Starting phenix.real_space_refine on Fri Feb 16 02:38:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/02_2024/6bze_7314.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/02_2024/6bze_7314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/02_2024/6bze_7314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/02_2024/6bze_7314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/02_2024/6bze_7314.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/02_2024/6bze_7314.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7072 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 4408 2.51 5 N 1296 2.21 5 O 1352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 11": "OE1" <-> "OE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "G GLU 11": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 30": "OE1" <-> "OE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7072 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "B" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "C" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "D" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "E" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "F" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "G" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "H" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Time building chain proxies: 4.32, per 1000 atoms: 0.61 Number of scatterers: 7072 At special positions: 0 Unit cell: (105.7, 105.7, 87.58, 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 16 16.00 O 1352 8.00 N 1296 7.00 C 4408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.5 seconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.778A pdb=" N VAL A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A 18 " --> pdb=" O THR A 14 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 38 through 44 removed outlier: 4.213A pdb=" N ARG A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.834A pdb=" N GLU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 73 removed outlier: 3.709A pdb=" N LEU A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.521A pdb=" N VAL A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 115 removed outlier: 3.568A pdb=" N LEU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 25 removed outlier: 3.691A pdb=" N VAL B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 38 through 44 removed outlier: 4.184A pdb=" N ARG B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 44 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.922A pdb=" N GLU B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 73 removed outlier: 3.927A pdb=" N LEU B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 95 through 115 removed outlier: 3.808A pdb=" N LEU B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 25 removed outlier: 3.634A pdb=" N VAL C 16 " --> pdb=" O ASP C 12 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 18 " --> pdb=" O THR C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.216A pdb=" N ARG C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 44 " --> pdb=" O HIS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 58 removed outlier: 3.844A pdb=" N GLU C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 removed outlier: 3.891A pdb=" N LEU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 removed outlier: 3.502A pdb=" N VAL C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 115 removed outlier: 3.649A pdb=" N LEU C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 25 removed outlier: 3.810A pdb=" N VAL D 16 " --> pdb=" O ASP D 12 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 38 through 44 removed outlier: 4.478A pdb=" N ARG D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS D 44 " --> pdb=" O HIS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 removed outlier: 3.530A pdb=" N GLU D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 75 removed outlier: 4.003A pdb=" N LEU D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN D 75 " --> pdb=" O TYR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 Processing helix chain 'D' and resid 95 through 115 removed outlier: 3.684A pdb=" N LEU D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 25 removed outlier: 3.736A pdb=" N VAL E 16 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 19 " --> pdb=" O GLU E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 38 Processing helix chain 'E' and resid 38 through 44 removed outlier: 4.343A pdb=" N ARG E 42 " --> pdb=" O PHE E 38 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS E 44 " --> pdb=" O HIS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 58 removed outlier: 3.862A pdb=" N GLU E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 72 removed outlier: 4.102A pdb=" N LEU E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 Processing helix chain 'E' and resid 95 through 115 removed outlier: 3.658A pdb=" N LEU E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 25 removed outlier: 3.650A pdb=" N VAL F 16 " --> pdb=" O ASP F 12 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 38 through 44 removed outlier: 4.390A pdb=" N ARG F 42 " --> pdb=" O PHE F 38 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 44 " --> pdb=" O HIS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.881A pdb=" N GLU F 53 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG F 58 " --> pdb=" O GLU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 4.089A pdb=" N LEU F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 87 Processing helix chain 'F' and resid 95 through 115 removed outlier: 3.702A pdb=" N LEU F 114 " --> pdb=" O LYS F 110 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.914A pdb=" N VAL G 16 " --> pdb=" O ASP G 12 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP G 19 " --> pdb=" O GLU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 38 Processing helix chain 'G' and resid 38 through 44 removed outlier: 4.369A pdb=" N ARG G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS G 44 " --> pdb=" O HIS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.820A pdb=" N GLU G 53 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 72 removed outlier: 4.103A pdb=" N LEU G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 87 Processing helix chain 'G' and resid 95 through 115 removed outlier: 3.580A pdb=" N LEU G 114 " --> pdb=" O LYS G 110 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 25 removed outlier: 3.699A pdb=" N VAL H 16 " --> pdb=" O ASP H 12 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 36 Processing helix chain 'H' and resid 38 through 44 removed outlier: 4.412A pdb=" N ARG H 42 " --> pdb=" O PHE H 38 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS H 44 " --> pdb=" O HIS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 58 removed outlier: 3.790A pdb=" N GLU H 53 " --> pdb=" O ARG H 49 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG H 58 " --> pdb=" O GLU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 72 removed outlier: 3.856A pdb=" N LEU H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 Processing helix chain 'H' and resid 95 through 115 removed outlier: 3.778A pdb=" N LEU H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 963 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: 1.67 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1247 1.28 - 1.41: 1457 1.41 - 1.54: 4361 1.54 - 1.68: 47 1.68 - 1.81: 16 Bond restraints: 7128 Sorted by residual: bond pdb=" C GLU B 74 " pdb=" O GLU B 74 " ideal model delta sigma weight residual 1.235 1.145 0.091 1.26e-02 6.30e+03 5.18e+01 bond pdb=" C GLU D 74 " pdb=" O GLU D 74 " ideal model delta sigma weight residual 1.235 1.151 0.084 1.26e-02 6.30e+03 4.49e+01 bond pdb=" C GLU A 74 " pdb=" O GLU A 74 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.26e-02 6.30e+03 3.46e+01 bond pdb=" C GLU C 74 " pdb=" O GLU C 74 " ideal model delta sigma weight residual 1.235 1.164 0.071 1.26e-02 6.30e+03 3.19e+01 bond pdb=" ND1 HIS G 40 " pdb=" CE1 HIS G 40 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.46e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 101.89 - 108.29: 242 108.29 - 114.69: 4360 114.69 - 121.09: 2852 121.09 - 127.49: 2040 127.49 - 133.89: 26 Bond angle restraints: 9520 Sorted by residual: angle pdb=" N THR F 100 " pdb=" CA THR F 100 " pdb=" C THR F 100 " ideal model delta sigma weight residual 111.36 101.89 9.47 1.09e+00 8.42e-01 7.55e+01 angle pdb=" N THR H 100 " pdb=" CA THR H 100 " pdb=" C THR H 100 " ideal model delta sigma weight residual 111.82 101.98 9.84 1.16e+00 7.43e-01 7.20e+01 angle pdb=" N THR G 100 " pdb=" CA THR G 100 " pdb=" C THR G 100 " ideal model delta sigma weight residual 111.36 102.22 9.14 1.09e+00 8.42e-01 7.03e+01 angle pdb=" N THR A 100 " pdb=" CA THR A 100 " pdb=" C THR A 100 " ideal model delta sigma weight residual 111.36 102.30 9.06 1.09e+00 8.42e-01 6.91e+01 angle pdb=" N THR C 100 " pdb=" CA THR C 100 " pdb=" C THR C 100 " ideal model delta sigma weight residual 111.36 102.68 8.68 1.09e+00 8.42e-01 6.35e+01 ... (remaining 9515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 3971 17.56 - 35.13: 430 35.13 - 52.69: 124 52.69 - 70.25: 42 70.25 - 87.81: 17 Dihedral angle restraints: 4584 sinusoidal: 2064 harmonic: 2520 Sorted by residual: dihedral pdb=" CA SER A 56 " pdb=" C SER A 56 " pdb=" N CYS A 57 " pdb=" CA CYS A 57 " ideal model delta harmonic sigma weight residual -180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" C PHE B 38 " pdb=" N PHE B 38 " pdb=" CA PHE B 38 " pdb=" CB PHE B 38 " ideal model delta harmonic sigma weight residual -122.60 -131.30 8.70 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" CG ARG D 49 " pdb=" CD ARG D 49 " pdb=" NE ARG D 49 " pdb=" CZ ARG D 49 " ideal model delta sinusoidal sigma weight residual 90.00 41.95 48.05 2 1.50e+01 4.44e-03 1.18e+01 ... (remaining 4581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 756 0.079 - 0.157: 286 0.157 - 0.236: 54 0.236 - 0.315: 5 0.315 - 0.394: 3 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CA PHE B 38 " pdb=" N PHE B 38 " pdb=" C PHE B 38 " pdb=" CB PHE B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA PHE D 38 " pdb=" N PHE D 38 " pdb=" C PHE D 38 " pdb=" CB PHE D 38 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA PHE A 38 " pdb=" N PHE A 38 " pdb=" C PHE A 38 " pdb=" CB PHE A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1101 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 94 " 0.036 2.00e-02 2.50e+03 2.58e-02 1.17e+01 pdb=" CG PHE F 94 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE F 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 94 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 94 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 92 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C GLN B 92 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN B 92 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN B 93 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS F 37 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C HIS F 37 " -0.053 2.00e-02 2.50e+03 pdb=" O HIS F 37 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE F 38 " 0.018 2.00e-02 2.50e+03 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 87 2.30 - 2.95: 4208 2.95 - 3.60: 11653 3.60 - 4.25: 17484 4.25 - 4.90: 26284 Nonbonded interactions: 59716 Sorted by model distance: nonbonded pdb=" OG SER D 48 " pdb=" NE2 HIS H 37 " model vdw 1.648 2.520 nonbonded pdb=" OD2 ASP A 70 " pdb=" NH2 ARG D 49 " model vdw 1.789 2.520 nonbonded pdb=" OG SER A 48 " pdb=" NE2 HIS E 37 " model vdw 1.793 2.520 nonbonded pdb=" O ARG F 49 " pdb=" NH1 ARG F 49 " model vdw 1.879 2.520 nonbonded pdb=" O ARG C 49 " pdb=" NH1 ARG C 49 " model vdw 1.883 2.520 ... (remaining 59711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.440 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4815 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 : 0.009 0.091 7128 Z= 0.563 Angle : 1.421 10.371 9520 Z= 1.027 Chirality : 0.082 0.394 1104 Planarity : 0.005 0.033 1216 Dihedral : 17.335 87.814 2920 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 79.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.22 % Favored : 86.42 % Rotamer: Outliers : 9.00 % Allowed : 19.62 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (0.22), residues: 832 helix: -4.12 (0.14), residues: 528 sheet: None (None), residues: 0 loop : -1.99 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS H 37 PHE 0.055 0.006 PHE F 94 TYR 0.006 0.001 TYR H 71 ARG 0.005 0.001 ARG G 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 426 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7730 (tm-30) REVERT: A 24 LEU cc_start: 0.7077 (tp) cc_final: 0.6803 (tt) REVERT: A 28 LEU cc_start: 0.4443 (tp) cc_final: 0.3725 (tp) REVERT: A 70 ASP cc_start: 0.7043 (t70) cc_final: 0.6809 (t70) REVERT: A 84 GLU cc_start: 0.7343 (tp30) cc_final: 0.7140 (pp20) REVERT: B 11 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8899 (tm-30) REVERT: B 12 ASP cc_start: 0.8451 (m-30) cc_final: 0.7930 (p0) REVERT: B 23 ASN cc_start: 0.6061 (m110) cc_final: 0.5856 (m-40) REVERT: B 37 HIS cc_start: 0.3331 (OUTLIER) cc_final: 0.2945 (m-70) REVERT: B 55 ILE cc_start: 0.7265 (mt) cc_final: 0.6801 (tt) REVERT: B 70 ASP cc_start: 0.7059 (t70) cc_final: 0.6615 (t0) REVERT: B 74 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7983 (mt-10) REVERT: B 84 GLU cc_start: 0.8286 (tp30) cc_final: 0.7993 (tp30) REVERT: B 107 ARG cc_start: 0.8124 (tpp-160) cc_final: 0.7894 (tpp80) REVERT: B 113 HIS cc_start: 0.8341 (t-170) cc_final: 0.8029 (t70) REVERT: C 11 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7568 (tm-30) REVERT: C 12 ASP cc_start: 0.8377 (m-30) cc_final: 0.7728 (p0) REVERT: C 16 VAL cc_start: 0.6605 (OUTLIER) cc_final: 0.6369 (p) REVERT: C 30 GLU cc_start: 0.4359 (mm-30) cc_final: 0.3486 (mt-10) REVERT: C 74 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7277 (tm-30) REVERT: D 30 GLU cc_start: 0.5060 (mm-30) cc_final: 0.4691 (mm-30) REVERT: D 35 GLU cc_start: 0.0530 (pt0) cc_final: 0.0044 (pt0) REVERT: D 70 ASP cc_start: 0.7040 (t70) cc_final: 0.6499 (t0) REVERT: D 73 GLN cc_start: 0.6688 (mt0) cc_final: 0.5842 (mt0) REVERT: D 74 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8160 (mt-10) REVERT: D 80 ASP cc_start: 0.7408 (m-30) cc_final: 0.7079 (m-30) REVERT: D 95 LEU cc_start: 0.8740 (tp) cc_final: 0.8530 (tp) REVERT: E 11 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8392 (tm-30) REVERT: E 16 VAL cc_start: 0.5912 (OUTLIER) cc_final: 0.5416 (p) REVERT: E 32 ILE cc_start: 0.4377 (mm) cc_final: 0.2905 (mm) REVERT: E 48 SER cc_start: 0.4230 (t) cc_final: 0.3264 (p) REVERT: E 49 ARG cc_start: 0.6146 (tpt90) cc_final: 0.5866 (tpt90) REVERT: E 80 ASP cc_start: 0.7311 (m-30) cc_final: 0.6582 (m-30) REVERT: E 84 GLU cc_start: 0.7833 (tp30) cc_final: 0.7390 (tm-30) REVERT: F 18 LYS cc_start: 0.7595 (mtmp) cc_final: 0.7208 (mtpp) REVERT: F 25 ARG cc_start: 0.5008 (OUTLIER) cc_final: 0.4575 (tmt170) REVERT: F 62 ARG cc_start: 0.7242 (mmt90) cc_final: 0.6865 (mmm-85) REVERT: F 69 LEU cc_start: 0.7620 (mp) cc_final: 0.7392 (mp) REVERT: F 104 LEU cc_start: 0.9153 (mt) cc_final: 0.8878 (mt) REVERT: G 16 VAL cc_start: 0.3522 (OUTLIER) cc_final: 0.3317 (p) REVERT: G 32 ILE cc_start: 0.2041 (mm) cc_final: 0.1805 (mm) REVERT: G 55 ILE cc_start: 0.6531 (mt) cc_final: 0.5707 (mt) REVERT: H 26 VAL cc_start: 0.8649 (t) cc_final: 0.8410 (p) REVERT: H 63 LYS cc_start: 0.6063 (mmtt) cc_final: 0.5595 (mtmm) REVERT: H 95 LEU cc_start: 0.8964 (tp) cc_final: 0.8630 (pt) REVERT: H 96 ILE cc_start: 0.6795 (mm) cc_final: 0.6407 (mm) outliers start: 72 outliers final: 18 residues processed: 470 average time/residue: 0.2761 time to fit residues: 156.4746 Evaluate side-chains 317 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 294 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 49 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 32 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 0.0570 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 overall best weight: 5.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 97 GLN B 92 GLN B 97 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 97 GLN D 37 HIS ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN E 40 HIS ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 113 HIS F 23 ASN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN F 113 HIS G 97 GLN G 113 HIS ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4943 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7128 Z= 0.289 Angle : 0.941 9.159 9520 Z= 0.506 Chirality : 0.051 0.346 1104 Planarity : 0.006 0.036 1216 Dihedral : 9.369 90.892 999 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 33.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 8.50 % Allowed : 25.25 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.26), residues: 832 helix: -1.83 (0.20), residues: 536 sheet: None (None), residues: 0 loop : -3.09 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 37 PHE 0.020 0.004 PHE H 94 TYR 0.015 0.002 TYR B 71 ARG 0.014 0.001 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 383 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7932 (m-30) cc_final: 0.7694 (p0) REVERT: A 30 GLU cc_start: 0.5141 (mm-30) cc_final: 0.4782 (mt-10) REVERT: A 63 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7912 (mtmt) REVERT: B 11 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8888 (tm-30) REVERT: B 22 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7351 (mm-30) REVERT: B 25 ARG cc_start: 0.2987 (OUTLIER) cc_final: 0.1899 (tpt-90) REVERT: B 28 LEU cc_start: 0.6345 (tt) cc_final: 0.5598 (tt) REVERT: B 42 ARG cc_start: 0.7847 (tpt-90) cc_final: 0.7499 (mmt180) REVERT: B 49 ARG cc_start: 0.6151 (tpt90) cc_final: 0.5792 (tmt-80) REVERT: B 70 ASP cc_start: 0.6989 (t70) cc_final: 0.6092 (t70) REVERT: B 84 GLU cc_start: 0.7757 (tp30) cc_final: 0.7327 (mm-30) REVERT: B 101 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7699 (t0) REVERT: B 107 ARG cc_start: 0.8012 (tpp-160) cc_final: 0.7800 (tpp80) REVERT: B 112 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8588 (tm-30) REVERT: B 113 HIS cc_start: 0.8263 (t-170) cc_final: 0.8037 (t-170) REVERT: C 11 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7664 (tm-30) REVERT: C 16 VAL cc_start: 0.7613 (OUTLIER) cc_final: 0.7330 (p) REVERT: C 23 ASN cc_start: 0.7791 (m-40) cc_final: 0.7569 (m-40) REVERT: C 24 LEU cc_start: 0.7333 (mm) cc_final: 0.6245 (mm) REVERT: C 35 GLU cc_start: 0.1010 (pt0) cc_final: 0.0342 (pt0) REVERT: C 55 ILE cc_start: 0.7619 (mt) cc_final: 0.7111 (tt) REVERT: C 105 LYS cc_start: 0.7505 (mmmt) cc_final: 0.7223 (mmmt) REVERT: C 109 ILE cc_start: 0.7306 (mp) cc_final: 0.6792 (mp) REVERT: C 112 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8702 (tm-30) REVERT: D 16 VAL cc_start: 0.6995 (OUTLIER) cc_final: 0.6668 (p) REVERT: D 28 LEU cc_start: 0.6332 (tp) cc_final: 0.5819 (tp) REVERT: D 35 GLU cc_start: 0.1764 (pt0) cc_final: 0.0437 (mt-10) REVERT: D 37 HIS cc_start: 0.1258 (OUTLIER) cc_final: 0.0568 (t-170) REVERT: D 56 SER cc_start: 0.8105 (t) cc_final: 0.7779 (p) REVERT: D 73 GLN cc_start: 0.6761 (mt0) cc_final: 0.6541 (mt0) REVERT: E 11 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8135 (tm-30) REVERT: E 58 ARG cc_start: 0.4811 (OUTLIER) cc_final: 0.4452 (ttt180) REVERT: E 79 LEU cc_start: 0.7888 (mt) cc_final: 0.7638 (tt) REVERT: E 84 GLU cc_start: 0.7873 (tp30) cc_final: 0.7378 (tm-30) REVERT: E 90 LYS cc_start: 0.3627 (mttt) cc_final: 0.2136 (mttt) REVERT: F 25 ARG cc_start: 0.4662 (OUTLIER) cc_final: 0.3682 (tmt170) REVERT: F 70 ASP cc_start: 0.7714 (t0) cc_final: 0.7510 (t0) REVERT: F 79 LEU cc_start: 0.7892 (mt) cc_final: 0.7654 (mm) REVERT: F 90 LYS cc_start: 0.0636 (ttmt) cc_final: 0.0300 (ttmt) REVERT: G 23 ASN cc_start: 0.8159 (m-40) cc_final: 0.7842 (m-40) REVERT: G 84 GLU cc_start: 0.7897 (tp30) cc_final: 0.7425 (tp30) REVERT: G 103 VAL cc_start: 0.8713 (t) cc_final: 0.8498 (t) REVERT: H 35 GLU cc_start: 0.5019 (OUTLIER) cc_final: 0.4601 (pm20) REVERT: H 39 ASP cc_start: 0.6616 (m-30) cc_final: 0.6380 (m-30) REVERT: H 63 LYS cc_start: 0.6256 (mmtt) cc_final: 0.5891 (mtmm) REVERT: H 83 VAL cc_start: 0.8648 (p) cc_final: 0.8374 (p) REVERT: H 105 LYS cc_start: 0.6935 (mmmt) cc_final: 0.6434 (mmmt) outliers start: 68 outliers final: 30 residues processed: 419 average time/residue: 0.2858 time to fit residues: 144.7303 Evaluate side-chains 321 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 283 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 29 CYS Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 60 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN C 113 HIS D 37 HIS ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN F 23 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN G 113 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5052 moved from start: 0.8345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7128 Z= 0.266 Angle : 0.865 11.960 9520 Z= 0.453 Chirality : 0.049 0.283 1104 Planarity : 0.005 0.050 1216 Dihedral : 8.103 59.444 967 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 8.38 % Allowed : 26.50 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.28), residues: 832 helix: -0.59 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -3.10 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 113 PHE 0.020 0.004 PHE E 38 TYR 0.007 0.001 TYR H 27 ARG 0.007 0.001 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 333 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.4964 (mm-30) cc_final: 0.4681 (mt-10) REVERT: A 42 ARG cc_start: 0.7599 (ttt-90) cc_final: 0.7170 (mmt180) REVERT: A 63 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7893 (mtmt) REVERT: A 107 ARG cc_start: 0.7761 (tmt-80) cc_final: 0.7561 (tpt90) REVERT: B 35 GLU cc_start: 0.2836 (pt0) cc_final: 0.2600 (pt0) REVERT: B 41 LEU cc_start: 0.8215 (tp) cc_final: 0.7788 (tt) REVERT: B 42 ARG cc_start: 0.7751 (tpt-90) cc_final: 0.7379 (mmt180) REVERT: B 52 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7340 (p) REVERT: C 16 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7416 (p) REVERT: C 24 LEU cc_start: 0.7061 (mm) cc_final: 0.6239 (mm) REVERT: C 25 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.5867 (mtp180) REVERT: C 40 HIS cc_start: 0.6301 (OUTLIER) cc_final: 0.6041 (m-70) REVERT: C 63 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7079 (mtmt) REVERT: C 70 ASP cc_start: 0.7907 (t70) cc_final: 0.7413 (t70) REVERT: C 107 ARG cc_start: 0.8740 (tpp80) cc_final: 0.8374 (tpp-160) REVERT: C 109 ILE cc_start: 0.7574 (mp) cc_final: 0.7359 (mp) REVERT: D 16 VAL cc_start: 0.7220 (OUTLIER) cc_final: 0.6841 (p) REVERT: D 73 GLN cc_start: 0.6581 (mt0) cc_final: 0.6181 (mt0) REVERT: D 112 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8070 (tm-30) REVERT: D 113 HIS cc_start: 0.8851 (t-90) cc_final: 0.8533 (t-170) REVERT: E 11 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8411 (tm-30) REVERT: E 15 GLU cc_start: 0.8495 (mp0) cc_final: 0.8198 (pm20) REVERT: E 30 GLU cc_start: 0.6300 (mm-30) cc_final: 0.6094 (mm-30) REVERT: E 79 LEU cc_start: 0.8375 (mt) cc_final: 0.8122 (tt) REVERT: E 108 ASN cc_start: 0.7809 (t0) cc_final: 0.7589 (t0) REVERT: F 25 ARG cc_start: 0.5198 (OUTLIER) cc_final: 0.4308 (tmt170) REVERT: F 42 ARG cc_start: 0.7165 (ttp80) cc_final: 0.6941 (ttp80) REVERT: F 63 LYS cc_start: 0.7375 (mmtt) cc_final: 0.6759 (mtpt) REVERT: G 15 GLU cc_start: 0.8194 (mp0) cc_final: 0.7610 (tm-30) REVERT: G 42 ARG cc_start: 0.7221 (ttt-90) cc_final: 0.6897 (ttt-90) REVERT: G 53 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6356 (tm-30) REVERT: G 81 THR cc_start: 0.7597 (p) cc_final: 0.7275 (m) REVERT: G 105 LYS cc_start: 0.7695 (mmmt) cc_final: 0.7486 (tppt) REVERT: H 105 LYS cc_start: 0.7273 (mmmt) cc_final: 0.6883 (mmmt) outliers start: 67 outliers final: 41 residues processed: 368 average time/residue: 0.2785 time to fit residues: 123.8507 Evaluate side-chains 327 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 280 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 80 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 0.0470 chunk 48 optimal weight: 0.0980 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 64 optimal weight: 8.9990 overall best weight: 2.6284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN F 113 HIS ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5047 moved from start: 0.9322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7128 Z= 0.206 Angle : 0.775 10.173 9520 Z= 0.404 Chirality : 0.045 0.221 1104 Planarity : 0.004 0.057 1216 Dihedral : 7.591 58.486 963 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 26.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 7.75 % Allowed : 28.88 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.29), residues: 832 helix: -0.14 (0.23), residues: 536 sheet: None (None), residues: 0 loop : -2.96 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS D 37 PHE 0.018 0.003 PHE E 38 TYR 0.007 0.001 TYR H 27 ARG 0.011 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 318 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.4664 (mm-30) cc_final: 0.4301 (mt-10) REVERT: A 42 ARG cc_start: 0.7613 (ttt-90) cc_final: 0.7025 (mmt180) REVERT: A 63 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7911 (mtmt) REVERT: A 74 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: A 84 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6039 (mm-30) REVERT: A 87 ARG cc_start: 0.8631 (ptt180) cc_final: 0.8422 (ptt180) REVERT: B 17 LYS cc_start: 0.8531 (mmmm) cc_final: 0.8040 (tmtt) REVERT: B 35 GLU cc_start: 0.3017 (pt0) cc_final: 0.2544 (pt0) REVERT: B 42 ARG cc_start: 0.7489 (tpt-90) cc_final: 0.7168 (mmt180) REVERT: C 24 LEU cc_start: 0.7348 (mm) cc_final: 0.6273 (mm) REVERT: C 25 ARG cc_start: 0.6529 (tpt90) cc_final: 0.5980 (mmm-85) REVERT: C 63 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7045 (mtmt) REVERT: C 109 ILE cc_start: 0.7232 (mp) cc_final: 0.7023 (mp) REVERT: D 16 VAL cc_start: 0.7159 (OUTLIER) cc_final: 0.6749 (p) REVERT: D 73 GLN cc_start: 0.6057 (mt0) cc_final: 0.5679 (mt0) REVERT: D 105 LYS cc_start: 0.7129 (mmtt) cc_final: 0.6896 (mmmt) REVERT: E 15 GLU cc_start: 0.8471 (mp0) cc_final: 0.8175 (mp0) REVERT: E 30 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6344 (tp30) REVERT: E 39 ASP cc_start: 0.6357 (m-30) cc_final: 0.6074 (m-30) REVERT: E 84 GLU cc_start: 0.8393 (tp30) cc_final: 0.7779 (tm-30) REVERT: E 105 LYS cc_start: 0.7064 (mmtt) cc_final: 0.6663 (tppt) REVERT: F 37 HIS cc_start: 0.3083 (t70) cc_final: 0.2530 (t70) REVERT: F 63 LYS cc_start: 0.7340 (mmtt) cc_final: 0.6708 (mtpt) REVERT: G 42 ARG cc_start: 0.7041 (ttt-90) cc_final: 0.6628 (ttt-90) REVERT: G 49 ARG cc_start: 0.7869 (tpt90) cc_final: 0.7418 (tpm170) REVERT: G 53 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6241 (tm-30) REVERT: G 81 THR cc_start: 0.7610 (p) cc_final: 0.7222 (m) REVERT: H 24 LEU cc_start: 0.7289 (mm) cc_final: 0.6844 (mm) REVERT: H 82 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8326 (mm) REVERT: H 105 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7556 (mtpp) REVERT: H 109 ILE cc_start: 0.7452 (mt) cc_final: 0.7086 (pt) outliers start: 62 outliers final: 32 residues processed: 348 average time/residue: 0.2774 time to fit residues: 116.6036 Evaluate side-chains 322 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 287 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 29 CYS Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 82 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN F 23 ASN ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5050 moved from start: 1.0076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7128 Z= 0.294 Angle : 0.819 8.656 9520 Z= 0.434 Chirality : 0.047 0.279 1104 Planarity : 0.006 0.071 1216 Dihedral : 7.459 60.198 955 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 34.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 8.50 % Allowed : 29.75 % Favored : 61.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.29), residues: 832 helix: -0.58 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -3.69 (0.33), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS D 37 PHE 0.017 0.003 PHE E 38 TYR 0.012 0.001 TYR B 27 ARG 0.008 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 293 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.4624 (mm-30) cc_final: 0.4252 (mt-10) REVERT: A 42 ARG cc_start: 0.7293 (ttt-90) cc_final: 0.6950 (mmt180) REVERT: A 84 GLU cc_start: 0.6590 (mt-10) cc_final: 0.5818 (mm-30) REVERT: B 17 LYS cc_start: 0.7750 (mmmm) cc_final: 0.7150 (tptp) REVERT: B 22 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7167 (tp30) REVERT: B 73 GLN cc_start: 0.7765 (mt0) cc_final: 0.7302 (mp10) REVERT: C 24 LEU cc_start: 0.6959 (mm) cc_final: 0.6242 (mm) REVERT: C 25 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6209 (mmm-85) REVERT: C 63 LYS cc_start: 0.7509 (mmtt) cc_final: 0.7241 (mtmt) REVERT: D 16 VAL cc_start: 0.7158 (OUTLIER) cc_final: 0.6743 (p) REVERT: D 73 GLN cc_start: 0.6404 (mt0) cc_final: 0.6153 (mt0) REVERT: D 112 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8068 (tm-30) REVERT: F 63 LYS cc_start: 0.7287 (mmtt) cc_final: 0.6696 (mtpt) REVERT: G 42 ARG cc_start: 0.7192 (ttt-90) cc_final: 0.6826 (ttt-90) REVERT: G 49 ARG cc_start: 0.7725 (tpt90) cc_final: 0.7520 (tpm170) REVERT: G 53 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6442 (tm-30) REVERT: G 105 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7816 (mtpp) REVERT: H 35 GLU cc_start: 0.5724 (OUTLIER) cc_final: 0.5378 (pm20) REVERT: H 82 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8448 (mm) REVERT: H 105 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7862 (mmmt) REVERT: H 109 ILE cc_start: 0.7418 (mt) cc_final: 0.7195 (pt) outliers start: 68 outliers final: 45 residues processed: 324 average time/residue: 0.2813 time to fit residues: 110.0349 Evaluate side-chains 320 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 271 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 102 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 50.0000 chunk 74 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5034 moved from start: 1.0511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7128 Z= 0.216 Angle : 0.779 8.837 9520 Z= 0.407 Chirality : 0.045 0.223 1104 Planarity : 0.004 0.049 1216 Dihedral : 7.192 61.328 955 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 29.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 6.88 % Allowed : 33.88 % Favored : 59.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.29), residues: 832 helix: -0.10 (0.23), residues: 544 sheet: None (None), residues: 0 loop : -3.21 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS G 113 PHE 0.013 0.002 PHE F 38 TYR 0.009 0.001 TYR B 27 ARG 0.009 0.001 ARG F 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 316 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.5432 (mm-30) cc_final: 0.5153 (mt-10) REVERT: A 42 ARG cc_start: 0.7737 (ttt-90) cc_final: 0.7389 (mmt180) REVERT: A 63 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7938 (mtmt) REVERT: A 84 GLU cc_start: 0.6478 (mt-10) cc_final: 0.6257 (mm-30) REVERT: B 17 LYS cc_start: 0.7680 (mmmm) cc_final: 0.6987 (tptp) REVERT: C 24 LEU cc_start: 0.7129 (mm) cc_final: 0.6670 (mm) REVERT: C 63 LYS cc_start: 0.7234 (mmtt) cc_final: 0.7020 (mtmt) REVERT: D 16 VAL cc_start: 0.7120 (OUTLIER) cc_final: 0.6585 (p) REVERT: D 28 LEU cc_start: 0.6025 (tp) cc_final: 0.5719 (tp) REVERT: D 84 GLU cc_start: 0.7191 (pp20) cc_final: 0.6783 (pp20) REVERT: D 112 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8153 (tm-30) REVERT: F 42 ARG cc_start: 0.7091 (ttp80) cc_final: 0.6881 (ttp80) REVERT: G 42 ARG cc_start: 0.7196 (ttt-90) cc_final: 0.6771 (ttt-90) REVERT: G 49 ARG cc_start: 0.7632 (tpt90) cc_final: 0.7307 (tpm170) REVERT: G 53 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6183 (tm-30) REVERT: G 105 LYS cc_start: 0.8321 (mmmt) cc_final: 0.8008 (mtpp) REVERT: G 113 HIS cc_start: 0.8743 (t-170) cc_final: 0.8527 (t70) REVERT: H 24 LEU cc_start: 0.7602 (mm) cc_final: 0.7123 (mm) REVERT: H 82 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8228 (mm) REVERT: H 109 ILE cc_start: 0.7366 (mt) cc_final: 0.7039 (pt) outliers start: 55 outliers final: 37 residues processed: 336 average time/residue: 0.2785 time to fit residues: 113.1381 Evaluate side-chains 314 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 275 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 82 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 43 optimal weight: 30.0000 chunk 65 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 50.0000 chunk 46 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5044 moved from start: 1.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7128 Z= 0.258 Angle : 0.824 12.218 9520 Z= 0.429 Chirality : 0.047 0.349 1104 Planarity : 0.005 0.057 1216 Dihedral : 7.172 57.948 955 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 30.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 7.38 % Allowed : 35.75 % Favored : 56.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.29), residues: 832 helix: -0.39 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -3.48 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 113 PHE 0.010 0.002 PHE F 38 TYR 0.009 0.001 TYR A 27 ARG 0.011 0.001 ARG H 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 289 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.5896 (mm-30) cc_final: 0.5623 (mt-10) REVERT: A 63 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7953 (mtmt) REVERT: B 17 LYS cc_start: 0.7626 (mmmm) cc_final: 0.7021 (tptp) REVERT: B 48 SER cc_start: 0.5030 (t) cc_final: 0.4743 (m) REVERT: B 73 GLN cc_start: 0.7689 (mt0) cc_final: 0.7374 (mp10) REVERT: C 24 LEU cc_start: 0.7368 (mm) cc_final: 0.6478 (mm) REVERT: D 16 VAL cc_start: 0.7123 (OUTLIER) cc_final: 0.6710 (p) REVERT: F 12 ASP cc_start: 0.8513 (m-30) cc_final: 0.8029 (p0) REVERT: F 90 LYS cc_start: 0.5324 (pttm) cc_final: 0.4879 (pttm) REVERT: F 95 LEU cc_start: 0.7424 (tp) cc_final: 0.7044 (tp) REVERT: G 42 ARG cc_start: 0.7256 (ttt-90) cc_final: 0.6868 (ttt-90) REVERT: G 49 ARG cc_start: 0.7639 (tpt90) cc_final: 0.7309 (tpm170) REVERT: G 53 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6217 (tm-30) REVERT: G 105 LYS cc_start: 0.8393 (mmmt) cc_final: 0.8102 (mtpp) outliers start: 59 outliers final: 46 residues processed: 313 average time/residue: 0.2733 time to fit residues: 103.8430 Evaluate side-chains 316 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 269 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 80 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 60 optimal weight: 40.0000 chunk 70 optimal weight: 40.0000 chunk 73 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS B 37 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5040 moved from start: 1.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7128 Z= 0.269 Angle : 0.849 14.248 9520 Z= 0.441 Chirality : 0.047 0.346 1104 Planarity : 0.005 0.038 1216 Dihedral : 7.296 58.545 955 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 30.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 7.25 % Allowed : 36.88 % Favored : 55.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.30), residues: 832 helix: -0.36 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -3.27 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS F 113 PHE 0.036 0.003 PHE E 94 TYR 0.009 0.001 TYR B 27 ARG 0.009 0.001 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 282 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.5806 (tp) cc_final: 0.5401 (tp) REVERT: A 30 GLU cc_start: 0.6114 (mm-30) cc_final: 0.5828 (mt-10) REVERT: A 32 ILE cc_start: 0.2442 (mm) cc_final: 0.2166 (mm) REVERT: A 63 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7926 (mtmt) REVERT: A 74 GLU cc_start: 0.7760 (mp0) cc_final: 0.7460 (pt0) REVERT: B 17 LYS cc_start: 0.7627 (mmmm) cc_final: 0.6835 (tptt) REVERT: C 24 LEU cc_start: 0.7309 (mm) cc_final: 0.6480 (mm) REVERT: D 16 VAL cc_start: 0.7069 (OUTLIER) cc_final: 0.6625 (p) REVERT: D 35 GLU cc_start: 0.7206 (pp20) cc_final: 0.6724 (pm20) REVERT: D 87 ARG cc_start: 0.8327 (tmm160) cc_final: 0.7662 (ptm-80) REVERT: E 35 GLU cc_start: 0.4555 (pt0) cc_final: 0.4207 (pt0) REVERT: E 62 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8189 (mmm-85) REVERT: F 12 ASP cc_start: 0.8460 (m-30) cc_final: 0.7950 (p0) REVERT: F 42 ARG cc_start: 0.6912 (ttp80) cc_final: 0.6701 (ttp80) REVERT: F 63 LYS cc_start: 0.7377 (mmtt) cc_final: 0.6912 (mtmm) REVERT: G 42 ARG cc_start: 0.7247 (ttt-90) cc_final: 0.6840 (ttt-90) REVERT: G 53 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6333 (tm-30) REVERT: G 70 ASP cc_start: 0.7630 (t0) cc_final: 0.7265 (t0) REVERT: G 73 GLN cc_start: 0.8091 (mt0) cc_final: 0.7864 (mt0) REVERT: G 105 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8192 (mtpp) REVERT: H 69 LEU cc_start: 0.7965 (tp) cc_final: 0.7493 (tp) outliers start: 58 outliers final: 47 residues processed: 304 average time/residue: 0.2696 time to fit residues: 100.0333 Evaluate side-chains 316 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 267 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 109 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 40.0000 chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS B 37 HIS ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5042 moved from start: 1.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7128 Z= 0.228 Angle : 0.875 14.585 9520 Z= 0.444 Chirality : 0.047 0.393 1104 Planarity : 0.004 0.038 1216 Dihedral : 7.155 60.040 954 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 29.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 6.75 % Allowed : 38.75 % Favored : 54.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.30), residues: 832 helix: -0.31 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -3.20 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS F 113 PHE 0.026 0.002 PHE E 94 TYR 0.012 0.001 TYR D 27 ARG 0.008 0.001 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 289 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6165 (mm-30) cc_final: 0.5943 (mt-10) REVERT: A 63 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7905 (mtmt) REVERT: B 17 LYS cc_start: 0.7674 (mmmm) cc_final: 0.6701 (tptt) REVERT: B 73 GLN cc_start: 0.7364 (mt0) cc_final: 0.7025 (mp10) REVERT: C 24 LEU cc_start: 0.7355 (mm) cc_final: 0.6562 (mm) REVERT: C 87 ARG cc_start: 0.8590 (mpt180) cc_final: 0.8380 (ptp-170) REVERT: C 109 ILE cc_start: 0.7132 (mp) cc_final: 0.6869 (mt) REVERT: D 16 VAL cc_start: 0.7112 (OUTLIER) cc_final: 0.6663 (p) REVERT: D 35 GLU cc_start: 0.7046 (pp20) cc_final: 0.6482 (pm20) REVERT: D 87 ARG cc_start: 0.8322 (tmm160) cc_final: 0.7772 (ptm-80) REVERT: E 30 GLU cc_start: 0.6175 (mm-30) cc_final: 0.5795 (tp30) REVERT: E 31 LYS cc_start: 0.6291 (mtpt) cc_final: 0.5974 (ttpt) REVERT: E 35 GLU cc_start: 0.4288 (pt0) cc_final: 0.3928 (pt0) REVERT: F 12 ASP cc_start: 0.8440 (m-30) cc_final: 0.7958 (p0) REVERT: F 42 ARG cc_start: 0.6993 (ttp80) cc_final: 0.6759 (ttp80) REVERT: F 63 LYS cc_start: 0.7306 (mmtt) cc_final: 0.6865 (mtmm) REVERT: G 42 ARG cc_start: 0.7228 (ttt-90) cc_final: 0.6885 (ttt-90) REVERT: G 53 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6657 (tm-30) REVERT: G 70 ASP cc_start: 0.7700 (t0) cc_final: 0.7329 (t0) REVERT: G 73 GLN cc_start: 0.8088 (mt0) cc_final: 0.7876 (mt0) REVERT: G 81 THR cc_start: 0.7714 (p) cc_final: 0.7314 (m) REVERT: G 88 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7691 (ttt90) REVERT: H 108 ASN cc_start: 0.8134 (m-40) cc_final: 0.7912 (p0) outliers start: 54 outliers final: 43 residues processed: 307 average time/residue: 0.2624 time to fit residues: 98.6950 Evaluate side-chains 322 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 278 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 40.0000 chunk 67 optimal weight: 0.2980 chunk 19 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 73 GLN A 108 ASN F 113 HIS G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5049 moved from start: 1.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7128 Z= 0.217 Angle : 0.899 16.338 9520 Z= 0.445 Chirality : 0.047 0.357 1104 Planarity : 0.004 0.037 1216 Dihedral : 6.812 56.443 952 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 27.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 5.25 % Allowed : 39.50 % Favored : 55.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.30), residues: 832 helix: -0.33 (0.23), residues: 592 sheet: None (None), residues: 0 loop : -3.05 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS G 113 PHE 0.028 0.002 PHE E 94 TYR 0.007 0.001 TYR F 27 ARG 0.009 0.001 ARG D 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 294 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.5360 (mm-30) cc_final: 0.5000 (pm20) REVERT: A 63 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7877 (mtmt) REVERT: B 17 LYS cc_start: 0.7416 (mmmm) cc_final: 0.6553 (tptt) REVERT: B 28 LEU cc_start: 0.6634 (tp) cc_final: 0.6340 (tt) REVERT: C 24 LEU cc_start: 0.7586 (mm) cc_final: 0.6766 (mm) REVERT: D 16 VAL cc_start: 0.7071 (OUTLIER) cc_final: 0.6659 (p) REVERT: E 18 LYS cc_start: 0.7546 (tttm) cc_final: 0.7317 (mmmt) REVERT: E 31 LYS cc_start: 0.6503 (mtpt) cc_final: 0.5910 (ttpt) REVERT: E 35 GLU cc_start: 0.4661 (pt0) cc_final: 0.4230 (pt0) REVERT: E 53 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6501 (mt-10) REVERT: E 84 GLU cc_start: 0.7983 (tp30) cc_final: 0.7730 (tm-30) REVERT: F 12 ASP cc_start: 0.8534 (m-30) cc_final: 0.8036 (p0) REVERT: F 42 ARG cc_start: 0.6802 (ttp80) cc_final: 0.6574 (ttp80) REVERT: G 42 ARG cc_start: 0.7188 (ttt-90) cc_final: 0.6853 (ttt-90) REVERT: G 53 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6592 (tm-30) REVERT: G 70 ASP cc_start: 0.7408 (t0) cc_final: 0.7050 (t0) REVERT: G 73 GLN cc_start: 0.8029 (mt0) cc_final: 0.7818 (mt0) REVERT: G 81 THR cc_start: 0.7718 (p) cc_final: 0.7328 (m) REVERT: G 88 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7696 (ttt90) outliers start: 42 outliers final: 35 residues processed: 310 average time/residue: 0.2657 time to fit residues: 101.2684 Evaluate side-chains 315 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 279 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 0.0170 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 108 ASN C 37 HIS D 40 HIS F 113 HIS ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.129957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.116814 restraints weight = 21019.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.119486 restraints weight = 13565.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.121334 restraints weight = 9569.505| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 1.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7128 Z= 0.252 Angle : 0.937 15.817 9520 Z= 0.464 Chirality : 0.049 0.334 1104 Planarity : 0.005 0.039 1216 Dihedral : 6.955 60.568 952 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 31.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 5.12 % Allowed : 40.12 % Favored : 54.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.30), residues: 832 helix: -0.37 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -3.12 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS F 113 PHE 0.025 0.002 PHE E 94 TYR 0.009 0.001 TYR D 27 ARG 0.010 0.001 ARG D 107 =============================================================================== Job complete usr+sys time: 2203.80 seconds wall clock time: 40 minutes 30.91 seconds (2430.91 seconds total)