Starting phenix.real_space_refine on Thu Sep 18 08:40:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k9f_9948/09_2025/6k9f_9948.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k9f_9948/09_2025/6k9f_9948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k9f_9948/09_2025/6k9f_9948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k9f_9948/09_2025/6k9f_9948.map" model { file = "/net/cci-nas-00/data/ceres_data/6k9f_9948/09_2025/6k9f_9948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k9f_9948/09_2025/6k9f_9948.cif" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8484 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 5244 2.51 5 N 1512 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8484 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "D" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "E" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "F" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "H" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "I" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "J" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "K" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Time building chain proxies: 2.12, per 1000 atoms: 0.25 Number of scatterers: 8484 At special positions: 0 Unit cell: (97.9, 96.8, 103.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1704 8.00 N 1512 7.00 C 5244 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: 0.79 Conformation dependent library (CDL) restraints added in 320.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 0 sheets defined 95.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 451 through 457 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 468 through 478 Processing helix chain 'A' and resid 482 through 492 removed outlier: 4.165A pdb=" N GLU A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.687A pdb=" N LYS A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 509 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 525 Processing helix chain 'A' and resid 525 through 537 removed outlier: 4.240A pdb=" N VAL A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A 530 " --> pdb=" O PRO A 526 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 468 through 478 Processing helix chain 'B' and resid 482 through 492 removed outlier: 4.227A pdb=" N GLU B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.664A pdb=" N LYS B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 509 " --> pdb=" O MET B 505 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 Processing helix chain 'B' and resid 525 through 537 removed outlier: 4.235A pdb=" N VAL B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 537 " --> pdb=" O ARG B 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 468 through 478 Processing helix chain 'C' and resid 482 through 492 removed outlier: 4.128A pdb=" N GLU C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.681A pdb=" N LYS C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 509 " --> pdb=" O MET C 505 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 525 Processing helix chain 'C' and resid 525 through 537 removed outlier: 4.223A pdb=" N VAL C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C 530 " --> pdb=" O PRO C 526 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 537 " --> pdb=" O ARG C 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 457 Processing helix chain 'D' and resid 457 through 465 Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 482 through 492 removed outlier: 4.056A pdb=" N GLU D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 510 removed outlier: 3.620A pdb=" N LYS D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS D 509 " --> pdb=" O MET D 505 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 525 Processing helix chain 'D' and resid 525 through 537 removed outlier: 4.252A pdb=" N VAL D 529 " --> pdb=" O ASP D 525 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER D 530 " --> pdb=" O PRO D 526 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 537 " --> pdb=" O ARG D 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 457 Processing helix chain 'E' and resid 457 through 465 Processing helix chain 'E' and resid 468 through 478 Processing helix chain 'E' and resid 482 through 492 removed outlier: 4.168A pdb=" N GLU E 492 " --> pdb=" O LEU E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 510 removed outlier: 3.691A pdb=" N LYS E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS E 509 " --> pdb=" O MET E 505 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY E 510 " --> pdb=" O VAL E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 525 Processing helix chain 'E' and resid 525 through 537 removed outlier: 4.258A pdb=" N VAL E 529 " --> pdb=" O ASP E 525 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER E 530 " --> pdb=" O PRO E 526 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 537 " --> pdb=" O ARG E 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 457 Processing helix chain 'F' and resid 457 through 465 Processing helix chain 'F' and resid 468 through 478 Processing helix chain 'F' and resid 482 through 492 removed outlier: 4.077A pdb=" N GLU F 492 " --> pdb=" O LEU F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 510 removed outlier: 3.719A pdb=" N LYS F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS F 509 " --> pdb=" O MET F 505 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY F 510 " --> pdb=" O VAL F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 525 Processing helix chain 'F' and resid 525 through 537 removed outlier: 4.148A pdb=" N VAL F 529 " --> pdb=" O ASP F 525 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER F 530 " --> pdb=" O PRO F 526 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 537 " --> pdb=" O ARG F 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 457 Processing helix chain 'G' and resid 457 through 465 Processing helix chain 'G' and resid 468 through 478 Processing helix chain 'G' and resid 482 through 492 removed outlier: 4.103A pdb=" N GLU G 492 " --> pdb=" O LEU G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 510 removed outlier: 3.752A pdb=" N LYS G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS G 509 " --> pdb=" O MET G 505 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY G 510 " --> pdb=" O VAL G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 525 Processing helix chain 'G' and resid 525 through 536 removed outlier: 4.316A pdb=" N VAL G 529 " --> pdb=" O ASP G 525 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER G 530 " --> pdb=" O PRO G 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 457 Processing helix chain 'H' and resid 457 through 465 Processing helix chain 'H' and resid 468 through 478 Processing helix chain 'H' and resid 482 through 492 removed outlier: 4.026A pdb=" N GLU H 492 " --> pdb=" O LEU H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 510 removed outlier: 3.729A pdb=" N LYS H 508 " --> pdb=" O SER H 504 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS H 509 " --> pdb=" O MET H 505 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY H 510 " --> pdb=" O VAL H 506 " (cutoff:3.500A) Processing helix chain 'H' and resid 510 through 525 Processing helix chain 'H' and resid 525 through 537 removed outlier: 4.228A pdb=" N VAL H 529 " --> pdb=" O ASP H 525 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER H 530 " --> pdb=" O PRO H 526 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU H 537 " --> pdb=" O ARG H 533 " (cutoff:3.500A) Processing helix chain 'I' and resid 452 through 457 Processing helix chain 'I' and resid 457 through 465 Processing helix chain 'I' and resid 468 through 478 Processing helix chain 'I' and resid 482 through 492 removed outlier: 4.179A pdb=" N GLU I 492 " --> pdb=" O LEU I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 510 removed outlier: 3.638A pdb=" N LYS I 508 " --> pdb=" O SER I 504 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS I 509 " --> pdb=" O MET I 505 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY I 510 " --> pdb=" O VAL I 506 " (cutoff:3.500A) Processing helix chain 'I' and resid 510 through 525 Processing helix chain 'I' and resid 525 through 537 removed outlier: 4.306A pdb=" N VAL I 529 " --> pdb=" O ASP I 525 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER I 530 " --> pdb=" O PRO I 526 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU I 537 " --> pdb=" O ARG I 533 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 457 Processing helix chain 'J' and resid 457 through 465 Processing helix chain 'J' and resid 468 through 478 Processing helix chain 'J' and resid 482 through 492 removed outlier: 4.123A pdb=" N GLU J 492 " --> pdb=" O LEU J 488 " (cutoff:3.500A) Processing helix chain 'J' and resid 494 through 510 removed outlier: 3.705A pdb=" N LYS J 508 " --> pdb=" O SER J 504 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS J 509 " --> pdb=" O MET J 505 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY J 510 " --> pdb=" O VAL J 506 " (cutoff:3.500A) Processing helix chain 'J' and resid 510 through 525 Processing helix chain 'J' and resid 525 through 537 removed outlier: 4.154A pdb=" N VAL J 529 " --> pdb=" O ASP J 525 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER J 530 " --> pdb=" O PRO J 526 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU J 537 " --> pdb=" O ARG J 533 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 457 Processing helix chain 'K' and resid 457 through 465 Processing helix chain 'K' and resid 468 through 478 Processing helix chain 'K' and resid 482 through 492 removed outlier: 4.276A pdb=" N GLU K 492 " --> pdb=" O LEU K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 494 through 510 removed outlier: 3.700A pdb=" N LYS K 508 " --> pdb=" O SER K 504 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS K 509 " --> pdb=" O MET K 505 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY K 510 " --> pdb=" O VAL K 506 " (cutoff:3.500A) Processing helix chain 'K' and resid 510 through 525 Processing helix chain 'K' and resid 525 through 537 removed outlier: 4.156A pdb=" N VAL K 529 " --> pdb=" O ASP K 525 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER K 530 " --> pdb=" O PRO K 526 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU K 537 " --> pdb=" O ARG K 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 457 Processing helix chain 'L' and resid 457 through 465 Processing helix chain 'L' and resid 468 through 478 Processing helix chain 'L' and resid 482 through 492 removed outlier: 4.140A pdb=" N GLU L 492 " --> pdb=" O LEU L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 510 removed outlier: 3.743A pdb=" N LYS L 508 " --> pdb=" O SER L 504 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS L 509 " --> pdb=" O MET L 505 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY L 510 " --> pdb=" O VAL L 506 " (cutoff:3.500A) Processing helix chain 'L' and resid 510 through 525 Processing helix chain 'L' and resid 525 through 537 removed outlier: 4.271A pdb=" N VAL L 529 " --> pdb=" O ASP L 525 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER L 530 " --> pdb=" O PRO L 526 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU L 537 " --> pdb=" O ARG L 533 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1731 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: 1.31 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3012 1.34 - 1.46: 628 1.46 - 1.57: 4856 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 8544 Sorted by residual: bond pdb=" C ASP J 525 " pdb=" O ASP J 525 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.75e-01 bond pdb=" C ASP K 525 " pdb=" O ASP K 525 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.35e-01 bond pdb=" CB LYS H 508 " pdb=" CG LYS H 508 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.37e-01 bond pdb=" CB LYS G 508 " pdb=" CG LYS G 508 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.10e-01 bond pdb=" C ASP B 525 " pdb=" O ASP B 525 " ideal model delta sigma weight residual 1.248 1.239 0.010 1.26e-02 6.30e+03 5.98e-01 ... (remaining 8539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 10529 0.75 - 1.49: 743 1.49 - 2.24: 131 2.24 - 2.99: 29 2.99 - 3.73: 16 Bond angle restraints: 11448 Sorted by residual: angle pdb=" CA LYS K 508 " pdb=" CB LYS K 508 " pdb=" CG LYS K 508 " ideal model delta sigma weight residual 114.10 117.48 -3.38 2.00e+00 2.50e-01 2.86e+00 angle pdb=" CA LYS B 508 " pdb=" CB LYS B 508 " pdb=" CG LYS B 508 " ideal model delta sigma weight residual 114.10 117.43 -3.33 2.00e+00 2.50e-01 2.77e+00 angle pdb=" CA LYS I 508 " pdb=" CB LYS I 508 " pdb=" CG LYS I 508 " ideal model delta sigma weight residual 114.10 117.36 -3.26 2.00e+00 2.50e-01 2.65e+00 angle pdb=" CB LYS H 508 " pdb=" CG LYS H 508 " pdb=" CD LYS H 508 " ideal model delta sigma weight residual 111.30 115.03 -3.73 2.30e+00 1.89e-01 2.63e+00 angle pdb=" CA LYS J 508 " pdb=" CB LYS J 508 " pdb=" CG LYS J 508 " ideal model delta sigma weight residual 114.10 117.30 -3.20 2.00e+00 2.50e-01 2.55e+00 ... (remaining 11443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.66: 4792 11.66 - 23.32: 416 23.32 - 34.98: 107 34.98 - 46.64: 73 46.64 - 58.30: 36 Dihedral angle restraints: 5424 sinusoidal: 2352 harmonic: 3072 Sorted by residual: dihedral pdb=" CA ALA I 463 " pdb=" C ALA I 463 " pdb=" N ARG I 464 " pdb=" CA ARG I 464 " ideal model delta harmonic sigma weight residual -180.00 -163.35 -16.65 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ALA H 463 " pdb=" C ALA H 463 " pdb=" N ARG H 464 " pdb=" CA ARG H 464 " ideal model delta harmonic sigma weight residual 180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ALA L 463 " pdb=" C ALA L 463 " pdb=" N ARG L 464 " pdb=" CA ARG L 464 " ideal model delta harmonic sigma weight residual -180.00 -163.75 -16.25 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 5421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.019: 704 0.019 - 0.039: 358 0.039 - 0.058: 140 0.058 - 0.077: 69 0.077 - 0.096: 25 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA GLU K 479 " pdb=" N GLU K 479 " pdb=" C GLU K 479 " pdb=" CB GLU K 479 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.32e-01 chirality pdb=" CA PRO H 526 " pdb=" N PRO H 526 " pdb=" C PRO H 526 " pdb=" CB PRO H 526 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.16e-01 chirality pdb=" CA PRO I 526 " pdb=" N PRO I 526 " pdb=" C PRO I 526 " pdb=" CB PRO I 526 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.14e-01 ... (remaining 1293 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 527 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C TYR A 527 " 0.020 2.00e-02 2.50e+03 pdb=" O TYR A 527 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU A 528 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR J 527 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" C TYR J 527 " -0.019 2.00e-02 2.50e+03 pdb=" O TYR J 527 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU J 528 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 527 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.23e+00 pdb=" C TYR H 527 " -0.019 2.00e-02 2.50e+03 pdb=" O TYR H 527 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU H 528 " 0.007 2.00e-02 2.50e+03 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 2776 2.86 - 3.37: 8644 3.37 - 3.88: 13602 3.88 - 4.39: 16015 4.39 - 4.90: 26417 Nonbonded interactions: 67454 Sorted by model distance: nonbonded pdb=" NE2 GLN H 476 " pdb=" OE1 GLU H 483 " model vdw 2.356 3.120 nonbonded pdb=" O GLU E 500 " pdb=" OG SER E 504 " model vdw 2.379 3.040 nonbonded pdb=" O GLU L 500 " pdb=" OG SER L 504 " model vdw 2.425 3.040 nonbonded pdb=" O PHE E 518 " pdb=" OG SER E 522 " model vdw 2.450 3.040 nonbonded pdb=" O GLU B 500 " pdb=" OG SER B 504 " model vdw 2.455 3.040 ... (remaining 67449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.640 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8544 Z= 0.113 Angle : 0.446 3.733 11448 Z= 0.277 Chirality : 0.030 0.096 1296 Planarity : 0.003 0.023 1524 Dihedral : 11.872 58.301 3408 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.23), residues: 1020 helix: 0.05 (0.15), residues: 900 sheet: None (None), residues: 0 loop : -3.46 (0.29), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 464 TYR 0.015 0.002 TYR B 531 PHE 0.013 0.002 PHE J 518 HIS 0.002 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8544) covalent geometry : angle 0.44592 (11448) hydrogen bonds : bond 0.13146 ( 577) hydrogen bonds : angle 6.51362 ( 1731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 GLU cc_start: 0.9625 (mt-10) cc_final: 0.9334 (mt-10) REVERT: A 498 LYS cc_start: 0.9749 (mttt) cc_final: 0.9469 (mttt) REVERT: A 503 LEU cc_start: 0.9742 (mt) cc_final: 0.9493 (mp) REVERT: B 461 LEU cc_start: 0.9684 (mt) cc_final: 0.9398 (mt) REVERT: B 462 GLN cc_start: 0.9387 (tt0) cc_final: 0.8999 (tp40) REVERT: B 464 ARG cc_start: 0.8437 (mtt-85) cc_final: 0.7981 (tpt170) REVERT: B 487 GLU cc_start: 0.9718 (mt-10) cc_final: 0.9375 (pt0) REVERT: B 496 GLN cc_start: 0.9590 (mp10) cc_final: 0.9243 (pm20) REVERT: B 503 LEU cc_start: 0.9685 (mt) cc_final: 0.9352 (mt) REVERT: C 462 GLN cc_start: 0.9502 (tt0) cc_final: 0.9144 (tp40) REVERT: C 502 LEU cc_start: 0.9815 (tp) cc_final: 0.9582 (mt) REVERT: D 461 LEU cc_start: 0.9815 (mt) cc_final: 0.9541 (mt) REVERT: D 462 GLN cc_start: 0.9465 (tt0) cc_final: 0.9063 (tp40) REVERT: D 503 LEU cc_start: 0.9803 (mt) cc_final: 0.9598 (mt) REVERT: E 461 LEU cc_start: 0.9742 (mt) cc_final: 0.9419 (mt) REVERT: E 462 GLN cc_start: 0.9608 (tt0) cc_final: 0.9233 (tp-100) REVERT: E 503 LEU cc_start: 0.9826 (mt) cc_final: 0.9567 (mt) REVERT: F 462 GLN cc_start: 0.9610 (tt0) cc_final: 0.9282 (tp40) REVERT: F 524 ARG cc_start: 0.9546 (tpm170) cc_final: 0.9343 (mmm160) REVERT: F 528 LEU cc_start: 0.9519 (tp) cc_final: 0.9277 (mp) REVERT: G 498 LYS cc_start: 0.9582 (mttt) cc_final: 0.9379 (mttm) REVERT: G 503 LEU cc_start: 0.9842 (mt) cc_final: 0.9586 (mp) REVERT: H 465 MET cc_start: 0.9234 (mtm) cc_final: 0.8904 (mtm) REVERT: H 503 LEU cc_start: 0.9874 (mt) cc_final: 0.9533 (mt) REVERT: H 506 VAL cc_start: 0.9868 (t) cc_final: 0.9587 (p) REVERT: H 528 LEU cc_start: 0.9497 (tp) cc_final: 0.9245 (mt) REVERT: I 461 LEU cc_start: 0.9680 (mt) cc_final: 0.9330 (mt) REVERT: I 462 GLN cc_start: 0.9555 (tt0) cc_final: 0.9099 (tp40) REVERT: I 496 GLN cc_start: 0.9660 (mp10) cc_final: 0.9374 (pm20) REVERT: I 503 LEU cc_start: 0.9719 (mt) cc_final: 0.9501 (mp) REVERT: I 532 LEU cc_start: 0.9772 (mt) cc_final: 0.9563 (pp) REVERT: J 461 LEU cc_start: 0.9726 (mt) cc_final: 0.9420 (mt) REVERT: J 462 GLN cc_start: 0.9375 (tt0) cc_final: 0.8923 (tp40) REVERT: J 496 GLN cc_start: 0.9620 (mp10) cc_final: 0.9253 (pm20) REVERT: J 503 LEU cc_start: 0.9697 (mt) cc_final: 0.9377 (mt) REVERT: K 461 LEU cc_start: 0.9817 (mt) cc_final: 0.9455 (mt) REVERT: K 462 GLN cc_start: 0.9534 (tt0) cc_final: 0.9216 (tp40) REVERT: K 498 LYS cc_start: 0.9678 (mttt) cc_final: 0.9434 (mttt) REVERT: K 503 LEU cc_start: 0.9552 (mt) cc_final: 0.9211 (mp) REVERT: L 462 GLN cc_start: 0.9311 (tt0) cc_final: 0.8974 (tp40) REVERT: L 464 ARG cc_start: 0.8618 (mtt-85) cc_final: 0.8020 (tpt170) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.1532 time to fit residues: 101.5004 Evaluate side-chains 285 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 50.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 GLN C 460 GLN G 460 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.077205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.069770 restraints weight = 71868.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.070928 restraints weight = 36901.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.071643 restraints weight = 21878.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.072126 restraints weight = 14177.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.072457 restraints weight = 9795.095| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8544 Z= 0.157 Angle : 0.868 12.900 11448 Z= 0.416 Chirality : 0.046 0.259 1296 Planarity : 0.004 0.040 1524 Dihedral : 4.314 18.459 1128 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.43 % Allowed : 19.09 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.25), residues: 1020 helix: 0.86 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.29 (0.25), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 533 TYR 0.006 0.001 TYR L 531 PHE 0.006 0.001 PHE A 453 HIS 0.003 0.001 HIS H 458 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8544) covalent geometry : angle 0.86766 (11448) hydrogen bonds : bond 0.03636 ( 577) hydrogen bonds : angle 4.24436 ( 1731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 LEU cc_start: 0.9637 (mt) cc_final: 0.9351 (mt) REVERT: B 485 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9208 (pt0) REVERT: C 486 LYS cc_start: 0.9602 (ttpt) cc_final: 0.9338 (ttmt) REVERT: D 485 GLU cc_start: 0.9498 (mt-10) cc_final: 0.9292 (pt0) REVERT: E 503 LEU cc_start: 0.9885 (mt) cc_final: 0.9674 (mt) REVERT: F 486 LYS cc_start: 0.9515 (ttpt) cc_final: 0.9242 (ttmt) REVERT: G 461 LEU cc_start: 0.9706 (mt) cc_final: 0.9420 (mt) REVERT: G 465 MET cc_start: 0.8193 (mtm) cc_final: 0.7964 (mtm) REVERT: G 486 LYS cc_start: 0.9676 (ttpt) cc_final: 0.9435 (ttmt) REVERT: G 492 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8750 (mp0) REVERT: H 486 LYS cc_start: 0.9650 (ttpt) cc_final: 0.9316 (ttmt) REVERT: I 462 GLN cc_start: 0.9326 (tt0) cc_final: 0.8962 (tp40) REVERT: I 465 MET cc_start: 0.7798 (mtp) cc_final: 0.7593 (mtm) REVERT: I 485 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9416 (pt0) REVERT: I 492 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8737 (mp0) REVERT: J 465 MET cc_start: 0.7826 (mtp) cc_final: 0.7017 (mtp) REVERT: K 465 MET cc_start: 0.7586 (mtp) cc_final: 0.6898 (mtp) REVERT: K 481 LEU cc_start: 0.9274 (pp) cc_final: 0.9002 (tt) REVERT: K 485 GLU cc_start: 0.9543 (mt-10) cc_final: 0.9287 (mt-10) REVERT: L 462 GLN cc_start: 0.9166 (tt0) cc_final: 0.8958 (tp40) REVERT: L 464 ARG cc_start: 0.8872 (mtt-85) cc_final: 0.8412 (tpt170) REVERT: L 517 LEU cc_start: 0.9903 (tp) cc_final: 0.9621 (pp) outliers start: 42 outliers final: 27 residues processed: 362 average time/residue: 0.1267 time to fit residues: 58.0389 Evaluate side-chains 249 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 492 GLU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 480 VAL Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 56 optimal weight: 50.0000 chunk 91 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 18 optimal weight: 50.0000 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 50.0000 chunk 49 optimal weight: 30.0000 chunk 10 optimal weight: 50.0000 chunk 77 optimal weight: 5.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 462 GLN D 476 GLN ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 GLN F 462 GLN G 476 GLN H 458 HIS H 476 GLN I 476 GLN J 460 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.067853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.061235 restraints weight = 79258.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.062243 restraints weight = 39879.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.062865 restraints weight = 23648.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.063263 restraints weight = 15470.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.063535 restraints weight = 10925.980| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.7757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8544 Z= 0.154 Angle : 0.889 13.812 11448 Z= 0.424 Chirality : 0.042 0.237 1296 Planarity : 0.004 0.029 1524 Dihedral : 4.422 20.624 1128 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 6.01 % Allowed : 21.41 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.25), residues: 1020 helix: 0.85 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.40 (0.25), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 533 TYR 0.011 0.001 TYR H 531 PHE 0.006 0.001 PHE I 453 HIS 0.002 0.001 HIS K 458 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8544) covalent geometry : angle 0.88893 (11448) hydrogen bonds : bond 0.03467 ( 577) hydrogen bonds : angle 4.24959 ( 1731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 247 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.8337 (mtm) cc_final: 0.7815 (mtt) REVERT: A 500 GLU cc_start: 0.9373 (mt-10) cc_final: 0.9052 (mm-30) REVERT: A 502 LEU cc_start: 0.9492 (mt) cc_final: 0.9246 (pp) REVERT: B 468 LEU cc_start: 0.9637 (mt) cc_final: 0.8218 (mp) REVERT: B 481 LEU cc_start: 0.9294 (pp) cc_final: 0.8515 (pp) REVERT: B 485 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9221 (pt0) REVERT: B 486 LYS cc_start: 0.9740 (ttpt) cc_final: 0.9497 (ttmt) REVERT: B 524 ARG cc_start: 0.9168 (mmm160) cc_final: 0.8874 (tpp80) REVERT: C 462 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8418 (tp40) REVERT: C 486 LYS cc_start: 0.9725 (ttpt) cc_final: 0.9351 (ttmt) REVERT: D 468 LEU cc_start: 0.9703 (mt) cc_final: 0.9474 (mt) REVERT: E 505 MET cc_start: 0.9455 (mmm) cc_final: 0.9254 (mmm) REVERT: F 462 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8449 (tp40) REVERT: F 481 LEU cc_start: 0.9359 (pp) cc_final: 0.9083 (tt) REVERT: F 486 LYS cc_start: 0.9638 (ttpt) cc_final: 0.9226 (tttt) REVERT: G 517 LEU cc_start: 0.9904 (tp) cc_final: 0.9670 (pp) REVERT: H 467 ASP cc_start: 0.8683 (t0) cc_final: 0.8479 (t0) REVERT: I 462 GLN cc_start: 0.9448 (tt0) cc_final: 0.8976 (tp40) REVERT: I 481 LEU cc_start: 0.9511 (pp) cc_final: 0.9244 (tt) REVERT: I 486 LYS cc_start: 0.9553 (ttpt) cc_final: 0.9342 (ptpt) REVERT: I 492 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8814 (mp0) outliers start: 57 outliers final: 35 residues processed: 284 average time/residue: 0.1202 time to fit residues: 43.5934 Evaluate side-chains 239 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 492 GLU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain H residue 492 GLU Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 ASN Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain J residue 480 VAL Chi-restraints excluded: chain J residue 484 ASN Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 8.9990 chunk 47 optimal weight: 50.0000 chunk 58 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 30.0000 chunk 57 optimal weight: 40.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 458 HIS ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.064189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.057770 restraints weight = 83703.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.058800 restraints weight = 41964.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.059413 restraints weight = 24790.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.059794 restraints weight = 16285.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.060052 restraints weight = 11728.620| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.8516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8544 Z= 0.142 Angle : 0.892 14.051 11448 Z= 0.422 Chirality : 0.044 0.313 1296 Planarity : 0.003 0.032 1524 Dihedral : 4.536 20.338 1128 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 6.33 % Allowed : 22.68 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.26), residues: 1020 helix: 0.71 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.32 (0.28), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 533 TYR 0.014 0.001 TYR J 531 PHE 0.007 0.001 PHE K 453 HIS 0.003 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8544) covalent geometry : angle 0.89176 (11448) hydrogen bonds : bond 0.03310 ( 577) hydrogen bonds : angle 4.27777 ( 1731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 232 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 GLU cc_start: 0.9364 (mt-10) cc_final: 0.9043 (mm-30) REVERT: B 474 ASP cc_start: 0.9610 (m-30) cc_final: 0.9288 (m-30) REVERT: C 462 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8536 (tp40) REVERT: E 481 LEU cc_start: 0.9592 (pp) cc_final: 0.9239 (tt) REVERT: E 505 MET cc_start: 0.9526 (mmm) cc_final: 0.9282 (mmm) REVERT: F 481 LEU cc_start: 0.9384 (pp) cc_final: 0.9144 (tt) REVERT: F 486 LYS cc_start: 0.9737 (ttpt) cc_final: 0.9359 (tttt) REVERT: G 517 LEU cc_start: 0.9896 (tp) cc_final: 0.9654 (pp) REVERT: G 531 TYR cc_start: 0.9348 (t80) cc_final: 0.8919 (t80) REVERT: H 467 ASP cc_start: 0.8633 (t0) cc_final: 0.8340 (t0) REVERT: H 517 LEU cc_start: 0.9918 (tp) cc_final: 0.9655 (pp) REVERT: K 481 LEU cc_start: 0.9458 (pp) cc_final: 0.9207 (tt) REVERT: K 486 LYS cc_start: 0.9778 (ttpt) cc_final: 0.9552 (ttmt) REVERT: K 492 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7579 (mp0) outliers start: 60 outliers final: 43 residues processed: 268 average time/residue: 0.1171 time to fit residues: 40.6226 Evaluate side-chains 237 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain H residue 484 ASN Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 480 VAL Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain J residue 480 VAL Chi-restraints excluded: chain J residue 484 ASN Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 492 GLU Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 30.0000 chunk 73 optimal weight: 20.0000 chunk 40 optimal weight: 50.0000 chunk 5 optimal weight: 8.9990 chunk 24 optimal weight: 50.0000 chunk 2 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 48 optimal weight: 7.9990 chunk 41 optimal weight: 50.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 462 GLN ** I 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.060533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.054664 restraints weight = 85383.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.055634 restraints weight = 41725.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.056214 restraints weight = 24338.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.056579 restraints weight = 15895.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.056822 restraints weight = 11494.182| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.9045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8544 Z= 0.147 Angle : 0.867 12.858 11448 Z= 0.429 Chirality : 0.042 0.261 1296 Planarity : 0.003 0.025 1524 Dihedral : 4.727 22.267 1128 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 6.65 % Allowed : 23.95 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.26), residues: 1020 helix: 0.55 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.98 (0.33), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 464 TYR 0.010 0.001 TYR J 531 PHE 0.006 0.001 PHE K 453 HIS 0.013 0.002 HIS I 458 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8544) covalent geometry : angle 0.86740 (11448) hydrogen bonds : bond 0.03329 ( 577) hydrogen bonds : angle 4.33395 ( 1731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 220 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.7630 (mtt) cc_final: 0.6607 (mtt) REVERT: A 502 LEU cc_start: 0.9307 (mt) cc_final: 0.9041 (pp) REVERT: B 474 ASP cc_start: 0.9536 (m-30) cc_final: 0.9329 (m-30) REVERT: B 487 GLU cc_start: 0.9443 (mt-10) cc_final: 0.9216 (pt0) REVERT: B 492 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7289 (mp0) REVERT: E 489 VAL cc_start: 0.9691 (t) cc_final: 0.9324 (p) REVERT: E 505 MET cc_start: 0.9606 (mmm) cc_final: 0.9379 (mmm) REVERT: F 462 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8202 (tp40) REVERT: F 481 LEU cc_start: 0.9385 (pp) cc_final: 0.9041 (pp) REVERT: F 486 LYS cc_start: 0.9776 (ttpt) cc_final: 0.9345 (tttt) REVERT: H 467 ASP cc_start: 0.8668 (t0) cc_final: 0.8243 (t0) REVERT: H 517 LEU cc_start: 0.9924 (tp) cc_final: 0.9672 (pp) REVERT: I 481 LEU cc_start: 0.9486 (pp) cc_final: 0.9233 (pp) REVERT: I 485 GLU cc_start: 0.9678 (pt0) cc_final: 0.9466 (pt0) REVERT: I 489 VAL cc_start: 0.9717 (t) cc_final: 0.9200 (p) REVERT: K 486 LYS cc_start: 0.9848 (ttpt) cc_final: 0.9637 (ttmt) outliers start: 63 outliers final: 46 residues processed: 262 average time/residue: 0.1171 time to fit residues: 39.5859 Evaluate side-chains 228 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 459 ARG Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain H residue 484 ASN Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 484 ASN Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain J residue 484 ASN Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 50 optimal weight: 30.0000 chunk 67 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 36 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 462 GLN C 476 GLN ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.058610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.052708 restraints weight = 86209.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.053658 restraints weight = 42130.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.054197 restraints weight = 24769.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.054546 restraints weight = 16190.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.054752 restraints weight = 11731.822| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.9451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8544 Z= 0.154 Angle : 0.898 13.268 11448 Z= 0.450 Chirality : 0.045 0.319 1296 Planarity : 0.004 0.032 1524 Dihedral : 4.791 23.775 1128 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 6.43 % Allowed : 25.53 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.26), residues: 1020 helix: 0.42 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.15 (0.34), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 495 TYR 0.009 0.001 TYR J 531 PHE 0.007 0.001 PHE D 453 HIS 0.014 0.002 HIS I 458 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8544) covalent geometry : angle 0.89777 (11448) hydrogen bonds : bond 0.03473 ( 577) hydrogen bonds : angle 4.40859 ( 1731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 199 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.7758 (mtt) cc_final: 0.6807 (mtt) REVERT: A 492 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7803 (mp0) REVERT: A 502 LEU cc_start: 0.9440 (mt) cc_final: 0.9164 (pp) REVERT: B 487 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9229 (pt0) REVERT: B 492 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7422 (mp0) REVERT: C 462 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8388 (tp40) REVERT: E 489 VAL cc_start: 0.9537 (t) cc_final: 0.9036 (p) REVERT: E 492 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7534 (mp0) REVERT: F 486 LYS cc_start: 0.9760 (ttpt) cc_final: 0.9515 (tttt) REVERT: G 517 LEU cc_start: 0.9905 (tp) cc_final: 0.9676 (pp) REVERT: H 467 ASP cc_start: 0.8724 (t0) cc_final: 0.8407 (t0) REVERT: H 517 LEU cc_start: 0.9926 (tp) cc_final: 0.9661 (pp) REVERT: I 481 LEU cc_start: 0.9509 (pp) cc_final: 0.9283 (pp) REVERT: I 489 VAL cc_start: 0.9575 (t) cc_final: 0.9353 (p) REVERT: J 467 ASP cc_start: 0.8528 (t0) cc_final: 0.8326 (t0) REVERT: K 485 GLU cc_start: 0.9610 (mt-10) cc_final: 0.9324 (pt0) REVERT: K 486 LYS cc_start: 0.9852 (ttpt) cc_final: 0.9606 (ttmt) outliers start: 61 outliers final: 51 residues processed: 246 average time/residue: 0.1080 time to fit residues: 34.5977 Evaluate side-chains 231 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 459 ARG Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain H residue 484 ASN Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 484 ASN Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.1980 chunk 28 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 66 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 462 GLN ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN ** J 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.059003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.053124 restraints weight = 86007.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.054072 restraints weight = 41552.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.054633 restraints weight = 24128.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.054968 restraints weight = 15782.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.055192 restraints weight = 11336.732| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.9696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8544 Z= 0.142 Angle : 0.937 14.464 11448 Z= 0.454 Chirality : 0.045 0.339 1296 Planarity : 0.003 0.017 1524 Dihedral : 4.770 23.957 1128 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 6.12 % Allowed : 26.27 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.26), residues: 1020 helix: 0.42 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.38 (0.34), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 524 TYR 0.008 0.001 TYR J 531 PHE 0.007 0.001 PHE D 453 HIS 0.013 0.002 HIS I 458 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8544) covalent geometry : angle 0.93738 (11448) hydrogen bonds : bond 0.03447 ( 577) hydrogen bonds : angle 4.42607 ( 1731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.7760 (mtt) cc_final: 0.6966 (mtt) REVERT: A 476 GLN cc_start: 0.9112 (tp40) cc_final: 0.8780 (tp40) REVERT: A 492 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7781 (mp0) REVERT: A 502 LEU cc_start: 0.9514 (mt) cc_final: 0.9310 (pp) REVERT: C 462 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8169 (tp40) REVERT: C 489 VAL cc_start: 0.9490 (p) cc_final: 0.8950 (m) REVERT: D 505 MET cc_start: 0.9410 (mmm) cc_final: 0.9210 (mmm) REVERT: E 489 VAL cc_start: 0.9569 (t) cc_final: 0.9198 (t) REVERT: F 462 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8474 (tp40) REVERT: F 486 LYS cc_start: 0.9786 (ttpt) cc_final: 0.9516 (tttt) REVERT: F 489 VAL cc_start: 0.9572 (p) cc_final: 0.9234 (m) REVERT: G 474 ASP cc_start: 0.9516 (m-30) cc_final: 0.9284 (m-30) REVERT: G 485 GLU cc_start: 0.9630 (pt0) cc_final: 0.9406 (pm20) REVERT: H 467 ASP cc_start: 0.8769 (t0) cc_final: 0.8148 (t0) REVERT: H 517 LEU cc_start: 0.9922 (tp) cc_final: 0.9659 (pp) REVERT: J 485 GLU cc_start: 0.9674 (pt0) cc_final: 0.9404 (pm20) REVERT: K 486 LYS cc_start: 0.9856 (ttpt) cc_final: 0.9641 (ttmt) REVERT: K 489 VAL cc_start: 0.9645 (t) cc_final: 0.9263 (p) outliers start: 58 outliers final: 50 residues processed: 262 average time/residue: 0.1158 time to fit residues: 38.8913 Evaluate side-chains 236 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 459 ARG Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 480 VAL Chi-restraints excluded: chain I residue 484 ASN Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 459 ARG Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 484 ASN Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 40 optimal weight: 50.0000 chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 30.0000 chunk 60 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 8 optimal weight: 50.0000 chunk 68 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 462 GLN ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN ** J 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.058725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.052843 restraints weight = 86298.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.053800 restraints weight = 41913.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.054346 restraints weight = 24647.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.054697 restraints weight = 16281.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.054919 restraints weight = 11765.201| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.9911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8544 Z= 0.157 Angle : 1.012 14.891 11448 Z= 0.496 Chirality : 0.046 0.259 1296 Planarity : 0.003 0.017 1524 Dihedral : 4.889 24.156 1128 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 6.33 % Allowed : 27.74 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.26), residues: 1020 helix: 0.30 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.49 (0.34), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 495 TYR 0.007 0.001 TYR J 531 PHE 0.007 0.001 PHE G 453 HIS 0.012 0.002 HIS I 458 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8544) covalent geometry : angle 1.01154 (11448) hydrogen bonds : bond 0.03742 ( 577) hydrogen bonds : angle 4.59740 ( 1731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 201 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.7662 (mtt) cc_final: 0.6942 (mtt) REVERT: A 476 GLN cc_start: 0.9149 (tp40) cc_final: 0.8825 (tp40) REVERT: C 462 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8415 (tp40) REVERT: C 465 MET cc_start: 0.9128 (ppp) cc_final: 0.8899 (ppp) REVERT: D 474 ASP cc_start: 0.9612 (m-30) cc_final: 0.9377 (m-30) REVERT: D 505 MET cc_start: 0.9434 (mmm) cc_final: 0.9225 (mmm) REVERT: E 487 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9132 (pt0) REVERT: F 462 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8455 (tp40) REVERT: F 465 MET cc_start: 0.7941 (ptp) cc_final: 0.7726 (ptp) REVERT: G 474 ASP cc_start: 0.9526 (m-30) cc_final: 0.9298 (m-30) REVERT: H 467 ASP cc_start: 0.8730 (t0) cc_final: 0.8170 (t0) REVERT: H 517 LEU cc_start: 0.9925 (tp) cc_final: 0.9667 (pp) REVERT: J 485 GLU cc_start: 0.9693 (pt0) cc_final: 0.9431 (pm20) REVERT: K 486 LYS cc_start: 0.9875 (ttpt) cc_final: 0.9627 (ttmt) outliers start: 60 outliers final: 47 residues processed: 246 average time/residue: 0.1112 time to fit residues: 35.4202 Evaluate side-chains 232 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 459 ARG Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 484 ASN Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.0770 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 61 optimal weight: 0.0170 chunk 20 optimal weight: 8.9990 chunk 75 optimal weight: 0.0770 chunk 43 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 462 GLN ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN ** K 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.060206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.054183 restraints weight = 84782.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.055167 restraints weight = 41342.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.055721 restraints weight = 24207.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.056059 restraints weight = 16052.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.056289 restraints weight = 11592.987| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 1.0053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8544 Z= 0.171 Angle : 1.111 15.980 11448 Z= 0.535 Chirality : 0.054 0.436 1296 Planarity : 0.003 0.030 1524 Dihedral : 5.011 24.163 1128 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.59 % Allowed : 31.65 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.26), residues: 1020 helix: 0.29 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.33 (0.39), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 524 TYR 0.007 0.001 TYR J 531 PHE 0.006 0.001 PHE B 453 HIS 0.012 0.002 HIS I 458 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8544) covalent geometry : angle 1.11062 (11448) hydrogen bonds : bond 0.03991 ( 577) hydrogen bonds : angle 4.61650 ( 1731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 ASP cc_start: 0.9562 (m-30) cc_final: 0.9359 (m-30) REVERT: B 489 VAL cc_start: 0.9467 (p) cc_final: 0.9239 (m) REVERT: C 462 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.5716 (tp40) REVERT: C 500 GLU cc_start: 0.9407 (pt0) cc_final: 0.9168 (mm-30) REVERT: C 528 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9388 (mm) REVERT: D 474 ASP cc_start: 0.9609 (m-30) cc_final: 0.9371 (m-30) REVERT: E 487 GLU cc_start: 0.9374 (mt-10) cc_final: 0.9168 (pt0) REVERT: F 465 MET cc_start: 0.8017 (ptp) cc_final: 0.7747 (ptp) REVERT: G 474 ASP cc_start: 0.9525 (m-30) cc_final: 0.9313 (m-30) REVERT: G 485 GLU cc_start: 0.9671 (pt0) cc_final: 0.9411 (pm20) REVERT: H 467 ASP cc_start: 0.8611 (t0) cc_final: 0.8259 (t0) REVERT: I 485 GLU cc_start: 0.9658 (pt0) cc_final: 0.9426 (pm20) REVERT: L 485 GLU cc_start: 0.9565 (pt0) cc_final: 0.9328 (pm20) outliers start: 34 outliers final: 25 residues processed: 232 average time/residue: 0.0964 time to fit residues: 30.2357 Evaluate side-chains 213 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 484 ASN Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 8.9990 chunk 50 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 2 optimal weight: 40.0000 chunk 71 optimal weight: 0.6980 chunk 85 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 overall best weight: 7.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 HIS ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.056969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.051190 restraints weight = 87474.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.052140 restraints weight = 42584.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.052674 restraints weight = 25190.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.053017 restraints weight = 16705.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.053241 restraints weight = 12175.806| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 1.0349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8544 Z= 0.171 Angle : 1.099 16.209 11448 Z= 0.543 Chirality : 0.052 0.368 1296 Planarity : 0.003 0.020 1524 Dihedral : 5.054 24.981 1128 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.38 % Allowed : 32.28 % Favored : 64.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.27), residues: 1020 helix: 0.27 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.42 (0.43), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 495 TYR 0.023 0.001 TYR L 531 PHE 0.007 0.001 PHE G 453 HIS 0.011 0.002 HIS I 458 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8544) covalent geometry : angle 1.09923 (11448) hydrogen bonds : bond 0.04200 ( 577) hydrogen bonds : angle 4.80318 ( 1731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 528 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9408 (mm) REVERT: D 474 ASP cc_start: 0.9582 (m-30) cc_final: 0.9357 (m-30) REVERT: E 487 GLU cc_start: 0.9390 (mt-10) cc_final: 0.9124 (pt0) REVERT: F 465 MET cc_start: 0.7969 (ptp) cc_final: 0.7261 (ptp) REVERT: G 474 ASP cc_start: 0.9510 (m-30) cc_final: 0.9305 (m-30) REVERT: G 485 GLU cc_start: 0.9665 (pt0) cc_final: 0.9393 (pm20) REVERT: G 517 LEU cc_start: 0.9898 (tp) cc_final: 0.9657 (pp) REVERT: H 467 ASP cc_start: 0.8710 (t0) cc_final: 0.8353 (t0) REVERT: H 517 LEU cc_start: 0.9921 (tp) cc_final: 0.9659 (pp) REVERT: I 493 LYS cc_start: 0.9582 (mmtm) cc_final: 0.9160 (ptmt) REVERT: J 464 ARG cc_start: 0.9594 (mtt-85) cc_final: 0.9285 (mtp-110) outliers start: 32 outliers final: 29 residues processed: 215 average time/residue: 0.0955 time to fit residues: 27.8899 Evaluate side-chains 201 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 484 ASN Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 484 ASN Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 484 ASN Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 31 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.057750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.051924 restraints weight = 86938.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.052876 restraints weight = 42067.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.053436 restraints weight = 24681.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.053767 restraints weight = 16378.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.054004 restraints weight = 11865.129| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 1.0478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8544 Z= 0.169 Angle : 1.149 16.050 11448 Z= 0.561 Chirality : 0.052 0.370 1296 Planarity : 0.003 0.046 1524 Dihedral : 5.068 24.433 1128 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.16 % Allowed : 33.44 % Favored : 63.40 % 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 aren not related in a simple way. whole: -0.31 (0.26), residues: 1020 helix: 0.18 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.40 (0.42), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 524 TYR 0.028 0.001 TYR L 531 PHE 0.007 0.001 PHE B 453 HIS 0.012 0.002 HIS I 458 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8544) covalent geometry : angle 1.14923 (11448) hydrogen bonds : bond 0.04266 ( 577) hydrogen bonds : angle 4.80004 ( 1731) =============================================================================== Job complete usr+sys time: 1461.02 seconds wall clock time: 26 minutes 9.03 seconds (1569.03 seconds total)