Starting phenix.real_space_refine on Mon Dec 30 13:43:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ho7_34921/12_2024/8ho7_34921_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ho7_34921/12_2024/8ho7_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_34921/12_2024/8ho7_34921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ho7_34921/12_2024/8ho7_34921.map" model { file = "/net/cci-nas-00/data/ceres_data/8ho7_34921/12_2024/8ho7_34921_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ho7_34921/12_2024/8ho7_34921_neut.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9.56, per 1000 atoms: 0.72 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: 3.18 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.81 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: 5.69 Time building geometry restraints manager: 3.70 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: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.350 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.500 ------------------------------------------------------------------------------- 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= 0.154 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 : 4.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (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 TRP 0.018 0.001 TRP A 716 HIS 0.003 0.001 HIS A 653 PHE 0.015 0.001 PHE A 369 TYR 0.011 0.001 TYR A 462 ARG 0.002 0.000 ARG A 571 *********************** 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 : 1.644 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: 1.6740 time to fit residues: 285.4087 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 : 1.853 ------------------------------------------------------------------------------- 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 136 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 0.0270 chunk 65 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.3444 ------------------------------------------------------------------------------- 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 388 GLN B 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 13461 Z= 0.305 Angle : 0.614 17.241 18208 Z= 0.331 Chirality : 0.048 0.148 1862 Planarity : 0.004 0.038 2371 Dihedral : 7.771 66.618 1846 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.25 % Allowed : 17.17 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1616 helix: 0.86 (0.23), residues: 493 sheet: 1.22 (0.30), residues: 281 loop : -0.72 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 331 HIS 0.006 0.001 HIS B 653 PHE 0.018 0.002 PHE A 369 TYR 0.017 0.002 TYR A 462 ARG 0.003 0.000 ARG A 326 *********************** 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 168 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 1.630 Fit side-chains REVERT: A 249 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: A 571 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7464 (mtp180) REVERT: B 70 ARG cc_start: 0.9340 (OUTLIER) cc_final: 0.8366 (mpt90) REVERT: B 303 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7982 (mt-10) outliers start: 45 outliers final: 18 residues processed: 157 average time/residue: 1.7090 time to fit residues: 288.7597 Evaluate side-chains 142 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 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 70 ARG 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 13461 Z= 0.289 Angle : 0.599 18.023 18208 Z= 0.324 Chirality : 0.048 0.147 1862 Planarity : 0.004 0.042 2371 Dihedral : 6.984 65.303 1822 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.11 % Allowed : 16.38 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1616 helix: 0.77 (0.23), residues: 499 sheet: 1.14 (0.30), residues: 282 loop : -0.70 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 331 HIS 0.005 0.001 HIS B 653 PHE 0.019 0.002 PHE A 369 TYR 0.017 0.002 TYR A 462 ARG 0.002 0.000 ARG A 571 *********************** 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 181 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 124 time to evaluate : 1.749 Fit side-chains REVERT: A 28 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.8788 (mt) REVERT: A 53 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8814 (tpp-160) REVERT: A 249 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: A 373 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8805 (pt) REVERT: A 571 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7430 (mtp180) REVERT: A 673 ASP cc_start: 0.8191 (m-30) cc_final: 0.7895 (m-30) REVERT: A 743 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8167 (ttpm) REVERT: B 90 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8440 (mtt180) REVERT: B 143 LYS cc_start: 0.8611 (mppt) cc_final: 0.8340 (mtmm) REVERT: B 303 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: B 373 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8622 (pt) REVERT: B 673 ASP cc_start: 0.8170 (m-30) cc_final: 0.7951 (m-30) outliers start: 57 outliers final: 26 residues processed: 171 average time/residue: 1.8040 time to fit residues: 333.7975 Evaluate side-chains 162 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL 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 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 743 LYS 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 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 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 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 145 optimal weight: 0.3980 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 13461 Z= 0.232 Angle : 0.565 18.196 18208 Z= 0.306 Chirality : 0.046 0.147 1862 Planarity : 0.004 0.043 2371 Dihedral : 6.473 63.142 1815 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.04 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1616 helix: 0.87 (0.23), residues: 497 sheet: 1.15 (0.30), residues: 282 loop : -0.69 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 716 HIS 0.004 0.001 HIS A 653 PHE 0.019 0.002 PHE A 369 TYR 0.016 0.001 TYR A 462 ARG 0.002 0.000 ARG A 571 *********************** 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 185 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 129 time to evaluate : 1.488 Fit side-chains REVERT: A 28 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.8824 (mt) REVERT: A 116 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8143 (mt-10) REVERT: A 249 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: A 571 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7461 (mtp180) REVERT: A 623 GLN cc_start: 0.9409 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: A 673 ASP cc_start: 0.8174 (m-30) cc_final: 0.7804 (m-30) REVERT: A 743 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8166 (ttpm) REVERT: B 116 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8181 (mt-10) REVERT: B 137 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: B 143 LYS cc_start: 0.8534 (mppt) cc_final: 0.8257 (mtmm) REVERT: B 229 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7695 (mttp) REVERT: B 271 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7077 (pt0) REVERT: B 303 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: B 373 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8629 (pt) REVERT: B 523 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7713 (ptmt) REVERT: B 673 ASP cc_start: 0.8223 (m-30) cc_final: 0.7915 (m-30) outliers start: 56 outliers final: 24 residues processed: 175 average time/residue: 1.6648 time to fit residues: 314.1770 Evaluate side-chains 161 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 161 MET 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 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 743 LYS Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 784 THR 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 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 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 130 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 13461 Z= 0.383 Angle : 0.641 18.929 18208 Z= 0.347 Chirality : 0.050 0.151 1862 Planarity : 0.005 0.048 2371 Dihedral : 6.452 64.529 1809 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.04 % Allowed : 16.74 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1616 helix: 0.71 (0.23), residues: 499 sheet: 1.11 (0.30), residues: 282 loop : -0.70 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 716 HIS 0.005 0.001 HIS B 244 PHE 0.018 0.002 PHE A 369 TYR 0.019 0.002 TYR A 462 ARG 0.003 0.000 ARG A 571 *********************** 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 183 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 127 time to evaluate : 1.626 Fit side-chains REVERT: A 28 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.8773 (mt) REVERT: A 53 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8598 (tpp-160) REVERT: A 116 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8151 (mt-10) REVERT: A 249 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: A 571 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7470 (mtp180) REVERT: A 743 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8184 (ttpm) REVERT: B 90 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8481 (mtt180) REVERT: B 116 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8164 (mt-10) REVERT: B 229 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7669 (mttp) REVERT: B 249 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: B 303 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: B 373 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8668 (pt) REVERT: B 673 ASP cc_start: 0.8248 (m-30) cc_final: 0.7918 (m-30) outliers start: 56 outliers final: 29 residues processed: 168 average time/residue: 1.7863 time to fit residues: 323.8472 Evaluate side-chains 168 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL 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 94 SER Chi-restraints excluded: chain A residue 161 MET 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 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 736 LYS Chi-restraints excluded: chain A residue 743 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 86 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 145 THR 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 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 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 52 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 156 optimal weight: 0.0030 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 406 ASN A 407 ASN B 77 ASN B 406 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 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 : 0.002 0.055 13461 Z= 0.152 Angle : 0.526 18.108 18208 Z= 0.284 Chirality : 0.045 0.148 1862 Planarity : 0.004 0.042 2371 Dihedral : 5.947 59.375 1809 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.25 % Allowed : 17.60 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1616 helix: 1.00 (0.23), residues: 498 sheet: 1.17 (0.31), residues: 281 loop : -0.67 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 716 HIS 0.003 0.001 HIS A 653 PHE 0.020 0.001 PHE A 369 TYR 0.014 0.001 TYR A 462 ARG 0.002 0.000 ARG B 189 *********************** 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 179 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 1.588 Fit side-chains REVERT: A 53 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8627 (tpp-160) REVERT: A 116 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8113 (mt-10) REVERT: A 571 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7439 (mtp180) REVERT: A 673 ASP cc_start: 0.8128 (m-30) cc_final: 0.7887 (m-30) REVERT: B 90 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8376 (mtt180) REVERT: B 116 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8111 (mt-10) REVERT: B 137 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: B 143 LYS cc_start: 0.8584 (mppt) cc_final: 0.8317 (mtmm) REVERT: B 229 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7740 (mttp) REVERT: B 236 ASP cc_start: 0.8338 (t0) cc_final: 0.8098 (t0) REVERT: B 303 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: B 568 ASP cc_start: 0.8423 (t70) cc_final: 0.8146 (t0) REVERT: B 673 ASP cc_start: 0.8193 (m-30) cc_final: 0.7832 (m-30) outliers start: 45 outliers final: 16 residues processed: 171 average time/residue: 1.7574 time to fit residues: 325.2021 Evaluate side-chains 150 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 670 MET Chi-restraints excluded: chain A residue 736 LYS 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 303 GLU Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 777 SER 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 151 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 156 optimal weight: 0.0770 chunk 97 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN B 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.0822 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= 0.278 Angle : 0.583 18.460 18208 Z= 0.314 Chirality : 0.047 0.147 1862 Planarity : 0.004 0.044 2371 Dihedral : 5.818 61.260 1804 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.89 % Allowed : 17.89 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1616 helix: 0.90 (0.23), residues: 497 sheet: 1.13 (0.30), residues: 282 loop : -0.66 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 331 HIS 0.004 0.001 HIS B 244 PHE 0.018 0.002 PHE A 369 TYR 0.016 0.001 TYR A 462 ARG 0.003 0.000 ARG A 57 *********************** 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 172 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.645 Fit side-chains REVERT: A 53 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8631 (tpp-160) REVERT: A 116 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 571 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7449 (mtp180) REVERT: A 673 ASP cc_start: 0.8196 (m-30) cc_final: 0.7893 (m-30) REVERT: B 90 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8422 (mtt180) REVERT: B 116 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8125 (mt-10) REVERT: B 137 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: B 229 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7796 (mttp) REVERT: B 236 ASP cc_start: 0.8194 (t0) cc_final: 0.7968 (t0) REVERT: B 303 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: B 373 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8623 (pt) REVERT: B 673 ASP cc_start: 0.8255 (m-30) cc_final: 0.7890 (m-30) outliers start: 40 outliers final: 24 residues processed: 161 average time/residue: 1.8422 time to fit residues: 319.5862 Evaluate side-chains 163 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 161 MET Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 206 ASP 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 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 229 LYS 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 373 ILE 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 652 CYS Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 777 SER 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 96 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 47 optimal weight: 0.0980 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 406 ASN A 407 ASN B 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13461 Z= 0.176 Angle : 0.541 18.014 18208 Z= 0.292 Chirality : 0.045 0.147 1862 Planarity : 0.004 0.042 2371 Dihedral : 5.589 58.750 1803 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.74 % Allowed : 18.18 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1616 helix: 1.03 (0.23), residues: 496 sheet: 1.12 (0.30), residues: 282 loop : -0.64 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 716 HIS 0.003 0.001 HIS A 653 PHE 0.019 0.001 PHE A 369 TYR 0.015 0.001 TYR A 462 ARG 0.002 0.000 ARG A 57 *********************** 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 171 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.486 Fit side-chains REVERT: A 53 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8644 (tpp-160) REVERT: A 116 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8086 (mt-10) REVERT: A 571 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7420 (mtp180) REVERT: A 673 ASP cc_start: 0.8167 (m-30) cc_final: 0.7832 (m-30) REVERT: B 90 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8377 (mtt180) REVERT: B 116 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 137 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: B 236 ASP cc_start: 0.8184 (t0) cc_final: 0.7931 (t0) REVERT: B 271 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7079 (pt0) REVERT: B 303 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: B 373 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8623 (pt) REVERT: B 449 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7231 (mtpt) REVERT: B 673 ASP cc_start: 0.8225 (m-30) cc_final: 0.7851 (m-30) outliers start: 38 outliers final: 20 residues processed: 163 average time/residue: 1.7073 time to fit residues: 299.2712 Evaluate side-chains 158 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 161 MET 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 670 MET Chi-restraints excluded: chain A residue 736 LYS 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 305 LYS Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 373 ILE 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 777 SER 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 149 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 145 optimal weight: 0.0050 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 131 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 406 ASN A 407 ASN B 77 ASN B 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 13461 Z= 0.156 Angle : 0.523 17.651 18208 Z= 0.282 Chirality : 0.044 0.147 1862 Planarity : 0.004 0.041 2371 Dihedral : 5.372 56.074 1802 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.74 % Allowed : 18.18 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1616 helix: 1.09 (0.23), residues: 495 sheet: 1.16 (0.30), residues: 281 loop : -0.62 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 331 HIS 0.003 0.001 HIS A 653 PHE 0.018 0.001 PHE A 369 TYR 0.014 0.001 TYR A 462 ARG 0.002 0.000 ARG B 189 *********************** 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 174 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.587 Fit side-chains REVERT: A 53 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8591 (tpp-160) REVERT: A 571 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7402 (mtp180) REVERT: A 673 ASP cc_start: 0.8168 (m-30) cc_final: 0.7815 (m-30) REVERT: B 90 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8366 (mtt180) REVERT: B 116 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8094 (mt-10) REVERT: B 137 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: B 143 LYS cc_start: 0.8556 (mppt) cc_final: 0.8299 (mtmm) REVERT: B 236 ASP cc_start: 0.8171 (t0) cc_final: 0.7896 (t0) REVERT: B 271 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7069 (pt0) REVERT: B 303 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: B 373 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8576 (pt) REVERT: B 449 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7236 (mtpt) REVERT: B 673 ASP cc_start: 0.8226 (m-30) cc_final: 0.7848 (m-30) outliers start: 38 outliers final: 20 residues processed: 164 average time/residue: 1.7281 time to fit residues: 306.4907 Evaluate side-chains 157 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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 161 MET 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 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 670 MET Chi-restraints excluded: chain A residue 736 LYS 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 271 GLU 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 373 ILE 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 777 SER 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 153 optimal weight: 0.2980 chunk 93 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13461 Z= 0.170 Angle : 0.531 17.623 18208 Z= 0.287 Chirality : 0.045 0.148 1862 Planarity : 0.004 0.041 2371 Dihedral : 5.281 55.763 1800 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.02 % Allowed : 18.98 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1616 helix: 1.09 (0.23), residues: 498 sheet: 1.19 (0.30), residues: 281 loop : -0.62 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 331 HIS 0.003 0.001 HIS A 653 PHE 0.018 0.001 PHE A 369 TYR 0.015 0.001 TYR A 462 ARG 0.002 0.000 ARG B 189 ********************** 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 155 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.379 Fit side-chains REVERT: A 53 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8636 (tpp-160) REVERT: A 571 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7404 (mtp180) REVERT: A 673 ASP cc_start: 0.8168 (m-30) cc_final: 0.7812 (m-30) REVERT: B 90 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8387 (mtt180) REVERT: B 116 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8098 (mt-10) REVERT: B 137 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: B 236 ASP cc_start: 0.8172 (t0) cc_final: 0.7894 (t0) REVERT: B 303 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: B 373 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8585 (pt) REVERT: B 449 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7227 (mtpt) REVERT: B 673 ASP cc_start: 0.8232 (m-30) cc_final: 0.7853 (m-30) outliers start: 28 outliers final: 19 residues processed: 148 average time/residue: 1.7806 time to fit residues: 283.3569 Evaluate side-chains 153 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.625 ------------------------------------------------------------------------------- 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 161 MET 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 670 MET Chi-restraints excluded: chain A residue 736 LYS 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 303 GLU Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 373 ILE 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 777 SER 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 136 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 53 optimal weight: 0.1980 chunk 132 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.2974 r_free = 0.2974 target = 0.096326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.084985 restraints weight = 15060.728| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.26 r_work: 0.2716 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 13461 Z= 0.185 Angle : 0.541 17.707 18208 Z= 0.291 Chirality : 0.045 0.148 1862 Planarity : 0.004 0.042 2371 Dihedral : 5.305 56.119 1800 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.31 % Allowed : 18.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1616 helix: 1.09 (0.23), residues: 497 sheet: 1.18 (0.30), residues: 282 loop : -0.62 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 716 HIS 0.003 0.001 HIS A 653 PHE 0.018 0.001 PHE A 369 TYR 0.015 0.001 TYR A 462 ARG 0.002 0.000 ARG A 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5277.81 seconds wall clock time: 96 minutes 57.45 seconds (5817.45 seconds total)