Starting phenix.real_space_refine on Fri Jun 13 21:47:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k9f_9948/06_2025/6k9f_9948.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k9f_9948/06_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_9948/06_2025/6k9f_9948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k9f_9948/06_2025/6k9f_9948.map" model { file = "/net/cci-nas-00/data/ceres_data/6k9f_9948/06_2025/6k9f_9948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k9f_9948/06_2025/6k9f_9948.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.02, per 1000 atoms: 0.59 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: 2.08 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.82 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: 2.12 Time building geometry restraints manager: 2.46 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: 0.01 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.760 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.620 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (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 HIS 0.002 0.001 HIS A 458 PHE 0.013 0.002 PHE J 518 TYR 0.015 0.002 TYR B 531 ARG 0.002 0.000 ARG F 464 Details of bonding type rmsd hydrogen bonds : bond 0.13146 ( 577) hydrogen bonds : angle 6.51362 ( 1731) covalent geometry : bond 0.00213 ( 8544) covalent geometry : angle 0.44592 (11448) *********************** 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 : 1.159 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: 0.3265 time to fit residues: 215.3595 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 : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 40.0000 chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 60.0000 chunk 24 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 0.0060 chunk 56 optimal weight: 60.0000 chunk 87 optimal weight: 20.0000 overall best weight: 8.8008 ------------------------------------------------------------------------------- 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 L 535 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.074277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.067027 restraints weight = 73451.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.068130 restraints weight = 37459.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.068856 restraints weight = 22123.289| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8544 Z= 0.172 Angle : 0.852 12.560 11448 Z= 0.418 Chirality : 0.045 0.240 1296 Planarity : 0.004 0.038 1524 Dihedral : 4.330 18.297 1128 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.75 % Allowed : 19.73 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1020 helix: 0.83 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.40 (0.25), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 458 PHE 0.007 0.001 PHE I 453 TYR 0.007 0.001 TYR L 531 ARG 0.008 0.001 ARG J 533 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 577) hydrogen bonds : angle 4.41173 ( 1731) covalent geometry : bond 0.00363 ( 8544) covalent geometry : angle 0.85210 (11448) *********************** 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 371 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 326 time to evaluate : 1.114 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: A 481 LEU cc_start: 0.8958 (tp) cc_final: 0.8146 (tp) REVERT: B 461 LEU cc_start: 0.9673 (mt) cc_final: 0.9432 (mt) REVERT: B 462 GLN cc_start: 0.9105 (tt0) cc_final: 0.8730 (tp40) REVERT: B 465 MET cc_start: 0.7221 (mtm) cc_final: 0.6843 (mtm) REVERT: B 485 GLU cc_start: 0.9577 (mt-10) cc_final: 0.9286 (pt0) REVERT: C 462 GLN cc_start: 0.9252 (tt0) cc_final: 0.9023 (tp40) REVERT: C 486 LYS cc_start: 0.9628 (ttpt) cc_final: 0.9397 (ttmt) REVERT: C 500 GLU cc_start: 0.9484 (pt0) cc_final: 0.9279 (pp20) REVERT: F 486 LYS cc_start: 0.9553 (ttpt) cc_final: 0.9202 (ttmt) REVERT: G 461 LEU cc_start: 0.9715 (mt) cc_final: 0.9400 (mt) REVERT: G 465 MET cc_start: 0.8181 (mtm) cc_final: 0.7942 (mtm) REVERT: G 486 LYS cc_start: 0.9702 (ttpt) cc_final: 0.9367 (ttmt) REVERT: G 492 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8774 (mp0) REVERT: H 486 LYS cc_start: 0.9662 (ttpt) cc_final: 0.9209 (ttmt) REVERT: I 462 GLN cc_start: 0.9351 (tt0) cc_final: 0.8970 (tp40) REVERT: I 465 MET cc_start: 0.7979 (mtp) cc_final: 0.7753 (mtm) REVERT: I 485 GLU cc_start: 0.9673 (mt-10) cc_final: 0.9420 (pt0) REVERT: I 492 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8702 (mp0) REVERT: J 465 MET cc_start: 0.7962 (mtp) cc_final: 0.7118 (mtp) REVERT: K 465 MET cc_start: 0.7760 (mtp) cc_final: 0.7282 (mtp) REVERT: L 462 GLN cc_start: 0.9189 (tt0) cc_final: 0.8958 (tp40) REVERT: L 464 ARG cc_start: 0.8943 (mtt-85) cc_final: 0.8462 (tpt170) REVERT: L 517 LEU cc_start: 0.9910 (tp) cc_final: 0.9635 (pp) outliers start: 45 outliers final: 31 residues processed: 357 average time/residue: 0.2877 time to fit residues: 128.3419 Evaluate side-chains 268 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 455 LYS 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 453 PHE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 487 GLU Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain J residue 487 GLU 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 K residue 488 LEU 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 9 optimal weight: 6.9990 chunk 49 optimal weight: 50.0000 chunk 18 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 88 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 7 optimal weight: 50.0000 overall best weight: 4.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 HIS E 476 GLN F 458 HIS 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 = 0.3584 r_free = 0.3584 target = 0.070013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.063106 restraints weight = 78665.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.064166 restraints weight = 39393.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.064812 restraints weight = 23157.762| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.7467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8544 Z= 0.139 Angle : 0.870 14.291 11448 Z= 0.410 Chirality : 0.042 0.233 1296 Planarity : 0.003 0.032 1524 Dihedral : 4.334 21.151 1128 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 5.70 % Allowed : 20.36 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1020 helix: 0.86 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.39 (0.26), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 458 PHE 0.007 0.001 PHE K 453 TYR 0.012 0.001 TYR H 531 ARG 0.006 0.000 ARG B 533 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 577) hydrogen bonds : angle 4.20981 ( 1731) covalent geometry : bond 0.00296 ( 8544) covalent geometry : angle 0.86977 (11448) *********************** 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 318 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 264 time to evaluate : 1.012 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: A 502 LEU cc_start: 0.9548 (mt) cc_final: 0.9206 (pp) REVERT: B 468 LEU cc_start: 0.9628 (mt) cc_final: 0.8438 (mt) REVERT: B 485 GLU cc_start: 0.9543 (mt-10) cc_final: 0.9242 (pt0) REVERT: B 486 LYS cc_start: 0.9731 (ttpt) cc_final: 0.9513 (ttmt) REVERT: C 465 MET cc_start: 0.8730 (tmm) cc_final: 0.8467 (tmm) REVERT: C 486 LYS cc_start: 0.9707 (ttpt) cc_final: 0.9321 (ttmt) REVERT: D 461 LEU cc_start: 0.9873 (mt) cc_final: 0.9247 (mt) REVERT: F 462 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8537 (tp40) REVERT: F 481 LEU cc_start: 0.9370 (pp) cc_final: 0.9151 (tt) REVERT: F 486 LYS cc_start: 0.9628 (ttpt) cc_final: 0.9374 (tttt) REVERT: H 493 LYS cc_start: 0.9528 (mmtm) cc_final: 0.9092 (mmtm) REVERT: H 517 LEU cc_start: 0.9914 (tp) cc_final: 0.9695 (pp) REVERT: I 462 GLN cc_start: 0.9452 (tt0) cc_final: 0.8969 (tp40) REVERT: I 481 LEU cc_start: 0.9530 (pp) cc_final: 0.9328 (tt) REVERT: K 481 LEU cc_start: 0.9539 (pp) cc_final: 0.9310 (tt) outliers start: 54 outliers final: 36 residues processed: 298 average time/residue: 0.2783 time to fit residues: 104.6017 Evaluate side-chains 243 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 480 VAL Chi-restraints excluded: chain C residue 529 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 455 LYS 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 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 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 480 VAL Chi-restraints excluded: chain J residue 481 LEU Chi-restraints excluded: chain J residue 487 GLU Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 488 LEU 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 38 optimal weight: 3.9990 chunk 72 optimal weight: 50.0000 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 50.0000 chunk 55 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 90 optimal weight: 50.0000 chunk 2 optimal weight: 40.0000 chunk 21 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 GLN D 499 ASN ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 534 GLN J 458 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.064198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.057741 restraints weight = 82224.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.058705 restraints weight = 41674.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.059325 restraints weight = 24871.760| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.8449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8544 Z= 0.146 Angle : 0.907 14.990 11448 Z= 0.429 Chirality : 0.044 0.305 1296 Planarity : 0.004 0.035 1524 Dihedral : 4.478 20.854 1128 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 6.96 % Allowed : 21.10 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1020 helix: 0.72 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.51 (0.26), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 458 PHE 0.006 0.001 PHE K 453 TYR 0.008 0.001 TYR H 531 ARG 0.008 0.001 ARG G 533 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 577) hydrogen bonds : angle 4.26721 ( 1731) covalent geometry : bond 0.00313 ( 8544) covalent geometry : angle 0.90676 (11448) *********************** 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 303 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 237 time to evaluate : 1.222 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: C 500 GLU cc_start: 0.9545 (pp20) cc_final: 0.9153 (pp20) REVERT: E 481 LEU cc_start: 0.9596 (pp) cc_final: 0.9247 (tt) REVERT: F 481 LEU cc_start: 0.9382 (pp) cc_final: 0.9152 (tt) REVERT: F 486 LYS cc_start: 0.9754 (ttpt) cc_final: 0.9396 (ttmt) REVERT: F 489 VAL cc_start: 0.9574 (t) cc_final: 0.8912 (p) REVERT: F 517 LEU cc_start: 0.9896 (tp) cc_final: 0.9618 (pp) REVERT: G 517 LEU cc_start: 0.9897 (tp) cc_final: 0.9622 (pp) REVERT: G 531 TYR cc_start: 0.9353 (t80) cc_final: 0.8928 (t80) REVERT: H 517 LEU cc_start: 0.9920 (tp) cc_final: 0.9706 (pp) REVERT: I 481 LEU cc_start: 0.9572 (pp) cc_final: 0.9306 (tt) REVERT: I 492 GLU cc_start: 0.9264 (mm-30) cc_final: 0.9001 (mt-10) REVERT: K 481 LEU cc_start: 0.9569 (pp) cc_final: 0.9153 (pp) REVERT: K 485 GLU cc_start: 0.9553 (mt-10) cc_final: 0.9341 (pt0) REVERT: K 492 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7607 (mp0) outliers start: 66 outliers final: 45 residues processed: 273 average time/residue: 0.2536 time to fit residues: 88.5411 Evaluate side-chains 237 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 484 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 468 LEU 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 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 455 LYS 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 484 ASN Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 480 VAL Chi-restraints excluded: chain J residue 481 LEU Chi-restraints excluded: chain J residue 487 GLU Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 488 LEU 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 9 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 59 optimal weight: 30.0000 chunk 40 optimal weight: 60.0000 chunk 84 optimal weight: 9.9990 chunk 93 optimal weight: 40.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 462 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.060905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.054902 restraints weight = 83838.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.055853 restraints weight = 41999.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.056428 restraints weight = 24914.723| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.9024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8544 Z= 0.149 Angle : 0.894 11.961 11448 Z= 0.437 Chirality : 0.044 0.307 1296 Planarity : 0.004 0.027 1524 Dihedral : 4.649 24.043 1128 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 6.54 % Allowed : 25.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1020 helix: 0.49 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.38 (0.27), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 458 PHE 0.006 0.001 PHE A 453 TYR 0.008 0.001 TYR A 531 ARG 0.005 0.001 ARG B 524 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 577) hydrogen bonds : angle 4.40784 ( 1731) covalent geometry : bond 0.00313 ( 8544) covalent geometry : angle 0.89386 (11448) *********************** 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 279 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 1.007 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: A 465 MET cc_start: 0.8077 (mtt) cc_final: 0.7229 (mtt) REVERT: A 476 GLN cc_start: 0.9062 (tp40) cc_final: 0.8683 (tp40) REVERT: A 502 LEU cc_start: 0.9389 (mt) cc_final: 0.9178 (pp) REVERT: E 489 VAL cc_start: 0.9773 (t) cc_final: 0.9543 (m) REVERT: F 462 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8404 (tp40) REVERT: F 486 LYS cc_start: 0.9821 (ttpt) cc_final: 0.9504 (ttmt) REVERT: G 492 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8701 (mp0) REVERT: G 531 TYR cc_start: 0.9341 (t80) cc_final: 0.8979 (t80) REVERT: H 517 LEU cc_start: 0.9925 (tp) cc_final: 0.9696 (pp) REVERT: I 481 LEU cc_start: 0.9571 (pp) cc_final: 0.9318 (pp) REVERT: I 489 VAL cc_start: 0.9696 (m) cc_final: 0.9322 (p) REVERT: K 481 LEU cc_start: 0.9497 (pp) cc_final: 0.8920 (pp) outliers start: 62 outliers final: 46 residues processed: 255 average time/residue: 0.2459 time to fit residues: 81.2396 Evaluate side-chains 229 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 455 LYS 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 462 GLN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 492 GLU 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 468 LEU 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 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 481 LEU Chi-restraints excluded: chain J residue 487 GLU 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 K residue 488 LEU 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 23 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 78 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 chunk 40 optimal weight: 70.0000 chunk 92 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.060141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.054267 restraints weight = 84359.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.055197 restraints weight = 41681.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.055747 restraints weight = 24501.142| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.9344 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= 0.145 Angle : 0.931 13.355 11448 Z= 0.452 Chirality : 0.046 0.424 1296 Planarity : 0.003 0.042 1524 Dihedral : 4.728 22.562 1128 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 5.49 % Allowed : 25.95 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1020 helix: 0.46 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.49 (0.31), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS I 458 PHE 0.007 0.001 PHE D 453 TYR 0.007 0.001 TYR D 531 ARG 0.005 0.001 ARG H 495 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 577) hydrogen bonds : angle 4.32626 ( 1731) covalent geometry : bond 0.00306 ( 8544) covalent geometry : angle 0.93074 (11448) *********************** 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 255 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 1.276 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 475 LEU cc_start: 0.9896 (OUTLIER) cc_final: 0.9601 (tp) REVERT: A 476 GLN cc_start: 0.9123 (tp40) cc_final: 0.8737 (tp40) REVERT: E 489 VAL cc_start: 0.9595 (t) cc_final: 0.9253 (m) REVERT: E 492 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7463 (mp0) REVERT: F 462 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8508 (tp40) REVERT: G 492 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8685 (mp0) REVERT: G 531 TYR cc_start: 0.9310 (t80) cc_final: 0.8994 (t80) REVERT: H 517 LEU cc_start: 0.9923 (tp) cc_final: 0.9692 (pp) REVERT: I 481 LEU cc_start: 0.9555 (pp) cc_final: 0.9351 (pp) REVERT: J 464 ARG cc_start: 0.9661 (mtt-85) cc_final: 0.9326 (mtp-110) REVERT: L 485 GLU cc_start: 0.9648 (mt-10) cc_final: 0.9411 (pt0) outliers start: 52 outliers final: 40 residues processed: 242 average time/residue: 0.2357 time to fit residues: 74.7036 Evaluate side-chains 225 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 459 ARG 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 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 455 LYS 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 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 494 THR 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 J residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 488 LEU 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 95 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 7 optimal weight: 40.0000 chunk 1 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 31 optimal weight: 40.0000 chunk 49 optimal weight: 50.0000 chunk 63 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.058655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.052752 restraints weight = 86278.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.053745 restraints weight = 42312.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.054267 restraints weight = 24479.182| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.9647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8544 Z= 0.152 Angle : 0.958 13.983 11448 Z= 0.474 Chirality : 0.048 0.346 1296 Planarity : 0.003 0.021 1524 Dihedral : 4.823 22.432 1128 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 6.43 % Allowed : 26.58 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.26), residues: 1020 helix: 0.39 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.36 (0.37), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS I 458 PHE 0.008 0.001 PHE A 453 TYR 0.005 0.001 TYR H 531 ARG 0.005 0.001 ARG F 464 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 577) hydrogen bonds : angle 4.54566 ( 1731) covalent geometry : bond 0.00319 ( 8544) covalent geometry : angle 0.95818 (11448) *********************** 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 265 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 1.120 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: A 475 LEU cc_start: 0.9894 (OUTLIER) cc_final: 0.9660 (tp) REVERT: A 476 GLN cc_start: 0.9159 (tp40) cc_final: 0.8763 (tp40) REVERT: A 502 LEU cc_start: 0.9397 (mt) cc_final: 0.9182 (pp) REVERT: D 474 ASP cc_start: 0.9613 (m-30) cc_final: 0.9350 (m-30) REVERT: E 489 VAL cc_start: 0.9637 (t) cc_final: 0.9138 (p) REVERT: F 462 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8636 (tp40) REVERT: F 485 GLU cc_start: 0.9642 (OUTLIER) cc_final: 0.9371 (mp0) REVERT: F 489 VAL cc_start: 0.9382 (m) cc_final: 0.8912 (p) REVERT: G 474 ASP cc_start: 0.9555 (m-30) cc_final: 0.9329 (m-30) REVERT: G 485 GLU cc_start: 0.9721 (pt0) cc_final: 0.9491 (pm20) REVERT: G 488 LEU cc_start: 0.9868 (OUTLIER) cc_final: 0.9470 (mm) REVERT: H 517 LEU cc_start: 0.9920 (tp) cc_final: 0.9697 (pp) REVERT: J 464 ARG cc_start: 0.9689 (mtt-85) cc_final: 0.9286 (mtp180) REVERT: K 489 VAL cc_start: 0.9694 (t) cc_final: 0.9328 (p) outliers start: 61 outliers final: 49 residues processed: 253 average time/residue: 0.2448 time to fit residues: 80.5090 Evaluate side-chains 231 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 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 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 455 LYS Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 485 GLU 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 488 LEU Chi-restraints excluded: chain G residue 494 THR 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 468 LEU Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain H residue 494 THR 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 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 K residue 488 LEU 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 529 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 30 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN ** F 499 ASN ** 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 = 0.3416 r_free = 0.3416 target = 0.058753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.052900 restraints weight = 86765.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.053858 restraints weight = 42358.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.054418 restraints weight = 24791.353| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.9874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8544 Z= 0.153 Angle : 1.040 16.482 11448 Z= 0.506 Chirality : 0.050 0.485 1296 Planarity : 0.003 0.016 1524 Dihedral : 4.870 21.853 1128 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 6.12 % Allowed : 27.00 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1020 helix: 0.38 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.47 (0.37), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS I 458 PHE 0.007 0.001 PHE B 453 TYR 0.005 0.001 TYR J 527 ARG 0.003 0.001 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 577) hydrogen bonds : angle 4.60150 ( 1731) covalent geometry : bond 0.00319 ( 8544) covalent geometry : angle 1.04046 (11448) *********************** 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 254 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 196 time to evaluate : 1.094 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 475 LEU cc_start: 0.9889 (OUTLIER) cc_final: 0.9660 (tp) REVERT: A 476 GLN cc_start: 0.9172 (tp40) cc_final: 0.8818 (tp40) REVERT: A 492 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8039 (mp0) REVERT: A 502 LEU cc_start: 0.9403 (mt) cc_final: 0.9176 (pp) REVERT: B 517 LEU cc_start: 0.9916 (tp) cc_final: 0.9710 (pp) REVERT: C 528 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9355 (mm) REVERT: D 474 ASP cc_start: 0.9609 (m-30) cc_final: 0.9370 (m-30) REVERT: E 487 GLU cc_start: 0.9483 (mt-10) cc_final: 0.9281 (mt-10) REVERT: F 485 GLU cc_start: 0.9663 (OUTLIER) cc_final: 0.9322 (mp0) REVERT: G 474 ASP cc_start: 0.9546 (m-30) cc_final: 0.9310 (m-30) REVERT: G 485 GLU cc_start: 0.9698 (pt0) cc_final: 0.9482 (pm20) REVERT: H 517 LEU cc_start: 0.9921 (tp) cc_final: 0.9691 (pp) REVERT: J 464 ARG cc_start: 0.9672 (mtt-85) cc_final: 0.9321 (mmm-85) REVERT: K 481 LEU cc_start: 0.9468 (pp) cc_final: 0.8810 (tt) REVERT: K 485 GLU cc_start: 0.9639 (pt0) cc_final: 0.9325 (pt0) outliers start: 58 outliers final: 47 residues processed: 239 average time/residue: 0.2545 time to fit residues: 79.3124 Evaluate side-chains 224 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 471 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 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 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 455 LYS 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 459 ARG Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain H residue 494 THR 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 J residue 471 VAL Chi-restraints excluded: chain J residue 488 LEU 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 K residue 488 LEU Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 484 ASN 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 82 optimal weight: 6.9990 chunk 70 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 73 optimal weight: 40.0000 chunk 81 optimal weight: 30.0000 chunk 43 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 40.0000 chunk 58 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 GLN ** 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 = 0.3389 r_free = 0.3389 target = 0.057355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.051577 restraints weight = 88064.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.052532 restraints weight = 42796.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.053034 restraints weight = 25352.883| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 1.0096 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= 0.157 Angle : 1.046 15.627 11448 Z= 0.512 Chirality : 0.050 0.440 1296 Planarity : 0.003 0.025 1524 Dihedral : 5.102 36.441 1128 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 5.27 % Allowed : 28.48 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1020 helix: 0.29 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.47 (0.36), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS I 458 PHE 0.008 0.001 PHE A 453 TYR 0.005 0.001 TYR C 527 ARG 0.004 0.001 ARG F 464 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 577) hydrogen bonds : angle 4.86291 ( 1731) covalent geometry : bond 0.00329 ( 8544) covalent geometry : angle 1.04586 (11448) *********************** 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: 50 poor density : 187 time to evaluate : 1.247 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: A 475 LEU cc_start: 0.9894 (OUTLIER) cc_final: 0.9673 (tp) REVERT: A 476 GLN cc_start: 0.9153 (tp40) cc_final: 0.8814 (tp40) REVERT: A 492 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8045 (mp0) REVERT: B 517 LEU cc_start: 0.9927 (tp) cc_final: 0.9720 (pp) REVERT: D 474 ASP cc_start: 0.9613 (m-30) cc_final: 0.9377 (m-30) REVERT: G 474 ASP cc_start: 0.9549 (m-30) cc_final: 0.9346 (m-30) REVERT: H 517 LEU cc_start: 0.9922 (tp) cc_final: 0.9692 (pp) REVERT: I 485 GLU cc_start: 0.9739 (pt0) cc_final: 0.9527 (pm20) outliers start: 50 outliers final: 47 residues processed: 226 average time/residue: 0.2599 time to fit residues: 75.8627 Evaluate side-chains 219 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 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 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 455 LYS Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 485 GLU 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 479 GLU Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain H residue 494 THR 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 J residue 459 ARG Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain J residue 488 LEU Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 484 ASN 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 38 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 42 optimal weight: 0.0170 chunk 22 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 chunk 25 optimal weight: 50.0000 chunk 28 optimal weight: 9.9990 chunk 84 optimal weight: 50.0000 chunk 46 optimal weight: 30.0000 overall best weight: 5.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** 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 = 0.3397 r_free = 0.3397 target = 0.057675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.051824 restraints weight = 86903.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.052758 restraints weight = 42536.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.053314 restraints weight = 24990.878| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 1.0305 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= 0.164 Angle : 1.099 16.115 11448 Z= 0.544 Chirality : 0.053 0.444 1296 Planarity : 0.004 0.045 1524 Dihedral : 5.134 31.868 1128 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.43 % Allowed : 29.85 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1020 helix: 0.21 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.42 (0.38), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS I 458 PHE 0.008 0.001 PHE B 453 TYR 0.005 0.001 TYR C 527 ARG 0.005 0.001 ARG C 524 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 577) hydrogen bonds : angle 4.84228 ( 1731) covalent geometry : bond 0.00342 ( 8544) covalent geometry : angle 1.09888 (11448) ********************** 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 232 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 1.109 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: A 475 LEU cc_start: 0.9899 (OUTLIER) cc_final: 0.9676 (tp) REVERT: A 476 GLN cc_start: 0.9206 (tp40) cc_final: 0.8856 (tp40) REVERT: A 492 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8073 (mp0) REVERT: A 502 LEU cc_start: 0.9381 (mt) cc_final: 0.9031 (pp) REVERT: B 517 LEU cc_start: 0.9929 (tp) cc_final: 0.9726 (pp) REVERT: D 474 ASP cc_start: 0.9633 (m-30) cc_final: 0.9392 (m-30) REVERT: E 485 GLU cc_start: 0.9717 (pt0) cc_final: 0.8960 (tp30) REVERT: E 487 GLU cc_start: 0.9456 (mt-10) cc_final: 0.9244 (pt0) REVERT: E 505 MET cc_start: 0.9231 (mpp) cc_final: 0.8709 (pmm) REVERT: G 474 ASP cc_start: 0.9547 (m-30) cc_final: 0.9343 (m-30) REVERT: G 485 GLU cc_start: 0.9706 (pt0) cc_final: 0.9471 (pm20) REVERT: H 517 LEU cc_start: 0.9926 (tp) cc_final: 0.9701 (pp) REVERT: I 489 VAL cc_start: 0.9712 (p) cc_final: 0.9502 (p) REVERT: K 481 LEU cc_start: 0.9456 (pp) cc_final: 0.9158 (tt) outliers start: 42 outliers final: 38 residues processed: 222 average time/residue: 0.2322 time to fit residues: 68.3565 Evaluate side-chains 212 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 480 VAL 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 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 471 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 485 GLU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain H residue 494 THR 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 J residue 471 VAL Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 484 ASN 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 23 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 64 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 1 optimal weight: 50.0000 chunk 76 optimal weight: 8.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 491 GLN ** K 499 ASN ** 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 = 0.3376 r_free = 0.3376 target = 0.056814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.050967 restraints weight = 89241.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.051902 restraints weight = 43347.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.052458 restraints weight = 25509.831| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 1.0539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8544 Z= 0.171 Angle : 1.137 16.246 11448 Z= 0.562 Chirality : 0.051 0.439 1296 Planarity : 0.004 0.031 1524 Dihedral : 5.239 33.390 1128 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.64 % Allowed : 30.70 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.26), residues: 1020 helix: 0.13 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.41 (0.40), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS I 458 PHE 0.009 0.001 PHE A 453 TYR 0.004 0.001 TYR C 527 ARG 0.005 0.001 ARG B 524 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 577) hydrogen bonds : angle 4.96508 ( 1731) covalent geometry : bond 0.00357 ( 8544) covalent geometry : angle 1.13746 (11448) =============================================================================== Job complete usr+sys time: 2885.23 seconds wall clock time: 51 minutes 26.19 seconds (3086.19 seconds total)