Starting phenix.real_space_refine on Wed Feb 4 14:56:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yka_73043/02_2026/9yka_73043.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yka_73043/02_2026/9yka_73043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yka_73043/02_2026/9yka_73043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yka_73043/02_2026/9yka_73043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yka_73043/02_2026/9yka_73043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yka_73043/02_2026/9yka_73043.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7002 2.51 5 N 1908 2.21 5 O 2193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11157 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 993 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 801 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 993 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 801 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 993 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 801 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1897 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 3 Chain: "B" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1897 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 3 Chain: "C" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1897 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.29, per 1000 atoms: 0.21 Number of scatterers: 11157 At special positions: 0 Unit cell: (115.692, 118.491, 128.754, 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 54 16.00 O 2193 8.00 N 1908 7.00 C 7002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 528 " distance=2.02 Simple disulfide: pdb=" SG CYS A 551 " - pdb=" SG CYS A 588 " distance=2.05 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 528 " distance=2.02 Simple disulfide: pdb=" SG CYS B 551 " - pdb=" SG CYS B 588 " distance=2.05 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 528 " distance=2.02 Simple disulfide: pdb=" SG CYS C 551 " - pdb=" SG CYS C 588 " distance=2.05 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 563 " " NAG A 802 " - " ASN A 629 " " NAG B 801 " - " ASN B 563 " " NAG B 802 " - " ASN B 629 " " NAG C 801 " - " ASN C 563 " " NAG C 802 " - " ASN C 629 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 385.3 milliseconds 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 39 sheets defined 16.6% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 100G through 100K removed outlier: 3.527A pdb=" N HIS F 100J" --> pdb=" O ASN F 100G" (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.761A pdb=" N VAL G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100G through 100K removed outlier: 3.609A pdb=" N HIS H 100J" --> pdb=" O ASN H 100G" (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR H 100K" --> pdb=" O GLY H 100H" (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 100G through 100K' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.761A pdb=" N VAL I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 100G through 100K removed outlier: 3.706A pdb=" N HIS D 100J" --> pdb=" O ASN D 100G" (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 100K" --> pdb=" O GLY D 100H" (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100G through 100K' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.761A pdb=" N VAL E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 501 removed outlier: 3.907A pdb=" N GLN A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 511 removed outlier: 3.843A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'B' and resid 456 through 501 removed outlier: 3.908A pdb=" N GLN B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 511 removed outlier: 3.843A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'C' and resid 456 through 501 removed outlier: 3.908A pdb=" N GLN C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 511 removed outlier: 3.843A pdb=" N VAL C 505 " --> pdb=" O ASN C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 619 No H-bonds generated for 'chain 'C' and resid 617 through 619' Processing sheet with id=AA1, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'F' and resid 56 through 59 removed outlier: 5.076A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 56 through 59 removed outlier: 5.076A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 100 through 100A Processing sheet with id=AA5, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.656A pdb=" N VAL G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.656A pdb=" N VAL G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 56 through 59 removed outlier: 5.118A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 56 through 59 removed outlier: 5.118A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 100 through 100A Processing sheet with id=AB3, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.555A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.823A pdb=" N SER I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'D' and resid 56 through 59 removed outlier: 5.219A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 56 through 59 removed outlier: 5.219A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 100A Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.582A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.805A pdb=" N SER E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'A' and resid 515 through 519 removed outlier: 7.206A pdb=" N LEU A 59 " --> pdb=" O ALA C 620 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU C 622 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG A 61 " --> pdb=" O LEU C 622 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AC7, first strand: chain 'A' and resid 537 through 538 Processing sheet with id=AC8, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AC9, first strand: chain 'A' and resid 593 through 598 removed outlier: 6.187A pdb=" N ILE A 602 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N THR A 613 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 604 " --> pdb=" O PHE A 611 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 620 through 622 removed outlier: 3.938A pdb=" N ALA A 620 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AD3, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AD4, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AD5, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AD6, first strand: chain 'B' and resid 593 through 598 removed outlier: 6.185A pdb=" N ILE B 602 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N THR B 613 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 604 " --> pdb=" O PHE B 611 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 620 through 622 removed outlier: 3.923A pdb=" N ALA B 620 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AD9, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AE1, first strand: chain 'C' and resid 537 through 538 Processing sheet with id=AE2, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AE3, first strand: chain 'C' and resid 593 through 598 removed outlier: 6.187A pdb=" N ILE C 602 " --> pdb=" O THR C 613 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR C 613 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 604 " --> pdb=" O PHE C 611 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2453 1.33 - 1.45: 2600 1.45 - 1.57: 6245 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 11379 Sorted by residual: bond pdb=" CA SER B 526 " pdb=" CB SER B 526 " ideal model delta sigma weight residual 1.534 1.478 0.056 1.45e-02 4.76e+03 1.49e+01 bond pdb=" CA SER A 526 " pdb=" CB SER A 526 " ideal model delta sigma weight residual 1.534 1.479 0.056 1.45e-02 4.76e+03 1.48e+01 bond pdb=" CA SER C 526 " pdb=" CB SER C 526 " ideal model delta sigma weight residual 1.534 1.479 0.056 1.45e-02 4.76e+03 1.48e+01 bond pdb=" N VAL A 529 " pdb=" CA VAL A 529 " ideal model delta sigma weight residual 1.460 1.489 -0.029 7.60e-03 1.73e+04 1.42e+01 bond pdb=" N VAL C 529 " pdb=" CA VAL C 529 " ideal model delta sigma weight residual 1.460 1.488 -0.028 7.60e-03 1.73e+04 1.39e+01 ... (remaining 11374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 10186 1.37 - 2.74: 4339 2.74 - 4.11: 832 4.11 - 5.47: 61 5.47 - 6.84: 2 Bond angle restraints: 15420 Sorted by residual: angle pdb=" CA GLY D 106 " pdb=" C GLY D 106 " pdb=" O GLY D 106 " ideal model delta sigma weight residual 121.77 118.37 3.40 8.60e-01 1.35e+00 1.57e+01 angle pdb=" CA GLY F 106 " pdb=" C GLY F 106 " pdb=" O GLY F 106 " ideal model delta sigma weight residual 121.77 118.38 3.39 8.60e-01 1.35e+00 1.56e+01 angle pdb=" N GLN A 490 " pdb=" CA GLN A 490 " pdb=" C GLN A 490 " ideal model delta sigma weight residual 112.54 107.81 4.73 1.22e+00 6.72e-01 1.50e+01 angle pdb=" N LEU A 628 " pdb=" CA LEU A 628 " pdb=" C LEU A 628 " ideal model delta sigma weight residual 113.28 108.63 4.65 1.22e+00 6.72e-01 1.45e+01 angle pdb=" CA ILE B 562 " pdb=" C ILE B 562 " pdb=" O ILE B 562 " ideal model delta sigma weight residual 121.41 117.46 3.95 1.04e+00 9.25e-01 1.44e+01 ... (remaining 15415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6233 17.96 - 35.91: 482 35.91 - 53.86: 38 53.86 - 71.82: 93 71.82 - 89.77: 3 Dihedral angle restraints: 6849 sinusoidal: 2739 harmonic: 4110 Sorted by residual: dihedral pdb=" CB CYS C 551 " pdb=" SG CYS C 551 " pdb=" SG CYS C 588 " pdb=" CB CYS C 588 " ideal model delta sinusoidal sigma weight residual -86.00 -175.77 89.77 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS A 551 " pdb=" SG CYS A 551 " pdb=" SG CYS A 588 " pdb=" CB CYS A 588 " ideal model delta sinusoidal sigma weight residual -86.00 -175.77 89.77 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS B 551 " pdb=" SG CYS B 551 " pdb=" SG CYS B 588 " pdb=" CB CYS B 588 " ideal model delta sinusoidal sigma weight residual -86.00 -175.76 89.76 1 1.00e+01 1.00e-02 9.56e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 805 0.074 - 0.148: 722 0.148 - 0.223: 226 0.223 - 0.297: 6 0.297 - 0.371: 2 Chirality restraints: 1761 Sorted by residual: chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 629 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" C1 NAG C 802 " pdb=" ND2 ASN C 629 " pdb=" C2 NAG C 802 " pdb=" O5 NAG C 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 629 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1758 not shown) Planarity restraints: 1977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " 0.095 2.00e-02 2.50e+03 7.90e-02 7.79e+01 pdb=" C7 NAG A 802 " -0.023 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " 0.070 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " -0.129 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 801 " 0.086 2.00e-02 2.50e+03 7.12e-02 6.34e+01 pdb=" C7 NAG C 801 " -0.025 2.00e-02 2.50e+03 pdb=" C8 NAG C 801 " 0.066 2.00e-02 2.50e+03 pdb=" N2 NAG C 801 " -0.113 2.00e-02 2.50e+03 pdb=" O7 NAG C 801 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 42 " 0.639 9.50e-02 1.11e+02 2.87e-01 5.01e+01 pdb=" NE ARG G 42 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG G 42 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG G 42 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG G 42 " 0.020 2.00e-02 2.50e+03 ... (remaining 1974 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4120 2.87 - 3.38: 10012 3.38 - 3.88: 20168 3.88 - 4.39: 22825 4.39 - 4.90: 38166 Nonbonded interactions: 95291 Sorted by model distance: nonbonded pdb=" OG SER C 627 " pdb=" OD1 ASN C 629 " model vdw 2.361 3.040 nonbonded pdb=" OG SER A 627 " pdb=" OD1 ASN A 629 " model vdw 2.387 3.040 nonbonded pdb=" O ARG C 495 " pdb=" OG1 THR C 498 " model vdw 2.403 3.040 nonbonded pdb=" O ARG A 495 " pdb=" OG1 THR A 498 " model vdw 2.403 3.040 nonbonded pdb=" O ARG B 495 " pdb=" OG1 THR B 498 " model vdw 2.403 3.040 ... (remaining 95286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.420 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.013 0.056 11397 Z= 0.959 Angle : 1.443 6.842 15462 Z= 1.099 Chirality : 0.098 0.371 1761 Planarity : 0.022 0.287 1971 Dihedral : 14.080 67.588 4167 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 7.64 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.21), residues: 1395 helix: 0.11 (0.39), residues: 153 sheet: -0.58 (0.23), residues: 462 loop : -1.08 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG H 94 TYR 0.024 0.002 TYR G 49 PHE 0.011 0.002 PHE D 63 TRP 0.011 0.003 TRP E 35 HIS 0.008 0.002 HIS H 100I Details of bonding type rmsd covalent geometry : bond 0.01270 (11379) covalent geometry : angle 1.44127 (15420) SS BOND : bond 0.01175 ( 12) SS BOND : angle 2.36375 ( 24) hydrogen bonds : bond 0.19724 ( 472) hydrogen bonds : angle 8.08529 ( 1299) link_NAG-ASN : bond 0.00428 ( 6) link_NAG-ASN : angle 1.66669 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 460 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 22 CYS cc_start: 0.8117 (t) cc_final: 0.7722 (t) REVERT: F 100 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8382 (mtm) REVERT: F 110 THR cc_start: 0.9050 (m) cc_final: 0.8771 (p) REVERT: G 89 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8594 (tm-30) REVERT: H 67 LEU cc_start: 0.9033 (tp) cc_final: 0.8819 (tm) REVERT: H 85 GLU cc_start: 0.8473 (mp0) cc_final: 0.8216 (mp0) REVERT: H 110 THR cc_start: 0.9068 (m) cc_final: 0.8834 (p) REVERT: I 72 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8593 (m) REVERT: D 77 THR cc_start: 0.8955 (m) cc_final: 0.8608 (p) REVERT: D 85 GLU cc_start: 0.8583 (mp0) cc_final: 0.8209 (pm20) REVERT: D 95 ASP cc_start: 0.8454 (m-30) cc_final: 0.8131 (m-30) REVERT: D 101 ASP cc_start: 0.7937 (p0) cc_final: 0.7631 (p0) REVERT: A 79 GLU cc_start: 0.6353 (tm-30) cc_final: 0.6134 (tm-30) REVERT: A 471 GLN cc_start: 0.8717 (mt0) cc_final: 0.8332 (mt0) REVERT: A 535 THR cc_start: 0.8631 (m) cc_final: 0.8399 (p) REVERT: A 593 GLN cc_start: 0.8370 (tt0) cc_final: 0.8162 (tt0) REVERT: A 628 LEU cc_start: 0.8484 (tp) cc_final: 0.8246 (tt) REVERT: B 471 GLN cc_start: 0.8600 (mt0) cc_final: 0.8182 (mt0) REVERT: B 569 GLU cc_start: 0.8316 (tt0) cc_final: 0.8048 (tt0) REVERT: C 52 GLU cc_start: 0.8219 (pt0) cc_final: 0.7992 (pt0) REVERT: C 471 GLN cc_start: 0.8588 (mt0) cc_final: 0.8169 (mt0) REVERT: C 487 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8135 (mm-40) REVERT: C 521 ASP cc_start: 0.8260 (m-30) cc_final: 0.7974 (m-30) REVERT: C 623 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7941 (mm-40) outliers start: 8 outliers final: 4 residues processed: 462 average time/residue: 0.5558 time to fit residues: 276.1348 Evaluate side-chains 359 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 353 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain A residue 551 CYS Chi-restraints excluded: chain B residue 551 CYS Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 551 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN F 6 GLN G 38 GLN I 6 GLN I 38 GLN I 89 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN A 576 ASN A 635 ASN ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN B 576 ASN B 623 GLN B 635 ASN ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.086685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.077511 restraints weight = 20048.186| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.05 r_work: 0.2944 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11397 Z= 0.162 Angle : 0.558 8.407 15462 Z= 0.303 Chirality : 0.044 0.198 1761 Planarity : 0.005 0.047 1971 Dihedral : 5.163 55.928 1671 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.17 % Allowed : 17.64 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1395 helix: 2.10 (0.36), residues: 156 sheet: 0.20 (0.24), residues: 447 loop : -0.80 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 94 TYR 0.011 0.002 TYR G 49 PHE 0.011 0.002 PHE C 638 TRP 0.014 0.001 TRP D 50 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00368 (11379) covalent geometry : angle 0.55456 (15420) SS BOND : bond 0.00986 ( 12) SS BOND : angle 1.06923 ( 24) hydrogen bonds : bond 0.04813 ( 472) hydrogen bonds : angle 5.35090 ( 1299) link_NAG-ASN : bond 0.00535 ( 6) link_NAG-ASN : angle 1.47750 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 310 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8798 (tt0) cc_final: 0.8560 (tt0) REVERT: G 38 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8833 (tt0) REVERT: H 46 GLU cc_start: 0.8795 (tt0) cc_final: 0.8545 (tt0) REVERT: H 75 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8701 (p) REVERT: H 85 GLU cc_start: 0.8637 (mp0) cc_final: 0.8287 (mp0) REVERT: H 110 THR cc_start: 0.9146 (m) cc_final: 0.8937 (p) REVERT: I 72 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8694 (m) REVERT: D 55 ASP cc_start: 0.8656 (t70) cc_final: 0.8417 (t70) REVERT: D 64 GLN cc_start: 0.8248 (tp40) cc_final: 0.7953 (tp-100) REVERT: D 75 THR cc_start: 0.9240 (m) cc_final: 0.9023 (p) REVERT: D 85 GLU cc_start: 0.8669 (mp0) cc_final: 0.8413 (mp0) REVERT: D 110 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8922 (p) REVERT: A 58 ASP cc_start: 0.8500 (m-30) cc_final: 0.8293 (m-30) REVERT: A 79 GLU cc_start: 0.6585 (tm-30) cc_final: 0.6375 (tm-30) REVERT: A 319 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7678 (p) REVERT: A 466 ASP cc_start: 0.8517 (m-30) cc_final: 0.8283 (m-30) REVERT: A 486 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: A 539 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7948 (mmm-85) REVERT: A 569 GLU cc_start: 0.8488 (tt0) cc_final: 0.8183 (tp30) REVERT: B 486 GLU cc_start: 0.7971 (tp30) cc_final: 0.7704 (tp30) REVERT: B 583 LYS cc_start: 0.9123 (pttm) cc_final: 0.8840 (pttt) REVERT: B 594 TYR cc_start: 0.8758 (m-10) cc_final: 0.8267 (m-10) REVERT: C 486 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: C 518 ARG cc_start: 0.8742 (mtp85) cc_final: 0.8510 (mtp85) REVERT: C 521 ASP cc_start: 0.8513 (m-30) cc_final: 0.8080 (m-30) REVERT: C 594 TYR cc_start: 0.8731 (m-10) cc_final: 0.8484 (m-10) outliers start: 39 outliers final: 16 residues processed: 330 average time/residue: 0.5806 time to fit residues: 205.7943 Evaluate side-chains 305 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 282 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 GLN Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 551 CYS Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 551 CYS Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 551 CYS Chi-restraints excluded: chain C residue 558 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.0010 chunk 100 optimal weight: 2.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN H 6 GLN I 38 GLN I 89 GLN D 100JHIS ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 GLN A 593 GLN ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN C 606 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.081940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.072693 restraints weight = 20161.496| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.08 r_work: 0.2887 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11397 Z= 0.222 Angle : 0.558 7.713 15462 Z= 0.301 Chirality : 0.046 0.198 1761 Planarity : 0.005 0.043 1971 Dihedral : 5.203 53.639 1666 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.23 % Allowed : 20.16 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.22), residues: 1395 helix: 2.47 (0.36), residues: 153 sheet: 0.11 (0.24), residues: 483 loop : -0.90 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 103 TYR 0.013 0.002 TYR G 49 PHE 0.013 0.002 PHE A 561 TRP 0.013 0.001 TRP D 50 HIS 0.004 0.001 HIS D 100I Details of bonding type rmsd covalent geometry : bond 0.00526 (11379) covalent geometry : angle 0.55227 (15420) SS BOND : bond 0.00553 ( 12) SS BOND : angle 1.48253 ( 24) hydrogen bonds : bond 0.04511 ( 472) hydrogen bonds : angle 4.90521 ( 1299) link_NAG-ASN : bond 0.00316 ( 6) link_NAG-ASN : angle 1.67972 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 286 time to evaluate : 0.437 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: F 46 GLU cc_start: 0.8801 (tt0) cc_final: 0.8485 (tt0) REVERT: F 87 THR cc_start: 0.9011 (t) cc_final: 0.8723 (p) REVERT: H 46 GLU cc_start: 0.8801 (tt0) cc_final: 0.8588 (tt0) REVERT: H 75 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8832 (p) REVERT: H 85 GLU cc_start: 0.8671 (mp0) cc_final: 0.8319 (mp0) REVERT: H 110 THR cc_start: 0.9288 (m) cc_final: 0.9012 (t) REVERT: I 74 THR cc_start: 0.9133 (p) cc_final: 0.8932 (m) REVERT: D 55 ASP cc_start: 0.8859 (t70) cc_final: 0.8616 (t70) REVERT: D 64 GLN cc_start: 0.8395 (tp40) cc_final: 0.8103 (tp-100) REVERT: D 85 GLU cc_start: 0.8699 (mp0) cc_final: 0.8457 (mp0) REVERT: D 107 THR cc_start: 0.8966 (m) cc_final: 0.8732 (m) REVERT: A 319 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7940 (p) REVERT: A 466 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8426 (m-30) REVERT: A 486 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: A 528 CYS cc_start: 0.7022 (m) cc_final: 0.6576 (m) REVERT: A 537 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8875 (p) REVERT: A 543 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.7873 (mtp180) REVERT: A 569 GLU cc_start: 0.8571 (tt0) cc_final: 0.8287 (tp30) REVERT: A 583 LYS cc_start: 0.9132 (pttm) cc_final: 0.8911 (pttt) REVERT: B 539 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.7904 (mmm-85) REVERT: B 554 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.6736 (mtm180) REVERT: B 583 LYS cc_start: 0.9186 (pttm) cc_final: 0.8877 (pttt) REVERT: B 636 ILE cc_start: 0.9177 (mt) cc_final: 0.8959 (mp) REVERT: C 309 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7908 (p) REVERT: C 486 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: C 521 ASP cc_start: 0.8557 (m-30) cc_final: 0.8160 (m-30) REVERT: C 583 LYS cc_start: 0.9177 (pttt) cc_final: 0.8977 (pttt) REVERT: C 586 GLU cc_start: 0.8501 (pt0) cc_final: 0.8276 (pt0) outliers start: 52 outliers final: 25 residues processed: 314 average time/residue: 0.5966 time to fit residues: 200.7352 Evaluate side-chains 304 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 551 CYS Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 551 CYS Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 551 CYS Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 116 optimal weight: 0.0020 chunk 70 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN G 38 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN D 100GASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN C 532 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.081877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.072576 restraints weight = 20676.725| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.20 r_work: 0.2886 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11397 Z= 0.135 Angle : 0.498 6.071 15462 Z= 0.269 Chirality : 0.044 0.192 1761 Planarity : 0.004 0.046 1971 Dihedral : 5.070 53.524 1665 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 3.58 % Allowed : 21.38 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.22), residues: 1395 helix: 2.73 (0.36), residues: 153 sheet: 0.29 (0.24), residues: 483 loop : -0.76 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 103 TYR 0.012 0.001 TYR I 49 PHE 0.012 0.001 PHE B 463 TRP 0.010 0.001 TRP D 50 HIS 0.002 0.000 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00310 (11379) covalent geometry : angle 0.49387 (15420) SS BOND : bond 0.00499 ( 12) SS BOND : angle 1.32070 ( 24) hydrogen bonds : bond 0.03893 ( 472) hydrogen bonds : angle 4.53288 ( 1299) link_NAG-ASN : bond 0.00376 ( 6) link_NAG-ASN : angle 1.45552 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8849 (tt0) cc_final: 0.8566 (tt0) REVERT: F 87 THR cc_start: 0.8957 (t) cc_final: 0.8710 (p) REVERT: H 46 GLU cc_start: 0.8832 (tt0) cc_final: 0.8582 (tt0) REVERT: H 75 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8785 (p) REVERT: H 85 GLU cc_start: 0.8675 (mp0) cc_final: 0.8337 (mp0) REVERT: H 110 THR cc_start: 0.9260 (m) cc_final: 0.8915 (p) REVERT: I 48 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8728 (mm) REVERT: I 78 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8304 (tt) REVERT: I 79 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8392 (mm110) REVERT: D 55 ASP cc_start: 0.8823 (t70) cc_final: 0.8584 (t70) REVERT: D 64 GLN cc_start: 0.8425 (tp40) cc_final: 0.8118 (tp-100) REVERT: D 85 GLU cc_start: 0.8717 (mp0) cc_final: 0.8485 (mp0) REVERT: D 107 THR cc_start: 0.9017 (m) cc_final: 0.8801 (m) REVERT: A 63 SER cc_start: 0.9129 (t) cc_final: 0.8685 (p) REVERT: A 486 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7850 (tp30) REVERT: A 528 CYS cc_start: 0.7009 (m) cc_final: 0.6577 (m) REVERT: A 583 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8836 (pttt) REVERT: B 539 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8240 (mmm-85) REVERT: B 569 GLU cc_start: 0.8545 (tt0) cc_final: 0.8268 (tp30) REVERT: B 583 LYS cc_start: 0.9161 (pttm) cc_final: 0.8885 (pttt) REVERT: C 486 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7895 (mm-30) REVERT: C 521 ASP cc_start: 0.8549 (m-30) cc_final: 0.8136 (m-30) REVERT: C 583 LYS cc_start: 0.9121 (pttt) cc_final: 0.8844 (ptmt) outliers start: 44 outliers final: 20 residues processed: 293 average time/residue: 0.5455 time to fit residues: 172.1086 Evaluate side-chains 304 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 551 CYS Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 551 CYS Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN I 89 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.078342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.069216 restraints weight = 20776.155| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.08 r_work: 0.2825 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 11397 Z= 0.323 Angle : 0.610 6.760 15462 Z= 0.325 Chirality : 0.047 0.221 1761 Planarity : 0.005 0.054 1971 Dihedral : 5.509 53.570 1664 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.80 % Allowed : 19.59 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.22), residues: 1395 helix: 2.62 (0.36), residues: 153 sheet: 0.19 (0.22), residues: 513 loop : -0.84 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 474 TYR 0.015 0.002 TYR G 49 PHE 0.012 0.002 PHE A 561 TRP 0.015 0.002 TRP H 50 HIS 0.005 0.001 HIS D 100I Details of bonding type rmsd covalent geometry : bond 0.00764 (11379) covalent geometry : angle 0.60256 (15420) SS BOND : bond 0.00676 ( 12) SS BOND : angle 1.79977 ( 24) hydrogen bonds : bond 0.04445 ( 472) hydrogen bonds : angle 4.82560 ( 1299) link_NAG-ASN : bond 0.00260 ( 6) link_NAG-ASN : angle 1.97601 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 283 time to evaluate : 0.327 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: F 46 GLU cc_start: 0.8805 (tt0) cc_final: 0.8505 (tt0) REVERT: F 87 THR cc_start: 0.9036 (t) cc_final: 0.8746 (p) REVERT: G 18 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8439 (ptm160) REVERT: H 46 GLU cc_start: 0.8866 (tt0) cc_final: 0.8624 (tt0) REVERT: H 75 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8954 (p) REVERT: H 85 GLU cc_start: 0.8675 (mp0) cc_final: 0.8365 (mp0) REVERT: D 64 GLN cc_start: 0.8493 (tp40) cc_final: 0.8211 (tp-100) REVERT: D 81 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: D 85 GLU cc_start: 0.8717 (mp0) cc_final: 0.8485 (mp0) REVERT: D 107 THR cc_start: 0.9061 (m) cc_final: 0.8855 (m) REVERT: E 31 ASP cc_start: 0.8364 (t0) cc_final: 0.8137 (t70) REVERT: A 63 SER cc_start: 0.9185 (t) cc_final: 0.8813 (p) REVERT: A 486 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7853 (tp30) REVERT: A 528 CYS cc_start: 0.7155 (m) cc_final: 0.6736 (m) REVERT: A 543 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.8106 (mtp180) REVERT: A 569 GLU cc_start: 0.8438 (tp30) cc_final: 0.8208 (tp30) REVERT: A 583 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8924 (pttt) REVERT: B 583 LYS cc_start: 0.9277 (pttm) cc_final: 0.8965 (pttt) REVERT: C 309 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8177 (p) REVERT: C 465 TYR cc_start: 0.8909 (t80) cc_final: 0.8544 (t80) REVERT: C 486 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7954 (tp30) REVERT: C 499 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8782 (mtmt) REVERT: C 583 LYS cc_start: 0.9179 (pttt) cc_final: 0.8952 (pttt) outliers start: 59 outliers final: 36 residues processed: 308 average time/residue: 0.5456 time to fit residues: 180.9036 Evaluate side-chains 319 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 274 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 GLN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 551 CYS Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 551 CYS Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 38 optimal weight: 0.7980 chunk 132 optimal weight: 0.0970 chunk 40 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 576 ASN A 606 ASN ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 606 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.080468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.071088 restraints weight = 20609.133| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.19 r_work: 0.2855 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11397 Z= 0.147 Angle : 0.513 5.756 15462 Z= 0.275 Chirality : 0.044 0.204 1761 Planarity : 0.005 0.052 1971 Dihedral : 5.172 52.997 1664 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.98 % Allowed : 21.71 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.22), residues: 1395 helix: 3.16 (0.36), residues: 144 sheet: 0.33 (0.23), residues: 513 loop : -0.71 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 103 TYR 0.013 0.001 TYR I 49 PHE 0.012 0.001 PHE B 463 TRP 0.011 0.001 TRP H 50 HIS 0.001 0.000 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00343 (11379) covalent geometry : angle 0.50833 (15420) SS BOND : bond 0.00507 ( 12) SS BOND : angle 1.30596 ( 24) hydrogen bonds : bond 0.03857 ( 472) hydrogen bonds : angle 4.52633 ( 1299) link_NAG-ASN : bond 0.00379 ( 6) link_NAG-ASN : angle 1.61781 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 282 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8859 (tt0) cc_final: 0.8548 (tt0) REVERT: F 87 THR cc_start: 0.8990 (t) cc_final: 0.8734 (p) REVERT: G 18 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8375 (ptm160) REVERT: H 46 GLU cc_start: 0.8813 (tt0) cc_final: 0.8570 (tt0) REVERT: H 75 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8886 (p) REVERT: H 85 GLU cc_start: 0.8682 (mp0) cc_final: 0.8360 (mp0) REVERT: I 78 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8284 (tt) REVERT: I 79 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8394 (mm110) REVERT: D 55 ASP cc_start: 0.8839 (t70) cc_final: 0.8590 (t70) REVERT: D 64 GLN cc_start: 0.8446 (tp40) cc_final: 0.8192 (tp-100) REVERT: D 85 GLU cc_start: 0.8740 (mp0) cc_final: 0.8512 (mp0) REVERT: D 107 THR cc_start: 0.9023 (m) cc_final: 0.8803 (m) REVERT: A 63 SER cc_start: 0.9173 (t) cc_final: 0.8805 (p) REVERT: A 486 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7804 (tp30) REVERT: A 528 CYS cc_start: 0.7096 (m) cc_final: 0.6658 (m) REVERT: A 548 GLU cc_start: 0.8133 (mp0) cc_final: 0.7779 (mp0) REVERT: A 583 LYS cc_start: 0.9172 (pttm) cc_final: 0.8902 (pttt) REVERT: B 309 THR cc_start: 0.8360 (p) cc_final: 0.8156 (p) REVERT: B 486 GLU cc_start: 0.8120 (tp30) cc_final: 0.7802 (mm-30) REVERT: B 539 ARG cc_start: 0.8560 (mmm-85) cc_final: 0.8334 (mmm-85) REVERT: B 554 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8924 (mtp-110) REVERT: B 569 GLU cc_start: 0.8539 (tt0) cc_final: 0.8273 (tp30) REVERT: B 583 LYS cc_start: 0.9191 (pttm) cc_final: 0.8877 (ptmt) REVERT: C 309 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8212 (p) REVERT: C 465 TYR cc_start: 0.8896 (t80) cc_final: 0.8643 (t80) REVERT: C 486 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: C 586 GLU cc_start: 0.8487 (pt0) cc_final: 0.8284 (pt0) outliers start: 49 outliers final: 20 residues processed: 304 average time/residue: 0.5416 time to fit residues: 177.1861 Evaluate side-chains 292 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 551 CYS Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 551 CYS Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 137 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 121 optimal weight: 0.0010 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 576 ASN ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.080516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.071432 restraints weight = 20639.853| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.08 r_work: 0.2866 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11397 Z= 0.143 Angle : 0.515 5.898 15462 Z= 0.274 Chirality : 0.044 0.204 1761 Planarity : 0.004 0.051 1971 Dihedral : 5.071 53.140 1664 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.58 % Allowed : 22.60 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.22), residues: 1395 helix: 3.26 (0.36), residues: 144 sheet: 0.42 (0.23), residues: 513 loop : -0.62 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 103 TYR 0.014 0.001 TYR I 49 PHE 0.011 0.001 PHE B 463 TRP 0.011 0.001 TRP H 50 HIS 0.002 0.000 HIS F 100J Details of bonding type rmsd covalent geometry : bond 0.00333 (11379) covalent geometry : angle 0.51008 (15420) SS BOND : bond 0.00507 ( 12) SS BOND : angle 1.27918 ( 24) hydrogen bonds : bond 0.03766 ( 472) hydrogen bonds : angle 4.38544 ( 1299) link_NAG-ASN : bond 0.00333 ( 6) link_NAG-ASN : angle 1.67283 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8851 (tt0) cc_final: 0.8567 (tt0) REVERT: F 87 THR cc_start: 0.9006 (t) cc_final: 0.8749 (p) REVERT: G 18 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8398 (ptm160) REVERT: H 75 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8944 (p) REVERT: H 85 GLU cc_start: 0.8636 (mp0) cc_final: 0.8353 (mp0) REVERT: I 79 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8441 (mm110) REVERT: D 55 ASP cc_start: 0.8845 (t70) cc_final: 0.8614 (t70) REVERT: D 64 GLN cc_start: 0.8386 (tp40) cc_final: 0.8161 (tp-100) REVERT: D 107 THR cc_start: 0.8992 (m) cc_final: 0.8787 (m) REVERT: A 63 SER cc_start: 0.9166 (t) cc_final: 0.8802 (p) REVERT: A 486 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7774 (tp30) REVERT: A 528 CYS cc_start: 0.7117 (m) cc_final: 0.6697 (m) REVERT: A 539 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.8170 (mtp85) REVERT: A 548 GLU cc_start: 0.8124 (mp0) cc_final: 0.7779 (mp0) REVERT: A 583 LYS cc_start: 0.9171 (pttm) cc_final: 0.8900 (pttt) REVERT: B 309 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 554 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8977 (mtp-110) REVERT: B 569 GLU cc_start: 0.8518 (tt0) cc_final: 0.8281 (tp30) REVERT: B 583 LYS cc_start: 0.9189 (pttm) cc_final: 0.8864 (ptpt) REVERT: C 309 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8258 (p) REVERT: C 465 TYR cc_start: 0.8810 (t80) cc_final: 0.8562 (t80) REVERT: C 486 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7917 (tp30) REVERT: C 521 ASP cc_start: 0.8642 (m-30) cc_final: 0.8134 (m-30) REVERT: C 535 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8789 (p) REVERT: C 583 LYS cc_start: 0.9111 (ptmt) cc_final: 0.8885 (ptpt) outliers start: 44 outliers final: 21 residues processed: 287 average time/residue: 0.5607 time to fit residues: 173.2100 Evaluate side-chains 300 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 GLN Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 chunk 109 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.070800 restraints weight = 20646.497| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.08 r_work: 0.2856 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11397 Z= 0.176 Angle : 0.546 8.161 15462 Z= 0.289 Chirality : 0.044 0.208 1761 Planarity : 0.005 0.053 1971 Dihedral : 5.029 53.143 1662 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.82 % Allowed : 22.60 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1395 helix: 3.29 (0.36), residues: 144 sheet: 0.75 (0.23), residues: 483 loop : -0.53 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 103 TYR 0.020 0.002 TYR A 465 PHE 0.010 0.001 PHE B 463 TRP 0.010 0.001 TRP H 50 HIS 0.002 0.000 HIS D 100I Details of bonding type rmsd covalent geometry : bond 0.00413 (11379) covalent geometry : angle 0.53354 (15420) SS BOND : bond 0.00588 ( 12) SS BOND : angle 2.69576 ( 24) hydrogen bonds : bond 0.03838 ( 472) hydrogen bonds : angle 4.38877 ( 1299) link_NAG-ASN : bond 0.00313 ( 6) link_NAG-ASN : angle 1.69697 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8846 (tt0) cc_final: 0.8546 (tt0) REVERT: F 87 THR cc_start: 0.9014 (t) cc_final: 0.8746 (p) REVERT: G 18 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8382 (ptm160) REVERT: H 75 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8938 (p) REVERT: H 85 GLU cc_start: 0.8628 (mp0) cc_final: 0.8342 (mp0) REVERT: I 78 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8320 (tt) REVERT: I 79 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8455 (mm110) REVERT: D 55 ASP cc_start: 0.8830 (t70) cc_final: 0.8587 (t70) REVERT: D 64 GLN cc_start: 0.8400 (tp40) cc_final: 0.8170 (tp-100) REVERT: D 107 THR cc_start: 0.9014 (m) cc_final: 0.8806 (m) REVERT: A 63 SER cc_start: 0.9178 (t) cc_final: 0.8821 (p) REVERT: A 486 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: A 528 CYS cc_start: 0.7130 (m) cc_final: 0.6711 (m) REVERT: A 539 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.8190 (mtp85) REVERT: A 543 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.7873 (mtp180) REVERT: A 548 GLU cc_start: 0.8224 (mp0) cc_final: 0.7029 (mp0) REVERT: A 583 LYS cc_start: 0.9177 (pttm) cc_final: 0.8897 (pttt) REVERT: B 309 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8313 (p) REVERT: B 539 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8307 (mtp85) REVERT: B 554 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8975 (mtp-110) REVERT: B 583 LYS cc_start: 0.9196 (pttm) cc_final: 0.8868 (ptpt) REVERT: C 486 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7955 (tp30) REVERT: C 535 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8834 (p) outliers start: 47 outliers final: 27 residues processed: 292 average time/residue: 0.5332 time to fit residues: 167.5276 Evaluate side-chains 303 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 GLN Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 115 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.082999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.073777 restraints weight = 20832.762| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.09 r_work: 0.2820 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 11397 Z= 0.296 Angle : 0.613 6.579 15462 Z= 0.325 Chirality : 0.047 0.224 1761 Planarity : 0.005 0.054 1971 Dihedral : 5.332 53.319 1662 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.98 % Allowed : 22.20 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.22), residues: 1395 helix: 2.71 (0.37), residues: 156 sheet: 0.35 (0.23), residues: 516 loop : -0.67 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 474 TYR 0.021 0.002 TYR A 465 PHE 0.011 0.001 PHE A 561 TRP 0.011 0.002 TRP H 50 HIS 0.003 0.001 HIS D 100I Details of bonding type rmsd covalent geometry : bond 0.00699 (11379) covalent geometry : angle 0.60251 (15420) SS BOND : bond 0.00709 ( 12) SS BOND : angle 2.28693 ( 24) hydrogen bonds : bond 0.04296 ( 472) hydrogen bonds : angle 4.64223 ( 1299) link_NAG-ASN : bond 0.00349 ( 6) link_NAG-ASN : angle 2.14339 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8818 (tt0) cc_final: 0.8535 (tt0) REVERT: F 87 THR cc_start: 0.9050 (t) cc_final: 0.8762 (p) REVERT: G 18 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8387 (ptm160) REVERT: H 75 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8977 (p) REVERT: H 85 GLU cc_start: 0.8663 (mp0) cc_final: 0.8352 (mp0) REVERT: I 78 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8250 (tt) REVERT: I 79 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8484 (mm110) REVERT: D 64 GLN cc_start: 0.8484 (tp40) cc_final: 0.8237 (tp-100) REVERT: D 107 THR cc_start: 0.9049 (m) cc_final: 0.8845 (m) REVERT: E 31 ASP cc_start: 0.8398 (t0) cc_final: 0.8129 (t70) REVERT: A 63 SER cc_start: 0.9177 (t) cc_final: 0.8830 (p) REVERT: A 486 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7827 (tp30) REVERT: A 528 CYS cc_start: 0.7178 (m) cc_final: 0.6744 (m) REVERT: A 539 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.8266 (mtp85) REVERT: A 543 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.7848 (mtp180) REVERT: A 548 GLU cc_start: 0.8320 (mp0) cc_final: 0.7258 (mp0) REVERT: A 583 LYS cc_start: 0.9196 (pttm) cc_final: 0.8897 (pttt) REVERT: B 309 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8340 (p) REVERT: B 486 GLU cc_start: 0.8354 (tp30) cc_final: 0.8141 (tp30) REVERT: B 539 ARG cc_start: 0.8591 (mmm-85) cc_final: 0.8363 (mtp85) REVERT: B 554 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.6599 (mtm180) REVERT: B 583 LYS cc_start: 0.9272 (pttm) cc_final: 0.8977 (pttt) REVERT: C 486 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7941 (tp30) REVERT: C 521 ASP cc_start: 0.8604 (m-30) cc_final: 0.8233 (m-30) REVERT: C 535 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8869 (p) outliers start: 49 outliers final: 29 residues processed: 301 average time/residue: 0.5067 time to fit residues: 164.3033 Evaluate side-chains 314 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 GLN Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 74 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 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 = 0.3144 r_free = 0.3144 target = 0.085053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.075846 restraints weight = 20756.243| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.11 r_work: 0.2859 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11397 Z= 0.145 Angle : 0.548 7.036 15462 Z= 0.290 Chirality : 0.044 0.209 1761 Planarity : 0.005 0.053 1971 Dihedral : 5.064 53.206 1662 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.93 % Allowed : 23.66 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.22), residues: 1395 helix: 2.43 (0.37), residues: 165 sheet: 0.44 (0.23), residues: 513 loop : -0.53 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 103 TYR 0.020 0.001 TYR C 465 PHE 0.012 0.001 PHE B 463 TRP 0.010 0.001 TRP D 50 HIS 0.001 0.000 HIS D 100I Details of bonding type rmsd covalent geometry : bond 0.00336 (11379) covalent geometry : angle 0.53827 (15420) SS BOND : bond 0.00542 ( 12) SS BOND : angle 1.83018 ( 24) hydrogen bonds : bond 0.03856 ( 472) hydrogen bonds : angle 4.42312 ( 1299) link_NAG-ASN : bond 0.00501 ( 6) link_NAG-ASN : angle 2.20417 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8841 (tt0) cc_final: 0.8597 (tt0) REVERT: F 87 THR cc_start: 0.8993 (t) cc_final: 0.8740 (p) REVERT: G 18 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8401 (ptm160) REVERT: H 75 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8953 (p) REVERT: H 85 GLU cc_start: 0.8622 (mp0) cc_final: 0.8331 (mp0) REVERT: I 78 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8304 (tt) REVERT: I 79 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8444 (mm110) REVERT: D 55 ASP cc_start: 0.8837 (t70) cc_final: 0.8602 (t70) REVERT: D 64 GLN cc_start: 0.8451 (tp40) cc_final: 0.8224 (tp-100) REVERT: D 107 THR cc_start: 0.9009 (m) cc_final: 0.8794 (m) REVERT: A 63 SER cc_start: 0.9147 (t) cc_final: 0.8802 (p) REVERT: A 486 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7768 (tp30) REVERT: A 490 GLN cc_start: 0.8573 (mt0) cc_final: 0.8316 (mt0) REVERT: A 528 CYS cc_start: 0.7122 (m) cc_final: 0.6704 (m) REVERT: A 539 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.8210 (mtp85) REVERT: A 543 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.8854 (mtt-85) REVERT: A 548 GLU cc_start: 0.8300 (mp0) cc_final: 0.7884 (mp0) REVERT: A 583 LYS cc_start: 0.9137 (pttm) cc_final: 0.8863 (pttt) REVERT: B 309 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8368 (p) REVERT: B 553 SER cc_start: 0.8910 (t) cc_final: 0.8599 (m) REVERT: B 554 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8953 (mtp-110) REVERT: B 583 LYS cc_start: 0.9223 (pttm) cc_final: 0.8902 (ptpt) REVERT: C 486 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: C 521 ASP cc_start: 0.8672 (m-30) cc_final: 0.8168 (m-30) REVERT: C 535 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8882 (p) outliers start: 36 outliers final: 21 residues processed: 288 average time/residue: 0.5641 time to fit residues: 174.1091 Evaluate side-chains 293 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 GLN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 GLN A 527 GLN A 576 ASN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN C 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.079404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.070308 restraints weight = 20822.496| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.07 r_work: 0.2847 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11397 Z= 0.183 Angle : 0.571 7.426 15462 Z= 0.301 Chirality : 0.045 0.218 1761 Planarity : 0.005 0.067 1971 Dihedral : 5.165 53.112 1662 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.09 % Allowed : 23.58 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.22), residues: 1395 helix: 2.34 (0.37), residues: 165 sheet: 0.43 (0.23), residues: 513 loop : -0.55 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 62 TYR 0.017 0.002 TYR A 465 PHE 0.010 0.001 PHE B 463 TRP 0.011 0.001 TRP H 50 HIS 0.002 0.000 HIS D 100I Details of bonding type rmsd covalent geometry : bond 0.00429 (11379) covalent geometry : angle 0.56240 (15420) SS BOND : bond 0.00571 ( 12) SS BOND : angle 1.82620 ( 24) hydrogen bonds : bond 0.03935 ( 472) hydrogen bonds : angle 4.45653 ( 1299) link_NAG-ASN : bond 0.00287 ( 6) link_NAG-ASN : angle 2.10557 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4399.28 seconds wall clock time: 75 minutes 43.76 seconds (4543.76 seconds total)