Starting phenix.real_space_refine on Sat Aug 23 16:11:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ho7_34921/08_2025/8ho7_34921_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ho7_34921/08_2025/8ho7_34921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ho7_34921/08_2025/8ho7_34921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ho7_34921/08_2025/8ho7_34921.map" model { file = "/net/cci-nas-00/data/ceres_data/8ho7_34921/08_2025/8ho7_34921_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ho7_34921/08_2025/8ho7_34921_neut.cif" } resolution = 2.59 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= 1.000 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8404 2.51 5 N 2186 2.21 5 O 2583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 13227 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6558 Classifications: {'peptide': 810} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 780} Chain: "B" Number of atoms: 6557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6557 Classifications: {'peptide': 810} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 780} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Time building chain proxies: 2.98, per 1000 atoms: 0.23 Number of scatterers: 13227 At special positions: 0 Unit cell: (135.29, 107.07, 97.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2583 8.00 N 2186 7.00 C 8404 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 715.3 nanoseconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 25 sheets defined 33.7% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.900A pdb=" N PHE A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 313 Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 330 through 343 Processing helix chain 'A' and resid 359 through 370 removed outlier: 3.652A pdb=" N LEU A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 387 removed outlier: 3.909A pdb=" N THR A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 4.018A pdb=" N TRP A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.734A pdb=" N ILE A 436 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.742A pdb=" N VAL A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.986A pdb=" N LYS A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 Processing helix chain 'A' and resid 585 through 594 removed outlier: 3.784A pdb=" N GLY A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 590 " --> pdb=" O GLU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 614 Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.895A pdb=" N TYR A 640 " --> pdb=" O ILE A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 removed outlier: 3.683A pdb=" N ALA A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TRP A 657 " --> pdb=" O HIS A 653 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 679 through 685 removed outlier: 4.039A pdb=" N GLU A 684 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP A 685 " --> pdb=" O TYR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 719 through 731 Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.517A pdb=" N PHE B 168 " --> pdb=" O PHE B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 222 through 228 Processing helix chain 'B' and resid 268 through 271 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 293 through 312 Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 359 through 370 removed outlier: 3.561A pdb=" N ASN B 363 " --> pdb=" O PHE B 359 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 removed outlier: 3.529A pdb=" N GLU B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.914A pdb=" N TRP B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 421 " --> pdb=" O PRO B 417 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.742A pdb=" N ILE B 436 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 removed outlier: 4.062A pdb=" N VAL B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 533 removed outlier: 4.031A pdb=" N LYS B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASP B 524 " --> pdb=" O PHE B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 585 through 594 Processing helix chain 'B' and resid 601 through 614 Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.901A pdb=" N TYR B 640 " --> pdb=" O ILE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 665 removed outlier: 3.890A pdb=" N TRP B 657 " --> pdb=" O HIS B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'B' and resid 679 through 685 removed outlier: 4.020A pdb=" N GLU B 684 " --> pdb=" O ALA B 681 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASP B 685 " --> pdb=" O TYR B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 719 through 731 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.651A pdb=" N SER A 94 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 3.777A pdb=" N HIS A 244 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER A 207 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER A 243 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE A 205 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 275 removed outlier: 6.897A pdb=" N VAL A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 315 through 318 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 440 through 443 removed outlier: 5.756A pdb=" N LYS A 449 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 510 through 511 removed outlier: 3.580A pdb=" N TYR A 566 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AB1, first strand: chain 'A' and resid 615 through 616 Processing sheet with id=AB2, first strand: chain 'A' and resid 650 through 651 removed outlier: 6.645A pdb=" N ALA A 698 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER A 715 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 735 through 738 removed outlier: 3.901A pdb=" N LEU A 742 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.599A pdb=" N SER B 94 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 25 through 28 Processing sheet with id=AB6, first strand: chain 'B' and resid 54 through 56 removed outlier: 5.312A pdb=" N ILE B 55 " --> pdb=" O CYS B 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 54 through 56 removed outlier: 5.312A pdb=" N ILE B 55 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS B 244 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER B 207 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER B 243 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE B 205 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.872A pdb=" N VAL B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 315 through 318 removed outlier: 6.616A pdb=" N THR B 765 " --> pdb=" O HIS B 804 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL B 806 " --> pdb=" O THR B 765 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU B 767 " --> pdb=" O VAL B 806 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL B 808 " --> pdb=" O GLU B 767 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR B 769 " --> pdb=" O VAL B 808 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE B 783 " --> pdb=" O ILE B 790 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AC2, first strand: chain 'B' and resid 440 through 443 removed outlier: 5.604A pdb=" N LYS B 449 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AC4, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AC5, first strand: chain 'B' and resid 615 through 616 Processing sheet with id=AC6, first strand: chain 'B' and resid 698 through 701 removed outlier: 6.534A pdb=" N ALA B 698 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER B 715 " --> pdb=" O ALA B 698 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 735 through 738 removed outlier: 3.929A pdb=" N LEU B 742 " --> pdb=" O LEU B 795 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1593 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: 2.87 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4243 1.34 - 1.46: 2993 1.46 - 1.58: 6139 1.58 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 13461 Sorted by residual: bond pdb=" CA ARG B 189 " pdb=" C ARG B 189 " ideal model delta sigma weight residual 1.523 1.538 -0.014 1.34e-02 5.57e+03 1.14e+00 bond pdb=" C ASP B 740 " pdb=" N GLY B 741 " ideal model delta sigma weight residual 1.319 1.334 -0.015 1.44e-02 4.82e+03 1.08e+00 bond pdb=" CB THR B 20 " pdb=" CG2 THR B 20 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.04e+00 bond pdb=" CA VAL A 686 " pdb=" CB VAL A 686 " ideal model delta sigma weight residual 1.540 1.553 -0.013 1.36e-02 5.41e+03 8.78e-01 bond pdb=" N GLY B 68 " pdb=" CA GLY B 68 " ideal model delta sigma weight residual 1.449 1.463 -0.014 1.45e-02 4.76e+03 8.71e-01 ... (remaining 13456 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 17992 1.94 - 3.88: 179 3.88 - 5.82: 31 5.82 - 7.76: 4 7.76 - 9.70: 2 Bond angle restraints: 18208 Sorted by residual: angle pdb=" N GLY B 741 " pdb=" CA GLY B 741 " pdb=" C GLY B 741 " ideal model delta sigma weight residual 110.20 118.44 -8.24 1.32e+00 5.74e-01 3.90e+01 angle pdb=" CA ARG B 189 " pdb=" C ARG B 189 " pdb=" N ARG B 190 " ideal model delta sigma weight residual 116.84 122.66 -5.82 1.71e+00 3.42e-01 1.16e+01 angle pdb=" CA VAL B 686 " pdb=" CB VAL B 686 " pdb=" CG1 VAL B 686 " ideal model delta sigma weight residual 110.40 115.94 -5.54 1.70e+00 3.46e-01 1.06e+01 angle pdb=" C VAL A 686 " pdb=" CA VAL A 686 " pdb=" CB VAL A 686 " ideal model delta sigma weight residual 111.29 116.61 -5.32 1.64e+00 3.72e-01 1.05e+01 angle pdb=" C VAL B 686 " pdb=" CA VAL B 686 " pdb=" CB VAL B 686 " ideal model delta sigma weight residual 111.29 116.60 -5.31 1.64e+00 3.72e-01 1.05e+01 ... (remaining 18203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 6777 17.74 - 35.48: 769 35.48 - 53.21: 269 53.21 - 70.95: 59 70.95 - 88.69: 22 Dihedral angle restraints: 7896 sinusoidal: 3194 harmonic: 4702 Sorted by residual: dihedral pdb=" CA ILE B 330 " pdb=" C ILE B 330 " pdb=" N TRP B 331 " pdb=" CA TRP B 331 " ideal model delta harmonic sigma weight residual -180.00 -158.96 -21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ILE A 330 " pdb=" C ILE A 330 " pdb=" N TRP A 331 " pdb=" CA TRP A 331 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHE B 413 " pdb=" C PHE B 413 " pdb=" N ASN B 414 " pdb=" CA ASN B 414 " ideal model delta harmonic sigma weight residual 180.00 -159.90 -20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 7893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1014 0.029 - 0.059: 535 0.059 - 0.088: 182 0.088 - 0.117: 108 0.117 - 0.146: 23 Chirality restraints: 1862 Sorted by residual: chirality pdb=" CA GLU B 249 " pdb=" N GLU B 249 " pdb=" C GLU B 249 " pdb=" CB GLU B 249 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA ILE B 262 " pdb=" N ILE B 262 " pdb=" C ILE B 262 " pdb=" CB ILE B 262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 1859 not shown) Planarity restraints: 2371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 679 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 680 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 680 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 680 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 22 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 23 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 23 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 23 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 624 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO B 625 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 625 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 625 " -0.019 5.00e-02 4.00e+02 ... (remaining 2368 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 281 2.67 - 3.23: 11735 3.23 - 3.79: 21602 3.79 - 4.34: 33058 4.34 - 4.90: 51809 Nonbonded interactions: 118485 Sorted by model distance: nonbonded pdb=" OH TYR A 644 " pdb=" OD2 ASP B 236 " model vdw 2.118 3.040 nonbonded pdb=" OD2 ASP B 321 " pdb=" OH TYR B 682 " model vdw 2.190 3.040 nonbonded pdb=" OD2 ASP B 558 " pdb=" O HOH B 901 " model vdw 2.217 3.040 nonbonded pdb=" O GLU B 684 " pdb=" OG SER B 687 " model vdw 2.222 3.040 nonbonded pdb=" O GLU A 684 " pdb=" OG SER A 687 " model vdw 2.230 3.040 ... (remaining 118480 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' and (resid 1 through 461 or (resid 462 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ or name OH )) or resid 463 through 810)) selection = chain 'B' } 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: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:7.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 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 : 0.002 0.034 13461 Z= 0.114 Angle : 0.532 9.698 18208 Z= 0.298 Chirality : 0.044 0.146 1862 Planarity : 0.004 0.041 2371 Dihedral : 17.786 88.688 4916 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.31 % Allowed : 19.19 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.25 (0.21), residues: 1616 helix: 1.07 (0.24), residues: 478 sheet: 1.26 (0.31), residues: 285 loop : -0.74 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.011 0.001 TYR A 462 PHE 0.015 0.001 PHE A 369 TRP 0.018 0.001 TRP A 716 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00244 (13461) covalent geometry : angle 0.53247 (18208) hydrogen bonds : bond 0.14161 ( 572) hydrogen bonds : angle 6.48870 ( 1593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.519 Fit side-chains REVERT: A 236 ASP cc_start: 0.8329 (t0) cc_final: 0.8119 (t0) outliers start: 32 outliers final: 27 residues processed: 158 average time/residue: 0.6664 time to fit residues: 113.2555 Evaluate side-chains 154 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 579 GLU Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 736 LYS Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 807 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 407 ASN B 77 ASN B 388 GLN B 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.094852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.083457 restraints weight = 15188.882| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.26 r_work: 0.2695 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 13461 Z= 0.158 Angle : 0.579 16.732 18208 Z= 0.313 Chirality : 0.047 0.148 1862 Planarity : 0.004 0.038 2371 Dihedral : 7.598 66.161 1846 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.32 % Allowed : 17.32 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.20 (0.21), residues: 1616 helix: 0.89 (0.23), residues: 499 sheet: 1.22 (0.31), residues: 281 loop : -0.70 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 326 TYR 0.017 0.001 TYR A 462 PHE 0.018 0.002 PHE A 369 TRP 0.019 0.002 TRP A 716 HIS 0.005 0.001 HIS B 653 Details of bonding type rmsd covalent geometry : bond 0.00374 (13461) covalent geometry : angle 0.57877 (18208) hydrogen bonds : bond 0.04855 ( 572) hydrogen bonds : angle 5.52095 ( 1593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 0.533 Fit side-chains REVERT: A 249 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7529 (mm-30) REVERT: A 571 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7224 (mtp180) REVERT: B 303 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: B 673 ASP cc_start: 0.7875 (m-30) cc_final: 0.7628 (m-30) outliers start: 46 outliers final: 18 residues processed: 161 average time/residue: 0.7429 time to fit residues: 128.3818 Evaluate side-chains 143 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 807 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 106 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 407 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.094086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.082626 restraints weight = 15280.510| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 1.27 r_work: 0.2680 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 13461 Z= 0.183 Angle : 0.592 17.789 18208 Z= 0.320 Chirality : 0.047 0.145 1862 Planarity : 0.004 0.041 2371 Dihedral : 6.623 65.206 1816 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.75 % Allowed : 16.81 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.16 (0.21), residues: 1616 helix: 0.82 (0.23), residues: 499 sheet: 1.13 (0.30), residues: 282 loop : -0.69 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.017 0.001 TYR A 462 PHE 0.018 0.002 PHE A 369 TRP 0.020 0.002 TRP A 331 HIS 0.005 0.001 HIS B 653 Details of bonding type rmsd covalent geometry : bond 0.00444 (13461) covalent geometry : angle 0.59248 (18208) hydrogen bonds : bond 0.04926 ( 572) hydrogen bonds : angle 5.45625 ( 1593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 0.550 Fit side-chains REVERT: A 249 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: A 373 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8454 (pt) REVERT: A 571 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7201 (mtp180) REVERT: A 623 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.7088 (pm20) REVERT: A 673 ASP cc_start: 0.7898 (m-30) cc_final: 0.7665 (m-30) REVERT: B 90 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8223 (mtt180) REVERT: B 137 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: B 143 LYS cc_start: 0.8498 (mppt) cc_final: 0.8108 (mtmm) REVERT: B 229 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7372 (mttp) REVERT: B 271 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.6629 (pt0) REVERT: B 303 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: B 373 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8365 (pt) REVERT: B 673 ASP cc_start: 0.7923 (m-30) cc_final: 0.7576 (m-30) outliers start: 52 outliers final: 21 residues processed: 169 average time/residue: 0.6803 time to fit residues: 123.6932 Evaluate side-chains 157 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 579 GLU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 807 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 131 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 44 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 406 ASN A 407 ASN B 77 ASN B 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.094879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.083530 restraints weight = 15254.874| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 1.26 r_work: 0.2694 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 13461 Z= 0.149 Angle : 0.561 17.972 18208 Z= 0.303 Chirality : 0.046 0.146 1862 Planarity : 0.004 0.041 2371 Dihedral : 6.253 62.645 1813 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.82 % Allowed : 16.88 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.22 (0.21), residues: 1616 helix: 0.91 (0.23), residues: 498 sheet: 1.16 (0.31), residues: 282 loop : -0.67 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 189 TYR 0.016 0.001 TYR A 462 PHE 0.019 0.002 PHE A 369 TRP 0.019 0.002 TRP A 716 HIS 0.004 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00355 (13461) covalent geometry : angle 0.56055 (18208) hydrogen bonds : bond 0.04472 ( 572) hydrogen bonds : angle 5.35894 ( 1593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 130 time to evaluate : 0.401 Fit side-chains REVERT: A 28 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8517 (mt) REVERT: A 53 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8423 (tpp-160) REVERT: A 116 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8143 (mt-10) REVERT: A 249 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: A 373 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8446 (pt) REVERT: A 571 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7245 (mtp180) REVERT: A 623 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: A 673 ASP cc_start: 0.7918 (m-30) cc_final: 0.7599 (m-30) REVERT: A 807 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: B 116 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8198 (mt-10) REVERT: B 137 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: B 143 LYS cc_start: 0.8457 (mppt) cc_final: 0.8088 (mtmm) REVERT: B 229 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7453 (mttp) REVERT: B 271 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.6619 (pt0) REVERT: B 282 LYS cc_start: 0.8381 (tttt) cc_final: 0.8119 (mtpp) REVERT: B 303 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: B 373 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8345 (pt) REVERT: B 673 ASP cc_start: 0.7928 (m-30) cc_final: 0.7540 (m-30) outliers start: 53 outliers final: 21 residues processed: 172 average time/residue: 0.6929 time to fit residues: 128.2284 Evaluate side-chains 160 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 579 GLU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 780 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 407 ASN B 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.093445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.082072 restraints weight = 15313.064| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.26 r_work: 0.2673 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 13461 Z= 0.195 Angle : 0.598 18.355 18208 Z= 0.324 Chirality : 0.048 0.146 1862 Planarity : 0.004 0.045 2371 Dihedral : 6.226 63.416 1809 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.75 % Allowed : 16.81 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.15 (0.21), residues: 1616 helix: 0.81 (0.23), residues: 499 sheet: 1.11 (0.30), residues: 282 loop : -0.68 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.017 0.002 TYR A 462 PHE 0.018 0.002 PHE A 369 TRP 0.020 0.002 TRP A 716 HIS 0.004 0.001 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00477 (13461) covalent geometry : angle 0.59841 (18208) hydrogen bonds : bond 0.04943 ( 572) hydrogen bonds : angle 5.43116 ( 1593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 127 time to evaluate : 0.537 Fit side-chains REVERT: A 53 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8418 (tpp-160) REVERT: A 116 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8108 (mt-10) REVERT: A 249 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: A 373 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8461 (pt) REVERT: A 571 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7236 (mtp180) REVERT: A 673 ASP cc_start: 0.7923 (m-30) cc_final: 0.7568 (m-30) REVERT: A 807 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: B 90 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8221 (mtt180) REVERT: B 116 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8201 (mt-10) REVERT: B 137 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: B 229 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7428 (mttp) REVERT: B 249 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: B 303 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: B 373 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8381 (pt) REVERT: B 673 ASP cc_start: 0.7959 (m-30) cc_final: 0.7553 (m-30) outliers start: 52 outliers final: 26 residues processed: 168 average time/residue: 0.6663 time to fit residues: 120.2245 Evaluate side-chains 164 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 579 GLU Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 807 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 132 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 41 optimal weight: 0.0040 chunk 125 optimal weight: 1.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 406 ASN A 407 ASN B 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.095128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.083806 restraints weight = 15191.979| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.25 r_work: 0.2699 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 13461 Z= 0.136 Angle : 0.550 18.081 18208 Z= 0.298 Chirality : 0.045 0.147 1862 Planarity : 0.004 0.043 2371 Dihedral : 6.017 60.874 1809 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.54 % Allowed : 17.53 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.23 (0.21), residues: 1616 helix: 0.95 (0.23), residues: 497 sheet: 1.12 (0.30), residues: 282 loop : -0.66 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.015 0.001 TYR A 462 PHE 0.019 0.002 PHE A 369 TRP 0.019 0.001 TRP A 716 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00318 (13461) covalent geometry : angle 0.55048 (18208) hydrogen bonds : bond 0.04301 ( 572) hydrogen bonds : angle 5.32589 ( 1593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 128 time to evaluate : 0.325 Fit side-chains REVERT: A 28 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8560 (mt) REVERT: A 53 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8422 (tpp-160) REVERT: A 116 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8126 (mt-10) REVERT: A 373 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8456 (pt) REVERT: A 571 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7242 (mtp180) REVERT: A 623 GLN cc_start: 0.9333 (OUTLIER) cc_final: 0.7086 (pm20) REVERT: A 807 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: B 90 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8161 (mtt180) REVERT: B 116 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8174 (mt-10) REVERT: B 137 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: B 229 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7475 (mttp) REVERT: B 271 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.6607 (pt0) REVERT: B 282 LYS cc_start: 0.8363 (tttt) cc_final: 0.8111 (mtpp) REVERT: B 303 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: B 373 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8356 (pt) REVERT: B 387 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8300 (p) REVERT: B 523 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7560 (ptmt) REVERT: B 673 ASP cc_start: 0.7928 (m-30) cc_final: 0.7524 (m-30) outliers start: 49 outliers final: 19 residues processed: 166 average time/residue: 0.6687 time to fit residues: 118.9536 Evaluate side-chains 161 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 579 GLU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 780 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 108 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 chunk 60 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 139 GLN A 407 ASN B 77 ASN B 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.096573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.085283 restraints weight = 15153.238| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.25 r_work: 0.2723 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13461 Z= 0.115 Angle : 0.525 17.505 18208 Z= 0.284 Chirality : 0.045 0.146 1862 Planarity : 0.004 0.041 2371 Dihedral : 5.731 57.438 1808 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.17 % Allowed : 17.89 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.30 (0.21), residues: 1616 helix: 1.05 (0.23), residues: 498 sheet: 1.15 (0.31), residues: 282 loop : -0.64 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 189 TYR 0.014 0.001 TYR A 462 PHE 0.019 0.001 PHE A 369 TRP 0.017 0.001 TRP A 716 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00263 (13461) covalent geometry : angle 0.52511 (18208) hydrogen bonds : bond 0.03929 ( 572) hydrogen bonds : angle 5.22792 ( 1593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 0.528 Fit side-chains REVERT: A 53 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8402 (tpp-160) REVERT: A 116 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8111 (mt-10) REVERT: A 571 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7222 (mtp180) REVERT: A 623 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.7129 (pm20) REVERT: A 717 LEU cc_start: 0.8106 (mt) cc_final: 0.7873 (mp) REVERT: A 771 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8378 (ptmt) REVERT: A 807 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7970 (mm-30) REVERT: B 90 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8146 (mtt180) REVERT: B 116 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8149 (mt-10) REVERT: B 137 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: B 282 LYS cc_start: 0.8329 (tttt) cc_final: 0.8101 (mtpp) REVERT: B 303 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: B 387 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8263 (p) REVERT: B 449 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6686 (mtpt) REVERT: B 673 ASP cc_start: 0.7910 (m-30) cc_final: 0.7499 (m-30) outliers start: 44 outliers final: 21 residues processed: 166 average time/residue: 0.6695 time to fit residues: 119.2839 Evaluate side-chains 158 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 579 GLU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 736 LYS Chi-restraints excluded: chain A residue 771 LYS Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 807 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 100 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 407 ASN B 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.092887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.081604 restraints weight = 15055.839| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 1.24 r_work: 0.2664 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 13461 Z= 0.242 Angle : 0.632 18.564 18208 Z= 0.341 Chirality : 0.050 0.149 1862 Planarity : 0.005 0.047 2371 Dihedral : 6.100 62.274 1806 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.32 % Allowed : 17.97 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.16 (0.21), residues: 1616 helix: 0.80 (0.23), residues: 499 sheet: 1.12 (0.30), residues: 282 loop : -0.66 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 571 TYR 0.019 0.002 TYR A 462 PHE 0.019 0.002 PHE A 369 TRP 0.020 0.002 TRP A 716 HIS 0.005 0.001 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00595 (13461) covalent geometry : angle 0.63191 (18208) hydrogen bonds : bond 0.05256 ( 572) hydrogen bonds : angle 5.45907 ( 1593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 0.408 Fit side-chains REVERT: A 53 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8379 (tpp-160) REVERT: A 116 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8113 (mt-10) REVERT: A 139 GLN cc_start: 0.8238 (mm-40) cc_final: 0.8009 (mp10) REVERT: A 174 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: A 249 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7578 (mm-30) REVERT: A 571 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7228 (mtp180) REVERT: A 623 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: A 807 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: B 90 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8265 (mtt180) REVERT: B 116 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8151 (mt-10) REVERT: B 282 LYS cc_start: 0.8412 (tttt) cc_final: 0.8163 (mtpp) REVERT: B 303 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: B 387 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8292 (p) REVERT: B 523 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7649 (ptmt) outliers start: 46 outliers final: 20 residues processed: 165 average time/residue: 0.6464 time to fit residues: 114.6979 Evaluate side-chains 157 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 579 GLU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 807 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 122 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 407 ASN B 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.094948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.083639 restraints weight = 15245.010| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.25 r_work: 0.2698 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 13461 Z= 0.143 Angle : 0.560 18.113 18208 Z= 0.303 Chirality : 0.046 0.152 1862 Planarity : 0.004 0.044 2371 Dihedral : 5.888 60.428 1806 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.74 % Allowed : 18.54 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.25 (0.21), residues: 1616 helix: 0.95 (0.23), residues: 496 sheet: 1.14 (0.30), residues: 282 loop : -0.65 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.015 0.001 TYR A 462 PHE 0.019 0.002 PHE A 369 TRP 0.019 0.002 TRP A 716 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00338 (13461) covalent geometry : angle 0.56044 (18208) hydrogen bonds : bond 0.04358 ( 572) hydrogen bonds : angle 5.33563 ( 1593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.491 Fit side-chains REVERT: A 53 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8431 (tpp-160) REVERT: A 571 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7242 (mtp180) REVERT: A 598 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8472 (mp) REVERT: A 623 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.7089 (pm20) REVERT: A 807 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8024 (mm-30) REVERT: B 90 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8188 (mtt180) REVERT: B 116 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8161 (mt-10) REVERT: B 137 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: B 271 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.6615 (pt0) REVERT: B 282 LYS cc_start: 0.8356 (tttt) cc_final: 0.8109 (mtpp) REVERT: B 303 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: B 373 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8343 (pt) REVERT: B 387 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8317 (p) outliers start: 38 outliers final: 21 residues processed: 155 average time/residue: 0.6787 time to fit residues: 112.8716 Evaluate side-chains 157 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 579 GLU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 736 LYS Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 807 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 144 optimal weight: 0.0050 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 407 ASN B 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.094929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.083627 restraints weight = 15202.758| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 1.25 r_work: 0.2697 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 13461 Z= 0.150 Angle : 0.567 18.137 18208 Z= 0.307 Chirality : 0.046 0.177 1862 Planarity : 0.004 0.044 2371 Dihedral : 5.867 60.001 1806 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.24 % Allowed : 18.83 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.23 (0.21), residues: 1616 helix: 0.95 (0.23), residues: 496 sheet: 1.11 (0.30), residues: 282 loop : -0.66 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.016 0.001 TYR A 462 PHE 0.018 0.002 PHE A 369 TRP 0.019 0.002 TRP A 331 HIS 0.004 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00357 (13461) covalent geometry : angle 0.56720 (18208) hydrogen bonds : bond 0.04421 ( 572) hydrogen bonds : angle 5.33652 ( 1593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.381 Fit side-chains REVERT: A 53 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8415 (tpp-160) REVERT: A 571 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7250 (mtp180) REVERT: A 598 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 623 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.7089 (pm20) REVERT: A 807 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: B 90 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8187 (mtt180) REVERT: B 116 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8142 (mt-10) REVERT: B 282 LYS cc_start: 0.8366 (tttt) cc_final: 0.8120 (mtpp) REVERT: B 303 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: B 373 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8335 (pt) REVERT: B 387 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8330 (p) REVERT: B 523 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7534 (ptmt) outliers start: 31 outliers final: 21 residues processed: 151 average time/residue: 0.7039 time to fit residues: 114.2566 Evaluate side-chains 156 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 579 GLU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 736 LYS Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 807 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 93 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 407 ASN B 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.095234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.083937 restraints weight = 15194.668| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.26 r_work: 0.2702 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 13461 Z= 0.143 Angle : 0.560 18.077 18208 Z= 0.303 Chirality : 0.046 0.169 1862 Planarity : 0.004 0.043 2371 Dihedral : 5.820 58.979 1806 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.81 % Allowed : 18.25 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.24 (0.21), residues: 1616 helix: 0.97 (0.23), residues: 496 sheet: 1.11 (0.30), residues: 282 loop : -0.66 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.015 0.001 TYR A 462 PHE 0.018 0.002 PHE A 369 TRP 0.019 0.002 TRP A 331 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00338 (13461) covalent geometry : angle 0.56040 (18208) hydrogen bonds : bond 0.04327 ( 572) hydrogen bonds : angle 5.31624 ( 1593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.31 seconds wall clock time: 65 minutes 41.18 seconds (3941.18 seconds total)