Starting phenix.real_space_refine on Sun Oct 25 12:08:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q5l_72239/10_2026/9q5l_72239.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q5l_72239/10_2026/9q5l_72239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q5l_72239/10_2026/9q5l_72239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q5l_72239/10_2026/9q5l_72239.map" model { file = "/net/cci-nas-00/data/ceres_data/9q5l_72239/10_2026/9q5l_72239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q5l_72239/10_2026/9q5l_72239.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 88 5.16 5 C 10382 2.51 5 N 2928 2.21 5 O 3068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16468 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5971 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 721} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5971 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 721} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2257 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 18, 'TRANS': 270} Chain: "D" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2257 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 18, 'TRANS': 270} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' ZN': 1, 'DMN': 1, 'FOR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' ZN': 1, 'DMN': 1, 'FOR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2031 SG CYS A 285 80.846 76.092 31.818 1.00 40.94 S ATOM 2156 SG CYS A 301 82.795 73.731 30.718 1.00 55.25 S ATOM 2655 SG CYS A 365 83.355 75.055 34.756 1.00 59.08 S ATOM 8002 SG CYS B 285 55.572 55.420 31.846 1.00 40.94 S ATOM 8127 SG CYS B 301 53.620 57.780 30.750 1.00 55.25 S ATOM 8626 SG CYS B 365 53.069 56.457 34.790 1.00 59.08 S Time building chain proxies: 3.16, per 1000 atoms: 0.19 Number of scatterers: 16468 At special positions: 0 Unit cell: (137.274, 132.342, 96.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 88 16.00 O 3068 8.00 N 2928 7.00 C 10382 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: 1.55 Conformation dependent library (CDL) restraints added in 791.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 285 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 301 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 365 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 285 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 301 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 365 " 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3848 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 26 sheets defined 23.2% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.837A pdb=" N TYR A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 523 through 537 removed outlier: 3.512A pdb=" N GLU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 529 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 565 removed outlier: 3.722A pdb=" N VAL A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 removed outlier: 4.415A pdb=" N ALA A 620 " --> pdb=" O PRO A 616 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 651 removed outlier: 3.650A pdb=" N LEU A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.836A pdb=" N TYR B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 523 through 537 removed outlier: 3.512A pdb=" N GLU B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET B 529 " --> pdb=" O GLY B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 565 removed outlier: 3.722A pdb=" N VAL B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 630 removed outlier: 4.415A pdb=" N ALA B 620 " --> pdb=" O PRO B 616 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU B 621 " --> pdb=" O LYS B 617 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 624 " --> pdb=" O ALA B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 651 removed outlier: 3.650A pdb=" N LEU B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 481 through 485 Processing helix chain 'C' and resid 523 through 536 removed outlier: 3.524A pdb=" N LEU C 536 " --> pdb=" O GLN C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 566 Processing helix chain 'C' and resid 615 through 628 removed outlier: 4.531A pdb=" N ALA C 620 " --> pdb=" O PRO C 616 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU C 621 " --> pdb=" O LYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 651 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 687 through 692 Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 481 through 485 Processing helix chain 'D' and resid 523 through 536 removed outlier: 3.523A pdb=" N LEU D 536 " --> pdb=" O GLN D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 566 Processing helix chain 'D' and resid 615 through 628 removed outlier: 4.530A pdb=" N ALA D 620 " --> pdb=" O PRO D 616 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU D 621 " --> pdb=" O LYS D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 651 Processing helix chain 'D' and resid 670 through 674 Processing helix chain 'D' and resid 687 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 3.891A pdb=" N LYS B 766 " --> pdb=" O LYS B 760 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N CYS B 716 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE B 724 " --> pdb=" O ASP B 746 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 742 " --> pdb=" O THR B 728 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA B 730 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE B 740 " --> pdb=" O ALA B 730 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TRP B 732 " --> pdb=" O LYS B 738 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS B 738 " --> pdb=" O TRP B 732 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN B 739 " --> pdb=" O ILE B 705 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 702 " --> pdb=" O THR B 773 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 37 removed outlier: 3.923A pdb=" N ASP A 130 " --> pdb=" O ASN A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 47 Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 192 removed outlier: 6.788A pdb=" N TYR A 349 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP A 273 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 351 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR A 259 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 189 through 192 removed outlier: 6.788A pdb=" N TYR A 349 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP A 273 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 351 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 197 through 202 Processing sheet with id=AA7, first strand: chain 'A' and resid 328 through 331 removed outlier: 4.423A pdb=" N ASN A 328 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 423 through 426 removed outlier: 8.047A pdb=" N ASP A 423 " --> pdb=" O ASN A 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 567 through 569 Processing sheet with id=AB1, first strand: chain 'A' and resid 490 through 496 removed outlier: 3.564A pdb=" N ASP A 504 " --> pdb=" O MET A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 21 through 22 removed outlier: 3.890A pdb=" N LYS A 766 " --> pdb=" O LYS A 760 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS A 716 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE A 724 " --> pdb=" O ASP A 746 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A 742 " --> pdb=" O THR A 728 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA A 730 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE A 740 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TRP A 732 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS A 738 " --> pdb=" O TRP A 732 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A 739 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 702 " --> pdb=" O THR A 773 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 32 through 37 removed outlier: 3.923A pdb=" N ASP B 130 " --> pdb=" O ASN B 57 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 42 through 47 Processing sheet with id=AB5, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.788A pdb=" N TYR B 349 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP B 273 " --> pdb=" O TYR B 349 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 351 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR B 259 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.788A pdb=" N TYR B 349 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP B 273 " --> pdb=" O TYR B 349 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 351 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 197 through 202 Processing sheet with id=AB8, first strand: chain 'B' and resid 328 through 331 removed outlier: 4.424A pdb=" N ASN B 328 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 423 through 426 removed outlier: 8.046A pdb=" N ASP B 423 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 567 through 569 Processing sheet with id=AC2, first strand: chain 'B' and resid 490 through 496 removed outlier: 3.564A pdb=" N ASP B 504 " --> pdb=" O MET B 495 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 424 through 427 Processing sheet with id=AC4, first strand: chain 'C' and resid 453 through 456 Processing sheet with id=AC5, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AC6, first strand: chain 'D' and resid 424 through 427 Processing sheet with id=AC7, first strand: chain 'D' and resid 453 through 456 Processing sheet with id=AC8, first strand: chain 'D' and resid 490 through 491 652 hydrogen bonds defined for protein. 1788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4953 1.33 - 1.45: 2752 1.45 - 1.57: 9043 1.57 - 1.69: 0 1.69 - 1.81: 146 Bond restraints: 16894 Sorted by residual: bond pdb=" C FOR A 802 " pdb=" O FOR A 802 " ideal model delta sigma weight residual 1.202 1.263 -0.061 2.00e-02 2.50e+03 9.22e+00 bond pdb=" C FOR B 802 " pdb=" O FOR B 802 " ideal model delta sigma weight residual 1.202 1.262 -0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" N GLN A 32 " pdb=" CA GLN A 32 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.23e-02 6.61e+03 6.67e+00 bond pdb=" N GLN B 32 " pdb=" CA GLN B 32 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.23e-02 6.61e+03 6.60e+00 bond pdb=" N ASN B 416 " pdb=" CA ASN B 416 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.30e-02 5.92e+03 5.99e+00 ... (remaining 16889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 22237 1.77 - 3.53: 618 3.53 - 5.30: 80 5.30 - 7.07: 15 7.07 - 8.84: 8 Bond angle restraints: 22958 Sorted by residual: angle pdb=" N GLN A 32 " pdb=" CA GLN A 32 " pdb=" CB GLN A 32 " ideal model delta sigma weight residual 110.42 118.07 -7.65 1.63e+00 3.76e-01 2.20e+01 angle pdb=" N GLN B 32 " pdb=" CA GLN B 32 " pdb=" CB GLN B 32 " ideal model delta sigma weight residual 110.42 118.04 -7.62 1.63e+00 3.76e-01 2.19e+01 angle pdb=" N ILE D 690 " pdb=" CA ILE D 690 " pdb=" C ILE D 690 " ideal model delta sigma weight residual 112.96 108.49 4.47 1.00e+00 1.00e+00 2.00e+01 angle pdb=" N ILE C 690 " pdb=" CA ILE C 690 " pdb=" C ILE C 690 " ideal model delta sigma weight residual 111.90 108.50 3.40 8.10e-01 1.52e+00 1.76e+01 angle pdb=" C GLN A 662 " pdb=" CA GLN A 662 " pdb=" CB GLN A 662 " ideal model delta sigma weight residual 109.38 116.08 -6.70 1.68e+00 3.54e-01 1.59e+01 ... (remaining 22953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 8398 17.08 - 34.16: 1140 34.16 - 51.24: 373 51.24 - 68.32: 77 68.32 - 85.39: 28 Dihedral angle restraints: 10016 sinusoidal: 3988 harmonic: 6028 Sorted by residual: dihedral pdb=" CA LYS C 636 " pdb=" C LYS C 636 " pdb=" N PRO C 637 " pdb=" CA PRO C 637 " ideal model delta harmonic sigma weight residual -180.00 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA LYS D 636 " pdb=" C LYS D 636 " pdb=" N PRO D 637 " pdb=" CA PRO D 637 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA TRP A 320 " pdb=" C TRP A 320 " pdb=" N MET A 321 " pdb=" CA MET A 321 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 10013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1429 0.035 - 0.069: 657 0.069 - 0.103: 224 0.103 - 0.138: 108 0.138 - 0.172: 12 Chirality restraints: 2430 Sorted by residual: chirality pdb=" CA ASN D 438 " pdb=" N ASN D 438 " pdb=" C ASN D 438 " pdb=" CB ASN D 438 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA ASN C 438 " pdb=" N ASN C 438 " pdb=" C ASN C 438 " pdb=" CB ASN C 438 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CB VAL C 465 " pdb=" CA VAL C 465 " pdb=" CG1 VAL C 465 " pdb=" CG2 VAL C 465 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 2427 not shown) Planarity restraints: 3064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 554 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C VAL D 554 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL D 554 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN D 555 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 554 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C VAL C 554 " -0.058 2.00e-02 2.50e+03 pdb=" O VAL C 554 " 0.022 2.00e-02 2.50e+03 pdb=" N GLN C 555 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 661 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C ASP A 661 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP A 661 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN A 662 " -0.014 2.00e-02 2.50e+03 ... (remaining 3061 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 75 2.63 - 3.20: 14203 3.20 - 3.77: 26211 3.77 - 4.33: 38287 4.33 - 4.90: 63386 Nonbonded interactions: 142162 Sorted by model distance: nonbonded pdb="ZN ZN A 801 " pdb=" O FOR A 802 " model vdw 2.066 2.230 nonbonded pdb="ZN ZN B 801 " pdb=" O FOR B 802 " model vdw 2.067 2.230 nonbonded pdb=" O PRO D 437 " pdb=" ND2 ASN D 438 " model vdw 2.392 3.120 nonbonded pdb=" O PRO C 437 " pdb=" ND2 ASN C 438 " model vdw 2.393 3.120 nonbonded pdb=" O GLU A 154 " pdb=" OE1 GLU A 154 " model vdw 2.508 3.040 ... (remaining 142157 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 2.170 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.030 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.007 0.375 16900 Z= 0.288 Angle : 0.696 8.835 22958 Z= 0.383 Chirality : 0.047 0.172 2430 Planarity : 0.006 0.051 3064 Dihedral : 17.917 85.394 6168 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.25 % Allowed : 31.88 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 2122 helix: -0.84 (0.23), residues: 536 sheet: -0.52 (0.22), residues: 508 loop : -1.24 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 353 TYR 0.015 0.002 TYR A 445 PHE 0.018 0.002 PHE B 659 TRP 0.011 0.002 TRP B 528 HIS 0.007 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.24 (16894) covalent geometry : angle 0.69616 / 0.38 (22958) hydrogen bonds : bond 0.13707 / 9.22 ( 618) hydrogen bonds : angle 6.90638 / 5.02 ( 1788) metal coordination : bond 0.25464 / 14.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6436 (mmm-85) cc_final: 0.5953 (mtm180) REVERT: A 63 ARG cc_start: 0.7660 (ttp80) cc_final: 0.6304 (ttm-80) REVERT: A 121 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7152 (mp) REVERT: A 203 ARG cc_start: 0.7735 (mtp180) cc_final: 0.7329 (mpt-90) REVERT: A 379 ASP cc_start: 0.8477 (m-30) cc_final: 0.8234 (m-30) REVERT: A 404 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: A 489 GLN cc_start: 0.8334 (mt0) cc_final: 0.7944 (mt0) REVERT: A 755 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7908 (mt-10) REVERT: B 52 ARG cc_start: 0.6257 (mmm-85) cc_final: 0.5680 (mpp-170) REVERT: B 63 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7343 (ttp-170) REVERT: B 121 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7341 (mp) REVERT: B 134 PHE cc_start: 0.6532 (m-80) cc_final: 0.6262 (m-80) REVERT: B 203 ARG cc_start: 0.7682 (mtp180) cc_final: 0.7341 (mpt-90) REVERT: B 379 ASP cc_start: 0.8368 (m-30) cc_final: 0.8145 (m-30) REVERT: B 454 MET cc_start: 0.6858 (ptm) cc_final: 0.6378 (ptt) REVERT: B 489 GLN cc_start: 0.8270 (mt0) cc_final: 0.7834 (mt0) REVERT: B 755 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7776 (mt-10) REVERT: C 455 MET cc_start: 0.6180 (ttp) cc_final: 0.4241 (mpp) REVERT: C 527 GLU cc_start: 0.6829 (tt0) cc_final: 0.6402 (tm-30) REVERT: C 649 GLU cc_start: 0.4182 (mt-10) cc_final: 0.3279 (tm-30) REVERT: C 667 GLU cc_start: 0.5683 (tt0) cc_final: 0.5107 (mt-10) REVERT: D 445 TYR cc_start: 0.3761 (OUTLIER) cc_final: 0.3176 (t80) REVERT: D 455 MET cc_start: 0.6205 (ttp) cc_final: 0.4247 (mpp) REVERT: D 649 GLU cc_start: 0.4270 (mt-10) cc_final: 0.3462 (tm-30) outliers start: 55 outliers final: 33 residues processed: 267 average time/residue: 0.5422 time to fit residues: 162.9164 Evaluate side-chains 243 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain D residue 438 ASN Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 676 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 392 GLN A 416 ASN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN B 392 GLN B 416 ASN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN C 548 GLN D 548 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.176192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.147732 restraints weight = 18839.271| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.60 r_work: 0.3565 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16900 Z= 0.109 Angle : 0.548 8.326 22958 Z= 0.279 Chirality : 0.044 0.151 2430 Planarity : 0.005 0.047 3064 Dihedral : 6.427 56.250 2400 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.55 % Allowed : 30.22 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.18), residues: 2122 helix: 0.02 (0.24), residues: 528 sheet: -0.44 (0.22), residues: 512 loop : -1.18 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 353 TYR 0.010 0.001 TYR B 445 PHE 0.018 0.001 PHE D 672 TRP 0.010 0.001 TRP D 528 HIS 0.004 0.001 HIS C 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (16894) covalent geometry : angle 0.54799 / 0.28 (22958) hydrogen bonds : bond 0.03101 / 2.14 ( 618) hydrogen bonds : angle 4.98509 / 3.58 ( 1788) metal coordination : bond 0.00422 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 233 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6448 (mmm-85) cc_final: 0.5944 (mtm180) REVERT: A 63 ARG cc_start: 0.7471 (ttp80) cc_final: 0.6140 (ttm-80) REVERT: A 137 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6801 (pp20) REVERT: A 203 ARG cc_start: 0.7712 (mtp180) cc_final: 0.7352 (mpt-90) REVERT: A 413 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: A 489 GLN cc_start: 0.8314 (mt0) cc_final: 0.7920 (mt0) REVERT: A 621 GLU cc_start: 0.6483 (tt0) cc_final: 0.6270 (tt0) REVERT: A 755 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7839 (mt-10) REVERT: B 52 ARG cc_start: 0.6277 (mmm-85) cc_final: 0.5697 (mtm180) REVERT: B 63 ARG cc_start: 0.7490 (ttp80) cc_final: 0.6050 (ttm-80) REVERT: B 134 PHE cc_start: 0.6497 (m-80) cc_final: 0.6248 (m-80) REVERT: B 137 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6804 (pp20) REVERT: B 203 ARG cc_start: 0.7654 (mtp180) cc_final: 0.7227 (mpt-90) REVERT: B 454 MET cc_start: 0.6817 (ptm) cc_final: 0.6309 (ptt) REVERT: B 489 GLN cc_start: 0.8257 (mt0) cc_final: 0.7829 (mt0) REVERT: B 731 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7889 (ptm) REVERT: B 755 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7721 (mt-10) REVERT: C 445 TYR cc_start: 0.3706 (OUTLIER) cc_final: 0.3145 (t80) REVERT: C 455 MET cc_start: 0.6002 (ttp) cc_final: 0.4160 (mpp) REVERT: C 649 GLU cc_start: 0.4096 (mt-10) cc_final: 0.3312 (tm-30) REVERT: C 667 GLU cc_start: 0.5572 (tt0) cc_final: 0.4996 (mt-10) REVERT: D 445 TYR cc_start: 0.3702 (OUTLIER) cc_final: 0.3063 (t80) REVERT: D 455 MET cc_start: 0.5994 (ttp) cc_final: 0.4050 (mpp) REVERT: D 534 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6332 (mt0) REVERT: D 649 GLU cc_start: 0.4161 (mt-10) cc_final: 0.3340 (pt0) outliers start: 94 outliers final: 28 residues processed: 303 average time/residue: 0.5187 time to fit residues: 177.5865 Evaluate side-chains 255 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 534 GLN Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 676 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [154, 107, 44, 132, 42, 69, 198, 5, 62, 129, 121] chunk 154 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 198 optimal weight: 0.0270 chunk 5 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN C 539 ASN C 548 GLN D 548 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.170914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.141696 restraints weight = 19197.849| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.62 r_work: 0.3517 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16900 Z= 0.177 Angle : 0.597 8.314 22958 Z= 0.307 Chirality : 0.045 0.151 2430 Planarity : 0.005 0.052 3064 Dihedral : 5.243 49.787 2346 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 6.97 % Allowed : 28.34 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 2122 helix: 0.04 (0.23), residues: 536 sheet: -0.36 (0.22), residues: 518 loop : -1.16 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 771 TYR 0.014 0.001 TYR B 445 PHE 0.018 0.002 PHE D 509 TRP 0.008 0.001 TRP D 568 HIS 0.005 0.001 HIS C 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (16894) covalent geometry : angle 0.59675 / 0.31 (22958) hydrogen bonds : bond 0.03646 / 2.55 ( 618) hydrogen bonds : angle 5.01425 / 3.59 ( 1788) metal coordination : bond 0.00487 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 227 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7753 (tt0) cc_final: 0.7439 (tm-30) REVERT: A 52 ARG cc_start: 0.6478 (mmm-85) cc_final: 0.5889 (mtm180) REVERT: A 63 ARG cc_start: 0.7477 (ttp80) cc_final: 0.6175 (ttm-80) REVERT: A 203 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7296 (mpt-90) REVERT: A 379 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8091 (m-30) REVERT: A 489 GLN cc_start: 0.8352 (mt0) cc_final: 0.8123 (mt0) REVERT: A 724 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8182 (pt) REVERT: A 746 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7230 (t70) REVERT: A 755 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7788 (mt-10) REVERT: B 32 GLN cc_start: 0.7698 (tt0) cc_final: 0.7279 (tm-30) REVERT: B 52 ARG cc_start: 0.6340 (mmm-85) cc_final: 0.5682 (mpp-170) REVERT: B 63 ARG cc_start: 0.7505 (ttp80) cc_final: 0.6068 (ttm-80) REVERT: B 203 ARG cc_start: 0.7694 (mtp180) cc_final: 0.7251 (mpt-90) REVERT: B 353 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7931 (ttp-110) REVERT: B 379 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: B 413 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: B 489 GLN cc_start: 0.8357 (mt0) cc_final: 0.7921 (mt0) REVERT: B 724 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8148 (pp) REVERT: B 746 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7270 (t70) REVERT: B 755 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7773 (mt-10) REVERT: C 445 TYR cc_start: 0.3714 (OUTLIER) cc_final: 0.3188 (t80) REVERT: C 455 MET cc_start: 0.6084 (ttp) cc_final: 0.4025 (mpp) REVERT: C 532 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7563 (mm110) REVERT: C 649 GLU cc_start: 0.4046 (mt-10) cc_final: 0.3318 (tm-30) REVERT: C 667 GLU cc_start: 0.5619 (tt0) cc_final: 0.5030 (mt-10) REVERT: D 445 TYR cc_start: 0.3776 (OUTLIER) cc_final: 0.3262 (t80) REVERT: D 455 MET cc_start: 0.6299 (ttp) cc_final: 0.4139 (mpp) REVERT: D 649 GLU cc_start: 0.4085 (mt-10) cc_final: 0.3373 (tm-30) outliers start: 118 outliers final: 55 residues processed: 321 average time/residue: 0.4802 time to fit residues: 175.5149 Evaluate side-chains 274 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 210 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 548 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 746 ASP Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [207, 63, 84, 102, 150, 121, 90, 14, 43, 3, 109] chunk 207 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 392 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN C 548 GLN D 548 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.173053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144318 restraints weight = 18966.587| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.60 r_work: 0.3535 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16900 Z= 0.132 Angle : 0.554 8.286 22958 Z= 0.282 Chirality : 0.044 0.145 2430 Planarity : 0.005 0.049 3064 Dihedral : 5.028 50.791 2342 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 6.61 % Allowed : 28.98 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.18), residues: 2122 helix: 0.34 (0.24), residues: 526 sheet: -0.30 (0.23), residues: 504 loop : -1.19 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 231 TYR 0.012 0.001 TYR B 445 PHE 0.015 0.001 PHE D 509 TRP 0.010 0.001 TRP D 528 HIS 0.004 0.001 HIS C 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (16894) covalent geometry : angle 0.55417 / 0.28 (22958) hydrogen bonds : bond 0.03078 / 2.14 ( 618) hydrogen bonds : angle 4.77097 / 3.40 ( 1788) metal coordination : bond 0.00303 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 224 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7732 (tt0) cc_final: 0.7507 (tm-30) REVERT: A 52 ARG cc_start: 0.6509 (mmm-85) cc_final: 0.5904 (mtm180) REVERT: A 63 ARG cc_start: 0.7462 (ttp80) cc_final: 0.6092 (ttm-80) REVERT: A 137 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6777 (pp20) REVERT: A 203 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7296 (mpt-90) REVERT: A 324 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8105 (m-40) REVERT: A 353 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7889 (ttp-110) REVERT: A 379 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8073 (m-30) REVERT: A 489 GLN cc_start: 0.8364 (mt0) cc_final: 0.7954 (mt0) REVERT: A 746 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7268 (t70) REVERT: A 755 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7801 (mt-10) REVERT: B 32 GLN cc_start: 0.7696 (tt0) cc_final: 0.7365 (tm-30) REVERT: B 52 ARG cc_start: 0.6393 (mmm-85) cc_final: 0.5905 (mtm180) REVERT: B 63 ARG cc_start: 0.7498 (ttp80) cc_final: 0.6069 (ttm-80) REVERT: B 120 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7797 (p) REVERT: B 121 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7268 (mt) REVERT: B 203 ARG cc_start: 0.7730 (mtp180) cc_final: 0.7277 (mpt-90) REVERT: B 324 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8060 (m-40) REVERT: B 353 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7912 (ttp-110) REVERT: B 379 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.8007 (m-30) REVERT: B 489 GLN cc_start: 0.8375 (mt0) cc_final: 0.7936 (mt0) REVERT: B 746 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7296 (t70) REVERT: B 755 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7787 (mt-10) REVERT: C 445 TYR cc_start: 0.3814 (OUTLIER) cc_final: 0.3292 (t80) REVERT: C 455 MET cc_start: 0.6219 (ttp) cc_final: 0.4159 (mpp) REVERT: C 558 LYS cc_start: 0.5739 (mtmt) cc_final: 0.5193 (mtmm) REVERT: C 649 GLU cc_start: 0.4120 (mt-10) cc_final: 0.3355 (tm-30) REVERT: C 667 GLU cc_start: 0.5633 (tt0) cc_final: 0.5040 (mt-10) REVERT: D 445 TYR cc_start: 0.3846 (OUTLIER) cc_final: 0.3257 (t80) REVERT: D 455 MET cc_start: 0.6275 (ttp) cc_final: 0.4139 (mpp) REVERT: D 558 LYS cc_start: 0.5628 (mtmt) cc_final: 0.5075 (mtmm) outliers start: 112 outliers final: 50 residues processed: 312 average time/residue: 0.4976 time to fit residues: 176.0910 Evaluate side-chains 276 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 215 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 548 GLN Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 746 ASP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 574 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [45, 26, 147, 186, 166, 127, 13, 125, 4, 63, 173] chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 392 GLN C 539 ASN C 548 GLN ** C 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.166920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.137461 restraints weight = 19162.950| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.61 r_work: 0.3446 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16900 Z= 0.294 Angle : 0.695 8.508 22958 Z= 0.361 Chirality : 0.050 0.161 2430 Planarity : 0.006 0.054 3064 Dihedral : 5.654 47.868 2342 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 7.85 % Allowed : 27.92 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.18), residues: 2122 helix: -0.12 (0.23), residues: 538 sheet: -0.50 (0.22), residues: 532 loop : -1.26 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 277 TYR 0.018 0.002 TYR A 445 PHE 0.022 0.002 PHE D 509 TRP 0.012 0.002 TRP D 568 HIS 0.008 0.002 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.29 (16894) covalent geometry : angle 0.69502 / 0.36 (22958) hydrogen bonds : bond 0.04215 / 2.97 ( 618) hydrogen bonds : angle 5.28717 / 3.77 ( 1788) metal coordination : bond 0.00760 / 0.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 216 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7798 (tt0) cc_final: 0.7388 (tm-30) REVERT: A 52 ARG cc_start: 0.6654 (mmm-85) cc_final: 0.5871 (mpp-170) REVERT: A 63 ARG cc_start: 0.7579 (ttp80) cc_final: 0.6338 (ttm-80) REVERT: A 121 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7168 (mp) REVERT: A 137 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6844 (pp20) REVERT: A 189 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: A 203 ARG cc_start: 0.7661 (mtp180) cc_final: 0.7244 (mpt-90) REVERT: A 608 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7758 (tp) REVERT: A 724 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8279 (pt) REVERT: B 32 GLN cc_start: 0.7787 (tt0) cc_final: 0.7398 (tm-30) REVERT: B 52 ARG cc_start: 0.6587 (mmm-85) cc_final: 0.5890 (mpp-170) REVERT: B 63 ARG cc_start: 0.7577 (ttp80) cc_final: 0.6231 (ttm-80) REVERT: B 120 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.7991 (p) REVERT: B 137 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6825 (pp20) REVERT: B 189 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: B 203 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7250 (mpt-90) REVERT: B 489 GLN cc_start: 0.8334 (mt0) cc_final: 0.8008 (mt0) REVERT: B 608 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7811 (tp) REVERT: B 724 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8250 (pt) REVERT: C 445 TYR cc_start: 0.3790 (OUTLIER) cc_final: 0.3320 (t80) REVERT: C 529 MET cc_start: 0.7581 (mtm) cc_final: 0.7274 (mtm) REVERT: C 558 LYS cc_start: 0.5856 (mtmt) cc_final: 0.5373 (mtmm) REVERT: C 649 GLU cc_start: 0.4077 (mt-10) cc_final: 0.3384 (tm-30) REVERT: D 445 TYR cc_start: 0.3888 (OUTLIER) cc_final: 0.3367 (t80) REVERT: D 558 LYS cc_start: 0.5841 (mtmt) cc_final: 0.5367 (mtmm) REVERT: D 649 GLU cc_start: 0.4148 (mt-10) cc_final: 0.3424 (tm-30) outliers start: 133 outliers final: 75 residues processed: 323 average time/residue: 0.4813 time to fit residues: 176.4603 Evaluate side-chains 292 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 205 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 548 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 746 ASP Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [164, 99, 131, 203, 88, 143, 181, 142, 159, 204, 115] chunk 164 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 204 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 392 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 392 GLN C 410 GLN C 548 GLN ** C 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 GLN ** D 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.173031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144424 restraints weight = 19024.457| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.60 r_work: 0.3537 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16900 Z= 0.119 Angle : 0.552 8.396 22958 Z= 0.282 Chirality : 0.044 0.149 2430 Planarity : 0.005 0.050 3064 Dihedral : 5.099 50.957 2342 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.43 % Allowed : 30.34 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.18), residues: 2122 helix: 0.55 (0.24), residues: 514 sheet: -0.32 (0.23), residues: 490 loop : -1.25 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 692 TYR 0.012 0.001 TYR B 445 PHE 0.014 0.001 PHE C 509 TRP 0.013 0.001 TRP D 528 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (16894) covalent geometry : angle 0.55213 / 0.28 (22958) hydrogen bonds : bond 0.02947 / 2.06 ( 618) hydrogen bonds : angle 4.75778 / 3.38 ( 1788) metal coordination : bond 0.00224 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 229 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7693 (tt0) cc_final: 0.7417 (tm-30) REVERT: A 52 ARG cc_start: 0.6531 (mmm-85) cc_final: 0.5940 (mtm180) REVERT: A 63 ARG cc_start: 0.7467 (ttp80) cc_final: 0.6118 (ttm-80) REVERT: A 137 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6767 (mm-30) REVERT: A 203 ARG cc_start: 0.7704 (mtp180) cc_final: 0.7308 (mpt-90) REVERT: A 353 ARG cc_start: 0.8181 (ttm170) cc_final: 0.7900 (ttp-170) REVERT: A 746 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7229 (t70) REVERT: A 755 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7822 (mt-10) REVERT: B 32 GLN cc_start: 0.7671 (tt0) cc_final: 0.7285 (tm-30) REVERT: B 52 ARG cc_start: 0.6441 (mmm-85) cc_final: 0.5910 (mtm180) REVERT: B 63 ARG cc_start: 0.7418 (ttp80) cc_final: 0.6054 (ttm-80) REVERT: B 120 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7907 (p) REVERT: B 203 ARG cc_start: 0.7687 (mtp180) cc_final: 0.7242 (mpt-90) REVERT: B 353 ARG cc_start: 0.8177 (ttm170) cc_final: 0.7910 (ttp-170) REVERT: B 489 GLN cc_start: 0.8303 (mt0) cc_final: 0.8079 (mt0) REVERT: B 608 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7770 (tp) REVERT: B 746 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7289 (t70) REVERT: B 755 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7799 (mt-10) REVERT: C 445 TYR cc_start: 0.3788 (OUTLIER) cc_final: 0.3323 (t80) REVERT: C 455 MET cc_start: 0.6406 (ttp) cc_final: 0.4168 (mpp) REVERT: C 529 MET cc_start: 0.7281 (mtm) cc_final: 0.7054 (mtm) REVERT: C 558 LYS cc_start: 0.5698 (mtmt) cc_final: 0.5329 (mtmp) REVERT: C 649 GLU cc_start: 0.3988 (mt-10) cc_final: 0.3321 (tm-30) REVERT: D 445 TYR cc_start: 0.3866 (OUTLIER) cc_final: 0.3358 (t80) REVERT: D 455 MET cc_start: 0.6539 (ttp) cc_final: 0.4202 (mpp) REVERT: D 558 LYS cc_start: 0.5698 (mtmt) cc_final: 0.5206 (mtmm) REVERT: D 649 GLU cc_start: 0.4143 (mt-10) cc_final: 0.3433 (tm-30) outliers start: 92 outliers final: 48 residues processed: 303 average time/residue: 0.4908 time to fit residues: 168.7614 Evaluate side-chains 266 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 548 GLN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 746 ASP Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 586 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [23, 139, 141, 40, 172, 125, 22, 109, 129, 7, 124] chunk 23 optimal weight: 0.2980 chunk 139 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 0.0000 chunk 129 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN C 548 GLN ** C 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 GLN D 548 GLN ** D 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.170723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.141761 restraints weight = 18908.380| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.60 r_work: 0.3507 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16900 Z= 0.172 Angle : 0.590 8.282 22958 Z= 0.302 Chirality : 0.045 0.148 2430 Planarity : 0.005 0.051 3064 Dihedral : 5.183 49.972 2342 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.25 % Allowed : 30.40 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.18), residues: 2122 helix: 0.22 (0.24), residues: 538 sheet: -0.24 (0.23), residues: 486 loop : -1.25 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 691 TYR 0.014 0.001 TYR B 445 PHE 0.018 0.002 PHE C 509 TRP 0.010 0.001 TRP D 528 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (16894) covalent geometry : angle 0.58994 / 0.30 (22958) hydrogen bonds : bond 0.03337 / 2.34 ( 618) hydrogen bonds : angle 4.86006 / 3.45 ( 1788) metal coordination : bond 0.00397 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 212 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6546 (mmm-85) cc_final: 0.5884 (mtm180) REVERT: A 63 ARG cc_start: 0.7462 (ttp80) cc_final: 0.6174 (ttm-80) REVERT: A 121 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7028 (mp) REVERT: A 137 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6759 (mm-30) REVERT: A 203 ARG cc_start: 0.7670 (mtp180) cc_final: 0.7243 (mpt-90) REVERT: A 353 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7940 (ttp-170) REVERT: A 413 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: A 608 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7729 (tp) REVERT: A 626 VAL cc_start: 0.7736 (t) cc_final: 0.7530 (t) REVERT: A 746 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7281 (t70) REVERT: A 755 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7817 (mt-10) REVERT: B 32 GLN cc_start: 0.7680 (tt0) cc_final: 0.7257 (tm-30) REVERT: B 52 ARG cc_start: 0.6441 (mmm-85) cc_final: 0.5902 (mtm180) REVERT: B 63 ARG cc_start: 0.7453 (ttp80) cc_final: 0.6081 (ttm-80) REVERT: B 120 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7903 (p) REVERT: B 137 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6796 (pp20) REVERT: B 203 ARG cc_start: 0.7655 (mtp180) cc_final: 0.7216 (mpt-90) REVERT: B 279 ASP cc_start: 0.8360 (t0) cc_final: 0.8156 (t70) REVERT: B 353 ARG cc_start: 0.8233 (ttm170) cc_final: 0.7956 (ttp-170) REVERT: B 413 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.6576 (m-80) REVERT: B 489 GLN cc_start: 0.8311 (mt0) cc_final: 0.8095 (mt0) REVERT: B 626 VAL cc_start: 0.7706 (t) cc_final: 0.7498 (t) REVERT: B 746 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7259 (t70) REVERT: B 755 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7777 (mt-10) REVERT: C 445 TYR cc_start: 0.3729 (OUTLIER) cc_final: 0.3240 (t80) REVERT: C 455 MET cc_start: 0.6393 (ttp) cc_final: 0.4083 (mpp) REVERT: C 558 LYS cc_start: 0.5720 (mtmt) cc_final: 0.5193 (mtmm) REVERT: C 649 GLU cc_start: 0.3994 (mt-10) cc_final: 0.3336 (tm-30) REVERT: D 440 SER cc_start: 0.5401 (OUTLIER) cc_final: 0.5178 (p) REVERT: D 445 TYR cc_start: 0.3910 (OUTLIER) cc_final: 0.3392 (t80) REVERT: D 455 MET cc_start: 0.6381 (ttp) cc_final: 0.4052 (mpp) REVERT: D 558 LYS cc_start: 0.5745 (mtmt) cc_final: 0.5228 (mtmm) REVERT: D 649 GLU cc_start: 0.4086 (mt-10) cc_final: 0.3379 (tm-30) outliers start: 89 outliers final: 50 residues processed: 285 average time/residue: 0.5268 time to fit residues: 169.2759 Evaluate side-chains 273 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 211 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 548 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 746 ASP Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 676 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [157, 36, 205, 42, 208, 28, 128, 140, 86, 148, 174] chunk 157 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 205 optimal weight: 0.0980 chunk 42 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN C 548 GLN ** C 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 GLN ** D 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.167817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138549 restraints weight = 19142.270| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.61 r_work: 0.3469 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16900 Z= 0.255 Angle : 0.661 8.373 22958 Z= 0.343 Chirality : 0.048 0.160 2430 Planarity : 0.006 0.052 3064 Dihedral : 5.557 48.369 2342 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 5.84 % Allowed : 29.75 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.18), residues: 2122 helix: -0.02 (0.24), residues: 532 sheet: -0.39 (0.22), residues: 518 loop : -1.23 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 345 TYR 0.017 0.002 TYR B 445 PHE 0.021 0.002 PHE C 509 TRP 0.011 0.002 TRP D 568 HIS 0.007 0.002 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.25 (16894) covalent geometry : angle 0.66125 / 0.34 (22958) hydrogen bonds : bond 0.03910 / 2.75 ( 618) hydrogen bonds : angle 5.15113 / 3.67 ( 1788) metal coordination : bond 0.00666 / 0.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 214 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7812 (tt0) cc_final: 0.7482 (tm-30) REVERT: A 52 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.6031 (mtm180) REVERT: A 63 ARG cc_start: 0.7513 (ttp80) cc_final: 0.7188 (ttp-170) REVERT: A 137 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6826 (mm-30) REVERT: A 608 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7736 (tt) REVERT: A 724 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8262 (pt) REVERT: A 755 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7834 (mt-10) REVERT: A 781 LYS cc_start: 0.7124 (mmtp) cc_final: 0.6733 (mmtm) REVERT: B 32 GLN cc_start: 0.7765 (tt0) cc_final: 0.7349 (tm-30) REVERT: B 52 ARG cc_start: 0.6533 (mmm-85) cc_final: 0.5938 (mtm180) REVERT: B 63 ARG cc_start: 0.7553 (ttp80) cc_final: 0.6238 (ttm-80) REVERT: B 120 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7967 (p) REVERT: B 137 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6897 (pp20) REVERT: B 724 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8191 (pp) REVERT: C 440 SER cc_start: 0.5411 (OUTLIER) cc_final: 0.5177 (p) REVERT: C 445 TYR cc_start: 0.3874 (OUTLIER) cc_final: 0.3385 (t80) REVERT: C 558 LYS cc_start: 0.5936 (mtmt) cc_final: 0.5417 (mtmm) REVERT: C 649 GLU cc_start: 0.4075 (mt-10) cc_final: 0.3395 (tm-30) REVERT: D 440 SER cc_start: 0.5517 (OUTLIER) cc_final: 0.5283 (p) REVERT: D 445 TYR cc_start: 0.3987 (OUTLIER) cc_final: 0.3513 (t80) REVERT: D 558 LYS cc_start: 0.5862 (mtmt) cc_final: 0.5280 (mtmm) REVERT: D 649 GLU cc_start: 0.4171 (mt-10) cc_final: 0.3431 (tm-30) outliers start: 99 outliers final: 63 residues processed: 298 average time/residue: 0.4841 time to fit residues: 163.7789 Evaluate side-chains 281 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 208 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 548 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 746 ASP Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [76, 36, 128, 23, 94, 174, 29, 65, 126, 37, 110] chunk 76 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 126 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN C 548 GLN ** C 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 GLN ** D 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.172087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.143341 restraints weight = 18992.909| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.60 r_work: 0.3525 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16900 Z= 0.129 Angle : 0.568 8.182 22958 Z= 0.290 Chirality : 0.044 0.148 2430 Planarity : 0.005 0.050 3064 Dihedral : 5.152 50.664 2342 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.49 % Allowed : 31.46 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.18), residues: 2122 helix: 0.32 (0.24), residues: 524 sheet: -0.30 (0.23), residues: 494 loop : -1.23 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 691 TYR 0.012 0.001 TYR B 445 PHE 0.014 0.001 PHE D 509 TRP 0.014 0.001 TRP D 528 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16894) covalent geometry : angle 0.56751 / 0.29 (22958) hydrogen bonds : bond 0.03069 / 2.14 ( 618) hydrogen bonds : angle 4.79599 / 3.40 ( 1788) metal coordination : bond 0.00258 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 219 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6547 (mmm-85) cc_final: 0.5978 (mtm180) REVERT: A 63 ARG cc_start: 0.7458 (ttp80) cc_final: 0.6199 (ttm-80) REVERT: A 353 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7957 (ttp-170) REVERT: A 608 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7746 (tp) REVERT: A 724 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8174 (pp) REVERT: A 746 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7270 (t70) REVERT: A 755 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7817 (mt-10) REVERT: B 52 ARG cc_start: 0.6418 (mmm-85) cc_final: 0.5905 (mtm180) REVERT: B 63 ARG cc_start: 0.7437 (ttp80) cc_final: 0.6086 (ttm-80) REVERT: B 120 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7923 (p) REVERT: B 137 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6873 (pp20) REVERT: B 203 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7273 (mpt90) REVERT: B 353 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7978 (ttp-170) REVERT: B 746 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7293 (t70) REVERT: B 755 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7804 (mt-10) REVERT: B 781 LYS cc_start: 0.7048 (mmtp) cc_final: 0.6647 (mmtm) REVERT: C 445 TYR cc_start: 0.3790 (OUTLIER) cc_final: 0.3304 (t80) REVERT: C 455 MET cc_start: 0.6573 (ttp) cc_final: 0.4097 (mpp) REVERT: C 558 LYS cc_start: 0.5702 (mtmt) cc_final: 0.5308 (mtmp) REVERT: C 649 GLU cc_start: 0.4039 (mt-10) cc_final: 0.3348 (tm-30) REVERT: D 445 TYR cc_start: 0.3957 (OUTLIER) cc_final: 0.3473 (t80) REVERT: D 455 MET cc_start: 0.6432 (ttp) cc_final: 0.4140 (mpp) REVERT: D 558 LYS cc_start: 0.5693 (mtmt) cc_final: 0.5186 (mtmm) REVERT: D 649 GLU cc_start: 0.4080 (mt-10) cc_final: 0.3377 (tm-30) outliers start: 76 outliers final: 45 residues processed: 285 average time/residue: 0.5477 time to fit residues: 175.1875 Evaluate side-chains 268 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 548 GLN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 746 ASP Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 676 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [38, 46, 156, 161, 120, 198, 96, 94, 80, 115, 182] chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 156 optimal weight: 0.0570 chunk 161 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 182 optimal weight: 6.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 392 GLN C 548 GLN ** C 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 GLN ** D 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.171453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.142595 restraints weight = 19023.158| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.61 r_work: 0.3526 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16900 Z= 0.149 Angle : 0.582 8.124 22958 Z= 0.298 Chirality : 0.045 0.148 2430 Planarity : 0.005 0.051 3064 Dihedral : 5.135 50.434 2342 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.96 % Allowed : 31.88 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.18), residues: 2122 helix: 0.29 (0.24), residues: 526 sheet: -0.29 (0.23), residues: 494 loop : -1.22 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 691 TYR 0.015 0.001 TYR C 610 PHE 0.024 0.002 PHE C 672 TRP 0.012 0.001 TRP D 528 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (16894) covalent geometry : angle 0.58221 / 0.30 (22958) hydrogen bonds : bond 0.03194 / 2.22 ( 618) hydrogen bonds : angle 4.80119 / 3.41 ( 1788) metal coordination : bond 0.00320 / 0.19 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4244 Ramachandran restraints generated. 2122 Oldfield, 0 Emsley, 2122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 222 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6550 (mmm-85) cc_final: 0.6011 (mtm180) REVERT: A 63 ARG cc_start: 0.7438 (ttp80) cc_final: 0.6149 (ttm-80) REVERT: A 121 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7080 (mp) REVERT: A 137 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6831 (pp20) REVERT: A 353 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7949 (ttp-110) REVERT: A 548 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7238 (mt0) REVERT: A 608 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7731 (tp) REVERT: A 724 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8225 (pt) REVERT: A 746 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7241 (t70) REVERT: A 755 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7792 (mt-10) REVERT: A 781 LYS cc_start: 0.7059 (mmtp) cc_final: 0.6649 (mmtm) REVERT: B 52 ARG cc_start: 0.6418 (mmm-85) cc_final: 0.5929 (mtm180) REVERT: B 63 ARG cc_start: 0.7444 (ttp80) cc_final: 0.6094 (ttm-80) REVERT: B 120 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7920 (p) REVERT: B 137 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6867 (pp20) REVERT: B 203 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7249 (mpt90) REVERT: B 353 ARG cc_start: 0.8219 (ttm170) cc_final: 0.7974 (ttp-110) REVERT: B 746 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7271 (t70) REVERT: B 755 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7785 (mt-10) REVERT: C 445 TYR cc_start: 0.3789 (OUTLIER) cc_final: 0.3299 (t80) REVERT: C 455 MET cc_start: 0.6558 (ttp) cc_final: 0.4067 (mpp) REVERT: C 558 LYS cc_start: 0.5703 (mtmt) cc_final: 0.5154 (mtmm) REVERT: C 649 GLU cc_start: 0.4075 (mt-10) cc_final: 0.3365 (tm-30) REVERT: D 445 TYR cc_start: 0.3986 (OUTLIER) cc_final: 0.3494 (t80) REVERT: D 455 MET cc_start: 0.6294 (ttp) cc_final: 0.4024 (mpp) REVERT: D 558 LYS cc_start: 0.5712 (mtmt) cc_final: 0.5182 (mtmm) REVERT: D 649 GLU cc_start: 0.4084 (mt-10) cc_final: 0.3371 (tm-30) outliers start: 67 outliers final: 48 residues processed: 279 average time/residue: 0.5155 time to fit residues: 162.2223 Evaluate side-chains 276 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 217 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 548 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 746 ASP Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 676 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [101, 140, 126, 67, 34, 73, 151, 191, 24, 63, 66] chunk 101 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 151 optimal weight: 0.0770 chunk 191 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.9498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN C 548 GLN ** C 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 GLN ** D 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.172996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.144288 restraints weight = 18962.934| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.60 r_work: 0.3535 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16900 Z= 0.127 Angle : 0.565 8.019 22958 Z= 0.288 Chirality : 0.044 0.149 2430 Planarity : 0.005 0.050 3064 Dihedral : 5.016 51.076 2342 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.84 % Allowed : 32.11 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2122 helix: 0.68 (0.25), residues: 502 sheet: -0.24 (0.23), residues: 494 loop : -1.17 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 691 TYR 0.011 0.001 TYR B 445 PHE 0.015 0.001 PHE C 509 TRP 0.014 0.001 TRP C 528 HIS 0.003 0.001 HIS A 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (16894) covalent geometry : angle 0.56491 / 0.29 (22958) hydrogen bonds : bond 0.03002 / 2.08 ( 618) hydrogen bonds : angle 4.68986 / 3.33 ( 1788) metal coordination : bond 0.00242 / 0.14 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5515.05 seconds wall clock time: 94 minutes 47.81 seconds (5687.81 seconds total)