Starting phenix.real_space_refine (version: dev) on Sat May 14 05:13:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/05_2022/6k9f_9948.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/05_2022/6k9f_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_9948/05_2022/6k9f_9948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/05_2022/6k9f_9948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/05_2022/6k9f_9948.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/05_2022/6k9f_9948.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "I PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 4.99, per 1000 atoms: 0.59 Number of scatterers: 8484 At special positions: 0 Unit cell: (97.9, 96.8, 103.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1704 8.00 N 1512 7.00 C 5244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.2 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 0 sheets defined 95.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 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: 2.09 Time building geometry restraints manager: 3.51 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: 100.41 - 106.60: 72 106.60 - 112.79: 4602 112.79 - 118.98: 2470 118.98 - 125.18: 4280 125.18 - 131.37: 24 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 2.520 nonbonded pdb=" O GLU E 500 " pdb=" OG SER E 504 " model vdw 2.379 2.440 nonbonded pdb=" O GLU L 500 " pdb=" OG SER L 504 " model vdw 2.425 2.440 nonbonded pdb=" O PHE E 518 " pdb=" OG SER E 522 " model vdw 2.450 2.440 nonbonded pdb=" O GLU B 500 " pdb=" OG SER B 504 " model vdw 2.455 2.440 ... (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 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 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. 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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.000 Extract box with map and model: 1.130 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 24.670 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 % 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 *********************** 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 : 1.314 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 outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.3070 time to fit residues: 203.4085 Evaluate side-chains 260 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5295 ------------------------------------------------------------------------------- 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: 6.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 60.0000 chunk 24 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 50.0000 chunk 87 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 HIS ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN I 458 HIS I 462 GLN ** L 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 535 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8544 Z= 0.225 Angle : 0.871 12.725 11448 Z= 0.420 Chirality : 0.046 0.248 1296 Planarity : 0.004 0.032 1524 Dihedral : 4.440 20.831 1128 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 25.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 4.85 % 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: 0.58 (0.25), residues: 1020 helix: 0.82 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.30 (0.26), residues: 96 *********************** 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 355 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 309 time to evaluate : 0.969 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 outliers start: 46 outliers final: 29 residues processed: 339 average time/residue: 0.2588 time to fit residues: 111.3401 Evaluate side-chains 247 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.0993 time to fit residues: 6.3719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 8.9990 chunk 27 optimal weight: 40.0000 chunk 72 optimal weight: 8.9990 chunk 59 optimal weight: 40.0000 chunk 24 optimal weight: 30.0000 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 458 HIS ** G 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 476 GLN H 458 HIS H 476 GLN I 476 GLN K 458 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.8072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8544 Z= 0.206 Angle : 0.852 12.824 11448 Z= 0.422 Chirality : 0.040 0.184 1296 Planarity : 0.003 0.031 1524 Dihedral : 4.590 23.201 1128 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer Outliers : 4.01 % 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: 0.55 (0.25), residues: 1020 helix: 0.78 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.13 (0.28), residues: 96 *********************** 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 274 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 1.142 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 outliers start: 38 outliers final: 18 residues processed: 261 average time/residue: 0.2462 time to fit residues: 83.1173 Evaluate side-chains 217 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1750 time to fit residues: 5.7346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 40.0000 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 40.0000 chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN D 499 ASN ** G 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.8873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8544 Z= 0.209 Angle : 0.869 13.705 11448 Z= 0.423 Chirality : 0.040 0.247 1296 Planarity : 0.003 0.027 1524 Dihedral : 4.564 25.266 1128 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 4.32 % 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: 0.35 (0.26), residues: 1020 helix: 0.65 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.18 (0.28), residues: 96 *********************** 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 268 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 227 time to evaluate : 1.185 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 outliers start: 41 outliers final: 20 residues processed: 242 average time/residue: 0.2245 time to fit residues: 71.5644 Evaluate side-chains 201 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 181 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1537 time to fit residues: 5.8271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 64 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 47 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 23 optimal weight: 50.0000 chunk 31 optimal weight: 20.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 535 GLN K 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.9480 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= 0.224 Angle : 0.878 14.357 11448 Z= 0.436 Chirality : 0.042 0.254 1296 Planarity : 0.003 0.025 1524 Dihedral : 4.725 25.603 1128 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 25.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 3.16 % 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: 0.04 (0.25), residues: 1020 helix: 0.38 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.86 (0.27), residues: 84 *********************** 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 225 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 1.033 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 outliers start: 30 outliers final: 17 residues processed: 216 average time/residue: 0.2295 time to fit residues: 65.4561 Evaluate side-chains 185 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1616 time to fit residues: 5.2607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 50.0000 chunk 18 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN L 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.9910 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= 0.194 Angle : 0.897 13.601 11448 Z= 0.437 Chirality : 0.041 0.302 1296 Planarity : 0.003 0.034 1524 Dihedral : 4.643 24.277 1128 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 2.32 % 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: 0.06 (0.26), residues: 1020 helix: 0.41 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.05 (0.28), residues: 84 *********************** 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 230 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 208 time to evaluate : 1.001 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 outliers start: 22 outliers final: 16 residues processed: 223 average time/residue: 0.2101 time to fit residues: 62.9049 Evaluate side-chains 191 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0838 time to fit residues: 3.8492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 50.0000 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 40.0000 chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 30.0000 chunk 42 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 1.0241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8544 Z= 0.196 Angle : 0.942 13.914 11448 Z= 0.453 Chirality : 0.043 0.372 1296 Planarity : 0.003 0.031 1524 Dihedral : 4.766 21.800 1128 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1020 helix: 0.31 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.01 (0.32), residues: 84 *********************** 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 213 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 1.104 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 outliers start: 15 outliers final: 7 residues processed: 206 average time/residue: 0.2217 time to fit residues: 60.8222 Evaluate side-chains 183 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1508 time to fit residues: 3.1327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 58 optimal weight: 40.0000 chunk 63 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 60.0000 chunk 72 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 457 ASN J 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 1.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8544 Z= 0.209 Angle : 0.957 15.834 11448 Z= 0.466 Chirality : 0.046 0.405 1296 Planarity : 0.003 0.034 1524 Dihedral : 4.895 23.762 1128 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.23 (0.26), residues: 1020 helix: 0.22 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.11 (0.35), residues: 84 *********************** 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 201 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 1.178 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 outliers start: 10 outliers final: 7 residues processed: 195 average time/residue: 0.2245 time to fit residues: 58.0418 Evaluate side-chains 178 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 171 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0848 time to fit residues: 2.5393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 50.0000 chunk 77 optimal weight: 8.9990 chunk 81 optimal weight: 40.0000 chunk 85 optimal weight: 8.9990 chunk 56 optimal weight: 50.0000 chunk 91 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 1.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8544 Z= 0.208 Angle : 0.974 17.305 11448 Z= 0.476 Chirality : 0.047 0.347 1296 Planarity : 0.003 0.029 1524 Dihedral : 4.918 24.616 1128 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 27.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1020 helix: 0.17 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.18 (0.36), residues: 84 *********************** 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 195 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 1.207 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 outliers start: 9 outliers final: 4 residues processed: 191 average time/residue: 0.2211 time to fit residues: 56.6743 Evaluate side-chains 168 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0854 time to fit residues: 2.1168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 7 optimal weight: 0.0670 chunk 58 optimal weight: 40.0000 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 HIS ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 1.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8544 Z= 0.211 Angle : 1.074 20.051 11448 Z= 0.509 Chirality : 0.051 0.438 1296 Planarity : 0.003 0.025 1524 Dihedral : 5.011 26.302 1128 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 0.42 % 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: -0.33 (0.26), residues: 1020 helix: 0.15 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.17 (0.36), residues: 84 ********************** 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 196 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 194 average time/residue: 0.2150 time to fit residues: 55.6821 Evaluate side-chains 167 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0800 time to fit residues: 1.5996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 76 optimal weight: 50.0000 chunk 31 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 0.0050 chunk 14 optimal weight: 7.9990 chunk 66 optimal weight: 0.0870 chunk 4 optimal weight: 8.9990 overall best weight: 4.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 ASN K 536 ASN ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.054969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.049552 restraints weight = 89019.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.050476 restraints weight = 43123.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.051030 restraints weight = 25407.208| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 1.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 8544 Z= 0.226 Angle : 1.073 16.870 11448 Z= 0.521 Chirality : 0.050 0.442 1296 Planarity : 0.003 0.032 1524 Dihedral : 5.012 26.647 1128 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 26.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 0.53 % 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: -0.41 (0.26), residues: 1020 helix: 0.10 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.14 (0.38), residues: 84 =============================================================================== Job complete usr+sys time: 1802.24 seconds wall clock time: 33 minutes 37.94 seconds (2017.94 seconds total)