Starting phenix.real_space_refine on Fri Sep 27 08:31:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/09_2024/6k9f_9948.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/09_2024/6k9f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/09_2024/6k9f_9948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/09_2024/6k9f_9948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/09_2024/6k9f_9948.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/09_2024/6k9f_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.17, per 1000 atoms: 0.61 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: 2.41 Conformation dependent library (CDL) restraints added in 965.3 milliseconds 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: 0.99 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: 2.14 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3012 1.34 - 1.46: 628 1.46 - 1.57: 4856 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 8544 Sorted by residual: bond pdb=" C ASP J 525 " pdb=" O ASP J 525 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.75e-01 bond pdb=" C ASP K 525 " pdb=" O ASP K 525 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.35e-01 bond pdb=" CB LYS H 508 " pdb=" CG LYS H 508 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.37e-01 bond pdb=" CB LYS G 508 " pdb=" CG LYS G 508 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.10e-01 bond pdb=" C ASP B 525 " pdb=" O ASP B 525 " ideal model delta sigma weight residual 1.248 1.239 0.010 1.26e-02 6.30e+03 5.98e-01 ... (remaining 8539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 10529 0.75 - 1.49: 743 1.49 - 2.24: 131 2.24 - 2.99: 29 2.99 - 3.73: 16 Bond angle restraints: 11448 Sorted by residual: angle pdb=" CA LYS K 508 " pdb=" CB LYS K 508 " pdb=" CG LYS K 508 " ideal model delta sigma weight residual 114.10 117.48 -3.38 2.00e+00 2.50e-01 2.86e+00 angle pdb=" CA LYS B 508 " pdb=" CB LYS B 508 " pdb=" CG LYS B 508 " ideal model delta sigma weight residual 114.10 117.43 -3.33 2.00e+00 2.50e-01 2.77e+00 angle pdb=" CA LYS I 508 " pdb=" CB LYS I 508 " pdb=" CG LYS I 508 " ideal model delta sigma weight residual 114.10 117.36 -3.26 2.00e+00 2.50e-01 2.65e+00 angle pdb=" CB LYS H 508 " pdb=" CG LYS H 508 " pdb=" CD LYS H 508 " ideal model delta sigma weight residual 111.30 115.03 -3.73 2.30e+00 1.89e-01 2.63e+00 angle pdb=" CA LYS J 508 " pdb=" CB LYS J 508 " pdb=" CG LYS J 508 " ideal model delta sigma weight residual 114.10 117.30 -3.20 2.00e+00 2.50e-01 2.55e+00 ... (remaining 11443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.66: 4792 11.66 - 23.32: 416 23.32 - 34.98: 107 34.98 - 46.64: 73 46.64 - 58.30: 36 Dihedral angle restraints: 5424 sinusoidal: 2352 harmonic: 3072 Sorted by residual: dihedral pdb=" CA ALA I 463 " pdb=" C ALA I 463 " pdb=" N ARG I 464 " pdb=" CA ARG I 464 " ideal model delta harmonic sigma weight residual -180.00 -163.35 -16.65 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ALA H 463 " pdb=" C ALA H 463 " pdb=" N ARG H 464 " pdb=" CA ARG H 464 " ideal model delta harmonic sigma weight residual 180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ALA L 463 " pdb=" C ALA L 463 " pdb=" N ARG L 464 " pdb=" CA ARG L 464 " ideal model delta harmonic sigma weight residual -180.00 -163.75 -16.25 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 5421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.019: 704 0.019 - 0.039: 358 0.039 - 0.058: 140 0.058 - 0.077: 69 0.077 - 0.096: 25 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA GLU K 479 " pdb=" N GLU K 479 " pdb=" C GLU K 479 " pdb=" CB GLU K 479 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.32e-01 chirality pdb=" CA PRO H 526 " pdb=" N PRO H 526 " pdb=" C PRO H 526 " pdb=" CB PRO H 526 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.16e-01 chirality pdb=" CA PRO I 526 " pdb=" N PRO I 526 " pdb=" C PRO I 526 " pdb=" CB PRO I 526 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.14e-01 ... (remaining 1293 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 527 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C TYR A 527 " 0.020 2.00e-02 2.50e+03 pdb=" O TYR A 527 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU A 528 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR J 527 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" C TYR J 527 " -0.019 2.00e-02 2.50e+03 pdb=" O TYR J 527 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU J 528 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 527 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.23e+00 pdb=" C TYR H 527 " -0.019 2.00e-02 2.50e+03 pdb=" O TYR H 527 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU H 528 " 0.007 2.00e-02 2.50e+03 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 2776 2.86 - 3.37: 8644 3.37 - 3.88: 13602 3.88 - 4.39: 16015 4.39 - 4.90: 26417 Nonbonded interactions: 67454 Sorted by model distance: nonbonded pdb=" NE2 GLN H 476 " pdb=" OE1 GLU H 483 " model vdw 2.356 3.120 nonbonded pdb=" O GLU E 500 " pdb=" OG SER E 504 " model vdw 2.379 3.040 nonbonded pdb=" O GLU L 500 " pdb=" OG SER L 504 " model vdw 2.425 3.040 nonbonded pdb=" O PHE E 518 " pdb=" OG SER E 522 " model vdw 2.450 3.040 nonbonded pdb=" O GLU B 500 " pdb=" OG SER B 504 " model vdw 2.455 3.040 ... (remaining 67449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.810 Find NCS groups from input model: 0.330 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- 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= 0.136 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 544 time to evaluate : 1.097 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: 0.3280 time to fit residues: 216.6112 Evaluate side-chains 285 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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= 0.235 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 *********************** 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 fitting. rotamer outliers: 45 poor density : 326 time to evaluate : 1.172 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: 0.9009 (tp) cc_final: 0.8663 (tp) REVERT: B 461 LEU cc_start: 0.9622 (mt) cc_final: 0.9412 (mt) REVERT: B 462 GLN cc_start: 0.9420 (tt0) cc_final: 0.9090 (tp40) REVERT: B 464 ARG cc_start: 0.8543 (mtt-85) cc_final: 0.8282 (tpt170) REVERT: B 465 MET cc_start: 0.8527 (mtm) cc_final: 0.7975 (mtm) REVERT: B 485 GLU cc_start: 0.9761 (mt-10) cc_final: 0.9550 (pt0) REVERT: B 524 ARG cc_start: 0.9756 (tpm170) cc_final: 0.9497 (mmm160) REVERT: C 462 GLN cc_start: 0.9542 (tt0) cc_final: 0.9275 (tp40) REVERT: C 486 LYS cc_start: 0.9560 (ttpt) cc_final: 0.9311 (ttmt) REVERT: F 486 LYS cc_start: 0.9563 (ttpt) cc_final: 0.9172 (ttmt) REVERT: F 524 ARG cc_start: 0.9589 (tpm170) cc_final: 0.9346 (mmm160) REVERT: G 461 LEU cc_start: 0.9675 (mt) cc_final: 0.9475 (mt) REVERT: G 465 MET cc_start: 0.9241 (mtm) cc_final: 0.8822 (mtm) REVERT: G 486 LYS cc_start: 0.9562 (ttpt) cc_final: 0.9143 (ttmt) REVERT: G 492 GLU cc_start: 0.9656 (mm-30) cc_final: 0.9228 (mp0) REVERT: H 486 LYS cc_start: 0.9473 (ttpt) cc_final: 0.9013 (ttmt) REVERT: H 492 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8937 (mt-10) REVERT: I 462 GLN cc_start: 0.9480 (tt0) cc_final: 0.9159 (tp40) REVERT: I 465 MET cc_start: 0.8705 (mtp) cc_final: 0.8300 (mtm) REVERT: I 485 GLU cc_start: 0.9805 (mt-10) cc_final: 0.9596 (pt0) REVERT: I 492 GLU cc_start: 0.9686 (mm-30) cc_final: 0.9374 (mp0) REVERT: J 465 MET cc_start: 0.9021 (mtp) cc_final: 0.8360 (mtp) REVERT: K 465 MET cc_start: 0.8753 (mtp) cc_final: 0.8368 (mtp) REVERT: L 464 ARG cc_start: 0.8806 (mtt-85) cc_final: 0.8173 (tpt170) REVERT: L 517 LEU cc_start: 0.9856 (tp) cc_final: 0.9501 (pp) outliers start: 45 outliers final: 31 residues processed: 357 average time/residue: 0.2786 time to fit residues: 123.9998 Evaluate side-chains 270 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 239 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 48 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 72 optimal weight: 50.0000 chunk 59 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 476 GLN F 458 HIS F 462 GLN G 476 GLN H 458 HIS H 476 GLN I 476 GLN J 460 GLN L 462 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.7478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8544 Z= 0.196 Angle : 0.857 14.606 11448 Z= 0.409 Chirality : 0.042 0.236 1296 Planarity : 0.003 0.036 1524 Dihedral : 4.365 21.258 1128 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 6.86 % Allowed : 20.04 % Favored : 73.10 % 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: 0.84 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.44 (0.25), 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 0.008 0.001 ARG B 533 *********************** 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 325 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 260 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.9178 (mtp) cc_final: 0.8599 (mtm) REVERT: A 502 LEU cc_start: 0.9396 (mt) cc_final: 0.9075 (pp) REVERT: B 464 ARG cc_start: 0.8767 (mtt-85) cc_final: 0.8496 (tpt170) REVERT: B 481 LEU cc_start: 0.9337 (pp) cc_final: 0.8979 (pp) REVERT: B 486 LYS cc_start: 0.9718 (ttpt) cc_final: 0.9442 (ttmt) REVERT: C 486 LYS cc_start: 0.9658 (ttpt) cc_final: 0.9396 (ttmt) REVERT: D 461 LEU cc_start: 0.9886 (mt) cc_final: 0.9414 (mt) REVERT: F 462 GLN cc_start: 0.9515 (OUTLIER) cc_final: 0.9044 (tp40) REVERT: F 486 LYS cc_start: 0.9662 (ttpt) cc_final: 0.9365 (tttt) REVERT: F 524 ARG cc_start: 0.9617 (tpm170) cc_final: 0.9388 (mmm160) REVERT: H 517 LEU cc_start: 0.9952 (tp) cc_final: 0.9725 (pp) REVERT: I 462 GLN cc_start: 0.9597 (tt0) cc_final: 0.9234 (tp40) REVERT: I 492 GLU cc_start: 0.9651 (mm-30) cc_final: 0.9407 (mp0) REVERT: K 481 LEU cc_start: 0.9476 (pp) cc_final: 0.9245 (tt) REVERT: K 485 GLU cc_start: 0.9686 (mt-10) cc_final: 0.9466 (mt-10) REVERT: K 486 LYS cc_start: 0.9743 (ttpt) cc_final: 0.9344 (ttmt) REVERT: L 524 ARG cc_start: 0.9656 (tpm170) cc_final: 0.9361 (mtp180) outliers start: 65 outliers final: 42 residues processed: 299 average time/residue: 0.2896 time to fit residues: 108.1921 Evaluate side-chains 245 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 202 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 471 VAL 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 459 ARG 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 G residue 471 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain 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 484 ASN 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 K residue 492 GLU 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 86 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 58 optimal weight: 40.0000 chunk 87 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 50.0000 chunk 25 optimal weight: 40.0000 chunk 77 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN D 499 ASN E 458 HIS ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 534 GLN L 462 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.8539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8544 Z= 0.193 Angle : 0.907 13.327 11448 Z= 0.432 Chirality : 0.044 0.296 1296 Planarity : 0.004 0.042 1524 Dihedral : 4.511 21.916 1128 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 7.17 % Allowed : 21.94 % Favored : 70.89 % 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: 0.37 (0.25), residues: 1020 helix: 0.70 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.50 (0.25), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 458 PHE 0.007 0.001 PHE K 453 TYR 0.009 0.001 TYR J 527 ARG 0.008 0.001 ARG G 533 *********************** 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 302 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 234 time to evaluate : 1.074 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: B 492 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9070 (mt-10) REVERT: D 492 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9214 (mt-10) REVERT: E 481 LEU cc_start: 0.9614 (pp) cc_final: 0.9322 (tt) REVERT: F 486 LYS cc_start: 0.9721 (ttpt) cc_final: 0.9495 (mtpp) REVERT: F 489 VAL cc_start: 0.9738 (t) cc_final: 0.9501 (p) REVERT: F 517 LEU cc_start: 0.9848 (tp) cc_final: 0.9470 (pp) REVERT: F 524 ARG cc_start: 0.9639 (tpm170) cc_final: 0.9350 (mmm160) REVERT: G 517 LEU cc_start: 0.9927 (tp) cc_final: 0.9681 (pp) REVERT: G 531 TYR cc_start: 0.9845 (t80) cc_final: 0.9598 (t80) REVERT: H 517 LEU cc_start: 0.9953 (tp) cc_final: 0.9714 (pp) REVERT: I 492 GLU cc_start: 0.9613 (mm-30) cc_final: 0.9372 (mp0) REVERT: L 462 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8810 (tp40) outliers start: 68 outliers final: 45 residues processed: 272 average time/residue: 0.2522 time to fit residues: 88.1654 Evaluate side-chains 244 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 198 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 468 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 459 ARG 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 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 488 LEU 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 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain L residue 462 GLN 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 52 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 64 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 47 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 476 GLN C 476 GLN F 462 GLN J 458 HIS ** L 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.9049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8544 Z= 0.197 Angle : 0.903 12.076 11448 Z= 0.441 Chirality : 0.044 0.285 1296 Planarity : 0.004 0.026 1524 Dihedral : 4.600 21.462 1128 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 6.33 % Allowed : 24.58 % Favored : 69.09 % 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: 0.16 (0.26), residues: 1020 helix: 0.49 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.19 (0.29), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS I 458 PHE 0.007 0.001 PHE G 453 TYR 0.009 0.001 TYR G 531 ARG 0.005 0.001 ARG L 533 *********************** 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 276 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 216 time to evaluate : 1.202 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: A 465 MET cc_start: 0.9166 (mtt) cc_final: 0.8741 (ptp) REVERT: A 476 GLN cc_start: 0.9475 (tp40) cc_final: 0.9247 (mm110) REVERT: D 492 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9087 (mt-10) REVERT: E 481 LEU cc_start: 0.9659 (pp) cc_final: 0.9424 (tt) REVERT: F 462 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.9222 (tp40) REVERT: F 486 LYS cc_start: 0.9836 (ttpt) cc_final: 0.9553 (mtpp) REVERT: H 517 LEU cc_start: 0.9954 (tp) cc_final: 0.9721 (pp) REVERT: H 532 LEU cc_start: 0.9759 (pp) cc_final: 0.9506 (mm) REVERT: I 492 GLU cc_start: 0.9658 (mm-30) cc_final: 0.9441 (mp0) REVERT: J 467 ASP cc_start: 0.8590 (t0) cc_final: 0.8342 (t0) REVERT: K 492 GLU cc_start: 0.9656 (mm-30) cc_final: 0.9398 (mt-10) outliers start: 60 outliers final: 47 residues processed: 257 average time/residue: 0.2541 time to fit residues: 84.3956 Evaluate side-chains 239 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 191 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 468 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 459 ARG 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 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 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 481 LEU Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain 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 83 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 77 optimal weight: 40.0000 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 0.2980 chunk 89 optimal weight: 9.9990 overall best weight: 7.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 462 GLN ** L 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.9409 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= 0.195 Angle : 0.934 13.978 11448 Z= 0.458 Chirality : 0.047 0.328 1296 Planarity : 0.003 0.037 1524 Dihedral : 4.627 20.765 1128 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 6.01 % Allowed : 25.32 % Favored : 68.67 % 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: 0.20 (0.26), residues: 1020 helix: 0.52 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.34 (0.34), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS I 458 PHE 0.007 0.001 PHE G 453 TYR 0.005 0.001 TYR H 531 ARG 0.004 0.001 ARG G 533 *********************** 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 272 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 215 time to evaluate : 1.105 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: A 475 LEU cc_start: 0.9927 (OUTLIER) cc_final: 0.9650 (tp) REVERT: F 486 LYS cc_start: 0.9853 (ttpt) cc_final: 0.9565 (mtpp) REVERT: H 517 LEU cc_start: 0.9953 (tp) cc_final: 0.9717 (pp) REVERT: J 467 ASP cc_start: 0.8516 (t0) cc_final: 0.8260 (t0) REVERT: K 485 GLU cc_start: 0.9738 (mt-10) cc_final: 0.9533 (pt0) outliers start: 57 outliers final: 50 residues processed: 257 average time/residue: 0.2481 time to fit residues: 82.2523 Evaluate side-chains 237 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 186 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 468 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 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 459 ARG Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 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 459 ARG Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 484 ASN 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 471 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 453 PHE 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 529 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 56 optimal weight: 40.0000 chunk 42 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.9711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8544 Z= 0.207 Angle : 0.959 14.721 11448 Z= 0.473 Chirality : 0.046 0.315 1296 Planarity : 0.004 0.047 1524 Dihedral : 4.770 21.203 1128 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 6.43 % Allowed : 26.48 % Favored : 67.09 % 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: -0.01 (0.26), residues: 1020 helix: 0.39 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.43 (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 D 453 TYR 0.008 0.001 TYR D 531 ARG 0.005 0.001 ARG F 464 *********************** 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 256 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 195 time to evaluate : 1.140 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: A 475 LEU cc_start: 0.9930 (OUTLIER) cc_final: 0.9694 (tp) REVERT: F 486 LYS cc_start: 0.9863 (ttpt) cc_final: 0.9647 (mtpp) REVERT: F 489 VAL cc_start: 0.9698 (m) cc_final: 0.9496 (p) REVERT: G 517 LEU cc_start: 0.9924 (tp) cc_final: 0.9659 (pp) REVERT: H 517 LEU cc_start: 0.9955 (tp) cc_final: 0.9720 (pp) outliers start: 61 outliers final: 51 residues processed: 244 average time/residue: 0.2461 time to fit residues: 77.8271 Evaluate side-chains 228 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 176 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 502 LEU Chi-restraints excluded: chain C residue 529 VAL 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 502 LEU Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 484 ASN 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 J residue 453 PHE 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 471 VAL 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 27 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 60.0000 chunk 72 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 462 GLN ** L 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.9883 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= 0.196 Angle : 1.038 14.693 11448 Z= 0.504 Chirality : 0.051 0.436 1296 Planarity : 0.003 0.020 1524 Dihedral : 4.760 22.927 1128 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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 : 0.00 % 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: -0.02 (0.26), residues: 1020 helix: 0.38 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.42 (0.40), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS I 458 PHE 0.007 0.001 PHE B 453 TYR 0.005 0.000 TYR H 531 ARG 0.004 0.001 ARG A 524 *********************** 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 248 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 206 time to evaluate : 1.078 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: A 475 LEU cc_start: 0.9931 (OUTLIER) cc_final: 0.9680 (tp) REVERT: C 471 VAL cc_start: 0.9775 (t) cc_final: 0.9496 (p) REVERT: F 462 GLN cc_start: 0.9483 (OUTLIER) cc_final: 0.9231 (tp40) REVERT: F 486 LYS cc_start: 0.9862 (ttpt) cc_final: 0.9626 (mtpp) REVERT: F 524 ARG cc_start: 0.9693 (tpm170) cc_final: 0.9376 (mtp180) REVERT: H 517 LEU cc_start: 0.9950 (tp) cc_final: 0.9711 (pp) outliers start: 42 outliers final: 34 residues processed: 240 average time/residue: 0.2178 time to fit residues: 69.5350 Evaluate side-chains 217 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 468 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 453 PHE 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 475 LEU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 484 ASN 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 475 LEU Chi-restraints excluded: chain G residue 484 ASN Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain H residue 484 ASN 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 J residue 453 PHE 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 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 86 optimal weight: 30.0000 chunk 88 optimal weight: 6.9990 chunk 51 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 56 optimal weight: 50.0000 chunk 91 optimal weight: 40.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 462 GLN ** I 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 1.0184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8544 Z= 0.223 Angle : 1.068 15.306 11448 Z= 0.527 Chirality : 0.050 0.354 1296 Planarity : 0.004 0.042 1524 Dihedral : 4.931 24.828 1128 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 5.06 % Allowed : 30.49 % Favored : 64.45 % 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: -0.19 (0.26), residues: 1020 helix: 0.27 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.49 (0.39), 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 0.009 0.001 ARG K 495 *********************** 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 236 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 188 time to evaluate : 1.084 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: C 471 VAL cc_start: 0.9800 (t) cc_final: 0.9534 (p) REVERT: D 492 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9133 (mp0) REVERT: F 462 GLN cc_start: 0.9488 (OUTLIER) cc_final: 0.9054 (tp40) REVERT: F 486 LYS cc_start: 0.9861 (ttpt) cc_final: 0.9612 (mtpp) REVERT: F 524 ARG cc_start: 0.9695 (tpm170) cc_final: 0.9373 (mtp180) REVERT: G 517 LEU cc_start: 0.9926 (tp) cc_final: 0.9686 (pp) REVERT: H 517 LEU cc_start: 0.9955 (tp) cc_final: 0.9723 (pp) outliers start: 48 outliers final: 41 residues processed: 225 average time/residue: 0.2279 time to fit residues: 67.8876 Evaluate side-chains 211 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 481 LEU 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 502 LEU Chi-restraints excluded: chain C residue 529 VAL 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 471 VAL Chi-restraints excluded: chain E residue 484 ASN 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 G residue 459 ARG Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 484 ASN 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 I residue 453 PHE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 459 ARG Chi-restraints excluded: chain L residue 471 VAL 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 55 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 58 optimal weight: 40.0000 chunk 46 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 491 GLN F 462 GLN ** I 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 1.0295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8544 Z= 0.227 Angle : 1.142 17.346 11448 Z= 0.557 Chirality : 0.051 0.360 1296 Planarity : 0.004 0.050 1524 Dihedral : 4.967 27.245 1128 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.01 % Allowed : 31.96 % Favored : 64.03 % 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: -0.22 (0.27), residues: 1020 helix: 0.25 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.46 (0.40), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS I 458 PHE 0.007 0.001 PHE A 453 TYR 0.005 0.001 TYR G 527 ARG 0.007 0.001 ARG K 495 ********************** 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 228 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 1.111 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: C 471 VAL cc_start: 0.9795 (t) cc_final: 0.9520 (p) REVERT: D 492 GLU cc_start: 0.9576 (mm-30) cc_final: 0.8637 (mp0) REVERT: D 493 LYS cc_start: 0.9723 (mmtm) cc_final: 0.9380 (tmtt) REVERT: F 462 GLN cc_start: 0.9487 (OUTLIER) cc_final: 0.9190 (tp40) REVERT: G 492 GLU cc_start: 0.9573 (mm-30) cc_final: 0.9302 (mp0) REVERT: G 517 LEU cc_start: 0.9924 (tp) cc_final: 0.9676 (pp) REVERT: H 517 LEU cc_start: 0.9952 (tp) cc_final: 0.9719 (pp) REVERT: K 503 LEU cc_start: 0.9610 (mt) cc_final: 0.9407 (mt) outliers start: 38 outliers final: 33 residues processed: 218 average time/residue: 0.2099 time to fit residues: 61.6030 Evaluate side-chains 204 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain C residue 453 PHE 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 471 VAL Chi-restraints excluded: chain E residue 484 ASN 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 G residue 459 ARG Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 484 ASN Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 471 VAL 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: 6.9990 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 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 458 HIS ** I 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.056406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.050668 restraints weight = 87315.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.051592 restraints weight = 42747.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.052158 restraints weight = 25132.320| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 1.0578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8544 Z= 0.233 Angle : 1.136 15.706 11448 Z= 0.561 Chirality : 0.051 0.363 1296 Planarity : 0.004 0.042 1524 Dihedral : 5.080 27.862 1128 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.54 % Allowed : 32.17 % Favored : 63.29 % 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: -0.24 (0.27), residues: 1020 helix: 0.24 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -3.47 (0.41), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS I 458 PHE 0.007 0.001 PHE B 453 TYR 0.007 0.001 TYR C 531 ARG 0.006 0.001 ARG K 495 =============================================================================== Job complete usr+sys time: 2080.46 seconds wall clock time: 37 minutes 38.97 seconds (2258.97 seconds total)