdb=" O PHE I 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 37 Proline residue: J 19 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.515A pdb=" N ALA A 322 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.514A pdb=" N ALA B 322 " --> pdb=" O VAL B 239 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 4.00 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 2 through 36 or resid 101)) selection = (chain 'E' and (resid 2 through 36 or resid 101)) selection = chain 'G' selection = (chain 'H' and (resid 2 through 36 or resid 101)) selection = (chain 'I' and (resid 2 through 36 or resid 101)) } 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: 0.730 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 30.270 Find NCS groups from input model: 0.460 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:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.950 ------------------------------------------------------------------------------- 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= 1.715 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 *********************** 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 : 1.411 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: 1.5411 time to fit residues: 375.2652 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 : 1.468 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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= 0.221 Angle : 0.599 6.896 18116 Z= 0.321 Chirality : 0.043 0.144 1938 Planarity : 0.005 0.044 2146 Dihedral : 14.729 174.673 2582 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.67 % Allowed : 6.67 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.21), residues: 1458 helix: 2.11 (0.15), residues: 1118 sheet: -0.87 (0.99), residues: 30 loop : 0.87 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 624 HIS 0.005 0.001 HIS A 379 PHE 0.022 0.002 PHE B 33 TYR 0.016 0.002 TYR A 261 ARG 0.007 0.001 ARG B 36 *********************** 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 : 1.396 Fit side-chains REVERT: A 389 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7068 (t80) REVERT: B 254 LYS cc_start: 0.8401 (mttt) cc_final: 0.8026 (mmmt) REVERT: B 389 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7072 (t80) REVERT: B 536 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7249 (tptt) outliers start: 34 outliers final: 2 residues processed: 170 average time/residue: 1.4009 time to fit residues: 258.4374 Evaluate side-chains 139 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2747 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= 0.219 Angle : 0.533 7.202 18116 Z= 0.279 Chirality : 0.041 0.147 1938 Planarity : 0.004 0.048 2146 Dihedral : 13.676 173.518 2582 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.35 % Allowed : 7.54 % Favored : 90.11 % 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: 2.81 (0.21), residues: 1458 helix: 2.23 (0.15), residues: 1142 sheet: -1.02 (1.01), residues: 30 loop : 0.82 (0.35), residues: 286 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 0.002 TYR B 261 ARG 0.004 0.000 ARG A 36 *********************** 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 200 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 1.407 Fit side-chains REVERT: A 389 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7053 (t80) REVERT: A 521 MET cc_start: 0.8916 (mtm) cc_final: 0.8679 (mtm) REVERT: B 254 LYS cc_start: 0.8383 (mttt) cc_final: 0.8031 (mmmt) REVERT: B 389 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7030 (t80) REVERT: E 12 TYR cc_start: 0.8974 (t80) cc_final: 0.8722 (t80) REVERT: I 12 TYR cc_start: 0.8986 (t80) cc_final: 0.8722 (t80) outliers start: 30 outliers final: 3 residues processed: 181 average time/residue: 1.3876 time to fit residues: 272.9357 Evaluate side-chains 150 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 417 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2993 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= 0.209 Angle : 0.513 7.426 18116 Z= 0.265 Chirality : 0.040 0.147 1938 Planarity : 0.004 0.046 2146 Dihedral : 13.092 162.744 2582 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.59 % Allowed : 8.79 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.88 (0.22), residues: 1458 helix: 2.32 (0.15), residues: 1130 sheet: -1.31 (1.00), residues: 30 loop : 0.73 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 624 HIS 0.007 0.001 HIS B 293 PHE 0.021 0.002 PHE A 33 TYR 0.020 0.002 TYR G 12 ARG 0.002 0.000 ARG A 357 *********************** 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 190 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.8419 (mttt) cc_final: 0.8026 (mmmt) REVERT: A 389 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7011 (t80) REVERT: A 448 MET cc_start: 0.9050 (mtp) cc_final: 0.8806 (mtm) REVERT: A 521 MET cc_start: 0.8923 (mtm) cc_final: 0.8713 (mtm) REVERT: B 254 LYS cc_start: 0.8420 (mttt) cc_final: 0.8038 (mmmt) REVERT: B 261 TYR cc_start: 0.8030 (t80) cc_final: 0.7804 (t80) REVERT: B 389 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7009 (t80) REVERT: B 448 MET cc_start: 0.9058 (mtp) cc_final: 0.8819 (mtm) REVERT: B 589 MET cc_start: 0.8589 (ttp) cc_final: 0.8289 (ttm) outliers start: 33 outliers final: 11 residues processed: 171 average time/residue: 1.4081 time to fit residues: 261.4179 Evaluate side-chains 159 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 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 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 D residue 34 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 0.0370 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13460 Z= 0.160 Angle : 0.489 7.380 18116 Z= 0.249 Chirality : 0.039 0.142 1938 Planarity : 0.004 0.045 2146 Dihedral : 12.340 147.526 2582 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.90 % Allowed : 9.58 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.22), residues: 1458 helix: 2.46 (0.15), residues: 1130 sheet: -1.34 (0.99), residues: 30 loop : 0.66 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 624 HIS 0.009 0.001 HIS A 293 PHE 0.016 0.001 PHE A 33 TYR 0.019 0.001 TYR A 261 ARG 0.003 0.000 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.8413 (mttt) cc_final: 0.8029 (mmmt) REVERT: A 255 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8217 (mt) REVERT: A 308 GLU cc_start: 0.7188 (tp30) cc_final: 0.6967 (tp30) REVERT: A 311 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: A 389 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.6965 (t80) REVERT: A 448 MET cc_start: 0.9044 (mtp) cc_final: 0.8789 (mtm) REVERT: A 521 MET cc_start: 0.8883 (mtm) cc_final: 0.8658 (mtm) REVERT: A 689 MET cc_start: 0.8907 (tpp) cc_final: 0.8586 (tpt) REVERT: B 254 LYS cc_start: 0.8424 (mttt) cc_final: 0.8041 (mmmt) REVERT: B 308 GLU cc_start: 0.7171 (tp30) cc_final: 0.6959 (tp30) REVERT: B 311 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: B 389 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.6965 (t80) REVERT: B 521 MET cc_start: 0.8882 (mtm) cc_final: 0.8616 (mtm) REVERT: B 589 MET cc_start: 0.8551 (ttp) cc_final: 0.8341 (ttm) REVERT: E 10 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8649 (ttpt) REVERT: H 34 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7717 (mtmm) REVERT: I 10 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8645 (ttpt) outliers start: 37 outliers final: 9 residues processed: 174 average time/residue: 1.3827 time to fit residues: 261.7129 Evaluate side-chains 166 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 587 THR 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 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 46 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 34 optimal weight: 0.4980 chunk 139 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS B 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3328 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= 0.170 Angle : 0.489 8.195 18116 Z= 0.248 Chirality : 0.039 0.145 1938 Planarity : 0.004 0.044 2146 Dihedral : 11.694 131.518 2582 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.75 % Allowed : 9.97 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.22), residues: 1458 helix: 2.51 (0.15), residues: 1130 sheet: -1.44 (0.99), residues: 30 loop : 0.61 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 624 HIS 0.009 0.001 HIS B 293 PHE 0.015 0.001 PHE A 33 TYR 0.020 0.001 TYR A 261 ARG 0.002 0.000 ARG A 198 *********************** 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 185 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.435 Fit side-chains REVERT: A 254 LYS cc_start: 0.8410 (mttt) cc_final: 0.8030 (mmmt) REVERT: A 255 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8211 (mt) REVERT: A 389 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7024 (t80) REVERT: A 448 MET cc_start: 0.9054 (mtp) cc_final: 0.8794 (mtm) REVERT: A 689 MET cc_start: 0.8922 (tpp) cc_final: 0.8577 (tpt) REVERT: B 254 LYS cc_start: 0.8419 (mttt) cc_final: 0.8040 (mmmt) REVERT: B 389 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7025 (t80) REVERT: B 521 MET cc_start: 0.8878 (mtm) cc_final: 0.8621 (mtm) REVERT: D 34 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7854 (mtmm) REVERT: E 10 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8646 (ttpt) REVERT: H 34 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7693 (mtmm) REVERT: I 10 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8639 (ttpt) outliers start: 35 outliers final: 11 residues processed: 163 average time/residue: 1.5121 time to fit residues: 268.5540 Evaluate side-chains 162 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 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 310 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 D residue 34 LYS Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 13 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 0.0060 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 0.0270 overall best weight: 0.4254 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13460 Z= 0.141 Angle : 0.485 8.116 18116 Z= 0.243 Chirality : 0.038 0.135 1938 Planarity : 0.004 0.043 2146 Dihedral : 10.929 120.817 2582 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.04 % Allowed : 10.68 % 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: 3.18 (0.22), residues: 1458 helix: 2.60 (0.15), residues: 1130 sheet: -1.46 (0.98), residues: 30 loop : 0.59 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 624 HIS 0.010 0.001 HIS B 293 PHE 0.014 0.001 PHE B 159 TYR 0.023 0.001 TYR B 261 ARG 0.002 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 255 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8216 (mt) REVERT: A 311 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: A 389 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7069 (t80) REVERT: A 448 MET cc_start: 0.9030 (mtp) cc_final: 0.8764 (mtm) REVERT: A 689 MET cc_start: 0.8927 (tpp) cc_final: 0.8609 (tpt) REVERT: B 254 LYS cc_start: 0.8415 (mttt) cc_final: 0.8034 (mmmt) REVERT: B 255 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8209 (mt) REVERT: B 311 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: B 389 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7064 (t80) REVERT: B 521 MET cc_start: 0.8859 (mtm) cc_final: 0.8638 (mtm) REVERT: B 689 MET cc_start: 0.8923 (tpp) cc_final: 0.8610 (tpt) REVERT: E 10 LYS cc_start: 0.8890 (tppp) cc_final: 0.8641 (ttpt) REVERT: H 34 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7713 (mtmm) REVERT: I 10 LYS cc_start: 0.8910 (tppp) cc_final: 0.8652 (ttpt) outliers start: 26 outliers final: 10 residues processed: 166 average time/residue: 1.3338 time to fit residues: 241.5983 Evaluate side-chains 157 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 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 D residue 34 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 55 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3501 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= 0.162 Angle : 0.485 7.753 18116 Z= 0.245 Chirality : 0.038 0.136 1938 Planarity : 0.004 0.044 2146 Dihedral : 10.585 111.252 2582 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.12 % Allowed : 10.99 % Favored : 86.89 % 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: 3.18 (0.22), residues: 1458 helix: 2.61 (0.15), residues: 1130 sheet: -1.41 (0.99), residues: 30 loop : 0.56 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 624 HIS 0.009 0.001 HIS B 293 PHE 0.021 0.001 PHE A 33 TYR 0.024 0.001 TYR B 261 ARG 0.001 0.000 ARG A 198 *********************** 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 172 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.378 Fit side-chains revert: symmetry clash REVERT: A 254 LYS cc_start: 0.8396 (mttt) cc_final: 0.8013 (mmmt) REVERT: A 255 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8220 (mt) REVERT: A 389 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7109 (t80) REVERT: A 689 MET cc_start: 0.8936 (tpp) cc_final: 0.8622 (tpt) REVERT: B 254 LYS cc_start: 0.8415 (mttt) cc_final: 0.8034 (mmmt) REVERT: B 255 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8207 (mt) REVERT: B 389 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7103 (t80) REVERT: B 646 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7300 (tt) REVERT: D 34 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7824 (mtmm) REVERT: E 10 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8645 (ttpt) REVERT: I 10 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8646 (ttpt) outliers start: 27 outliers final: 12 residues processed: 157 average time/residue: 1.3628 time to fit residues: 235.0570 Evaluate side-chains 162 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 643 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 310 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 D residue 34 LYS 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 132 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13460 Z= 0.189 Angle : 0.504 7.221 18116 Z= 0.253 Chirality : 0.039 0.136 1938 Planarity : 0.004 0.045 2146 Dihedral : 10.529 108.789 2582 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.43 % Allowed : 10.99 % 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: 3.15 (0.22), residues: 1458 helix: 2.57 (0.15), residues: 1130 sheet: -1.45 (0.99), residues: 30 loop : 0.59 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 624 HIS 0.011 0.001 HIS B 293 PHE 0.020 0.001 PHE A 33 TYR 0.027 0.001 TYR B 261 ARG 0.002 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.8409 (mttt) cc_final: 0.8032 (mmmt) REVERT: A 255 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8232 (mt) REVERT: A 389 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7082 (t80) REVERT: A 448 MET cc_start: 0.9014 (mtp) cc_final: 0.8747 (mtm) REVERT: B 254 LYS cc_start: 0.8414 (mttt) cc_final: 0.8034 (mmmt) REVERT: B 255 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8213 (mt) REVERT: B 389 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7074 (t80) REVERT: B 646 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7408 (tt) REVERT: E 10 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8649 (ttpt) REVERT: I 10 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8649 (ttpt) outliers start: 31 outliers final: 14 residues processed: 155 average time/residue: 1.4107 time to fit residues: 237.4852 Evaluate side-chains 160 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 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 389 PHE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain D residue 34 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3535 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= 0.176 Angle : 0.509 8.749 18116 Z= 0.255 Chirality : 0.039 0.133 1938 Planarity : 0.004 0.044 2146 Dihedral : 10.396 106.409 2582 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.04 % Allowed : 11.62 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.22), residues: 1458 helix: 2.60 (0.15), residues: 1130 sheet: -1.46 (0.99), residues: 30 loop : 0.62 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.011 0.001 HIS A 293 PHE 0.020 0.001 PHE A 33 TYR 0.027 0.001 TYR A 261 ARG 0.003 0.000 ARG A 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.8407 (mttt) cc_final: 0.8029 (mmmt) REVERT: A 255 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8228 (mt) REVERT: A 389 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7059 (t80) REVERT: A 646 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7347 (tt) REVERT: B 254 LYS cc_start: 0.8407 (mttt) cc_final: 0.8026 (mmmt) REVERT: B 255 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8210 (mt) REVERT: B 389 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7099 (t80) REVERT: B 646 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7455 (tt) REVERT: E 10 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8650 (ttpt) REVERT: I 10 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8651 (ttpt) outliers start: 26 outliers final: 9 residues processed: 152 average time/residue: 1.3419 time to fit residues: 222.4733 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 : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 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 389 PHE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain D residue 34 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 21 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS B 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.083702 restraints weight = 17627.651| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.66 r_work: 0.2888 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: 0.8372 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13460 Z= 0.173 Angle : 0.515 9.727 18116 Z= 0.255 Chirality : 0.039 0.131 1938 Planarity : 0.004 0.044 2146 Dihedral : 10.260 103.648 2582 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.96 % Allowed : 12.09 % 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: 3.20 (0.22), residues: 1458 helix: 2.62 (0.15), residues: 1130 sheet: -1.45 (1.00), residues: 30 loop : 0.58 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.011 0.001 HIS A 293 PHE 0.020 0.001 PHE A 33 TYR 0.028 0.001 TYR A 261 ARG 0.001 0.000 ARG A 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4669.14 seconds wall clock time: 84 minutes 32.61 seconds (5072.61 seconds total)