Starting phenix.real_space_refine on Fri Mar 15 14:30:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6see_10153/03_2024/6see_10153.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6see_10153/03_2024/6see_10153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6see_10153/03_2024/6see_10153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6see_10153/03_2024/6see_10153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6see_10153/03_2024/6see_10153.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6see_10153/03_2024/6see_10153.pdb" } resolution = 4.2 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 10 5.16 5 C 6628 2.51 5 N 2240 2.21 5 O 2783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "H ASP 68": "OD1" <-> "OD2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "V ARG 525": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11949 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "B" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 637 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 731 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "F" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "V" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 160 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Time building chain proxies: 6.46, per 1000 atoms: 0.54 Number of scatterers: 11949 At special positions: 0 Unit cell: (78, 120.9, 115.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2783 8.00 N 2240 7.00 C 6628 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: 6.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 71.4% alpha, 1.6% beta 144 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 6.56 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.515A pdb=" N GLU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.161A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 117 removed outlier: 3.507A pdb=" N LEU A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.592A pdb=" N ARG A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.379A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.531A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 removed outlier: 4.715A pdb=" N ALA C 21 " --> pdb=" O SER C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.750A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.351A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.858A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.919A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.509A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 80 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.943A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 4.543A pdb=" N LYS E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.881A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 117 removed outlier: 3.667A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.782A pdb=" N ARG E 131 " --> pdb=" O GLN E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 4.116A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.958A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.345A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.585A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG G 88 " --> pdb=" O GLN G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.916A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.648A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 122 removed outlier: 3.748A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR H 122 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.114A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'E' and resid 120 through 121 removed outlier: 3.681A pdb=" N LEU E 121 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.842A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 78 373 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 359 hydrogen bonds 686 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 7.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2239 1.33 - 1.45: 4367 1.45 - 1.57: 5561 1.57 - 1.69: 576 1.69 - 1.81: 18 Bond restraints: 12761 Sorted by residual: bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.24e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.71e+00 bond pdb=" C3' DG J 21 " pdb=" O3' DG J 21 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.44e+00 bond pdb=" C3' DC I -29 " pdb=" O3' DC I -29 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.44e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.25e+00 ... (remaining 12756 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.59: 1494 105.59 - 113.25: 7158 113.25 - 120.91: 6230 120.91 - 128.56: 3301 128.56 - 136.22: 293 Bond angle restraints: 18476 Sorted by residual: angle pdb=" CA LEU G 116 " pdb=" CB LEU G 116 " pdb=" CG LEU G 116 " ideal model delta sigma weight residual 116.30 129.74 -13.44 3.50e+00 8.16e-02 1.48e+01 angle pdb=" C3' DG I -30 " pdb=" O3' DG I -30 " pdb=" P DC I -29 " ideal model delta sigma weight residual 120.20 125.48 -5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " pdb=" P DC I 5 " ideal model delta sigma weight residual 120.20 125.45 -5.25 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C3' DG J 21 " pdb=" O3' DG J 21 " pdb=" P DT J 22 " ideal model delta sigma weight residual 120.20 125.41 -5.21 1.50e+00 4.44e-01 1.21e+01 angle pdb=" C3' DC I -29 " pdb=" O3' DC I -29 " pdb=" P DT I -28 " ideal model delta sigma weight residual 120.20 125.36 -5.16 1.50e+00 4.44e-01 1.18e+01 ... (remaining 18471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 5514 35.82 - 71.64: 1344 71.64 - 107.46: 15 107.46 - 143.29: 6 143.29 - 179.11: 2 Dihedral angle restraints: 6881 sinusoidal: 4708 harmonic: 2173 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual -140.00 39.11 -179.11 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 75.64 144.36 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 93.35 126.65 1 3.50e+01 8.16e-04 1.25e+01 ... (remaining 6878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1652 0.065 - 0.130: 389 0.130 - 0.195: 43 0.195 - 0.260: 6 0.260 - 0.325: 1 Chirality restraints: 2091 Sorted by residual: chirality pdb=" CB ILE V 523 " pdb=" CA ILE V 523 " pdb=" CG1 ILE V 523 " pdb=" CG2 ILE V 523 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1' DT I 68 " pdb=" O4' DT I 68 " pdb=" C2' DT I 68 " pdb=" N1 DT I 68 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2088 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " -0.052 2.00e-02 2.50e+03 2.39e-02 1.72e+01 pdb=" N9 DG I 26 " 0.061 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " -0.016 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " -0.040 2.00e-02 2.50e+03 1.84e-02 1.01e+01 pdb=" N9 DG I 28 " 0.043 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " -0.018 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " 0.005 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 95 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C VAL D 95 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL D 95 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG D 96 " 0.017 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2368 2.78 - 3.31: 10294 3.31 - 3.84: 24661 3.84 - 4.37: 27163 4.37 - 4.90: 38345 Nonbonded interactions: 102831 Sorted by model distance: nonbonded pdb=" N2 DG I -58 " pdb=" O2 DC J 58 " model vdw 2.252 2.496 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.258 2.440 nonbonded pdb=" O2 DC I -4 " pdb=" N2 DG J 4 " model vdw 2.271 2.496 nonbonded pdb=" O2 DC I -62 " pdb=" N2 DG J 62 " model vdw 2.274 2.496 nonbonded pdb=" O2 DC I 5 " pdb=" N2 DG J -5 " model vdw 2.279 2.496 ... (remaining 102826 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 'E' } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 110) } ncs_group { reference = (chain 'D' and resid 32 through 121) 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.680 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 40.540 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.008 0.062 12761 Z= 0.412 Angle : 0.935 13.444 18476 Z= 0.540 Chirality : 0.055 0.325 2091 Planarity : 0.006 0.035 1328 Dihedral : 27.452 179.107 5481 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.26), residues: 738 helix: -0.62 (0.19), residues: 512 sheet: None (None), residues: 0 loop : -2.17 (0.34), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP V 531 HIS 0.010 0.002 HIS H 49 PHE 0.020 0.003 PHE E 84 TYR 0.018 0.003 TYR F 72 ARG 0.006 0.001 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 0.814 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: A 49 LYS cc_start: 0.9342 (mmtm) cc_final: 0.8984 (pttp) REVERT: A 67 PHE cc_start: 0.9233 (t80) cc_final: 0.9029 (t80) REVERT: A 83 ASP cc_start: 0.6939 (t70) cc_final: 0.6475 (t0) REVERT: A 86 TRP cc_start: 0.8802 (m100) cc_final: 0.8502 (m-10) REVERT: A 95 GLN cc_start: 0.9341 (tt0) cc_final: 0.8566 (tt0) REVERT: A 96 GLU cc_start: 0.8607 (tp30) cc_final: 0.8368 (tp30) REVERT: A 99 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8057 (mt-10) REVERT: A 104 HIS cc_start: 0.8917 (m-70) cc_final: 0.8611 (t-170) REVERT: A 107 GLU cc_start: 0.8469 (pp20) cc_final: 0.8136 (pp20) REVERT: A 111 LEU cc_start: 0.9375 (mm) cc_final: 0.9020 (mm) REVERT: A 130 ARG cc_start: 0.8849 (mtp180) cc_final: 0.8450 (ttt-90) REVERT: B 31 LYS cc_start: 0.9316 (mttp) cc_final: 0.9116 (ttpt) REVERT: B 63 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8684 (tm-30) REVERT: B 79 LYS cc_start: 0.9403 (mttp) cc_final: 0.9029 (mtmt) REVERT: C 38 ASN cc_start: 0.8818 (m-40) cc_final: 0.7530 (p0) REVERT: C 73 ASN cc_start: 0.9059 (t0) cc_final: 0.8587 (t0) REVERT: C 82 HIS cc_start: 0.8710 (m170) cc_final: 0.8425 (m-70) REVERT: C 95 LYS cc_start: 0.9487 (tttm) cc_final: 0.9124 (mttm) REVERT: D 39 TYR cc_start: 0.8793 (t80) cc_final: 0.8183 (t80) REVERT: D 43 LYS cc_start: 0.9079 (tttt) cc_final: 0.8683 (tppt) REVERT: D 56 MET cc_start: 0.9129 (tpp) cc_final: 0.8923 (tpp) REVERT: D 65 ASP cc_start: 0.9180 (t0) cc_final: 0.8913 (t0) REVERT: D 68 GLU cc_start: 0.9034 (tt0) cc_final: 0.8169 (tm-30) REVERT: D 69 ARG cc_start: 0.8660 (mtp180) cc_final: 0.8131 (mtm180) REVERT: E 55 GLN cc_start: 0.9177 (mt0) cc_final: 0.8526 (mm-40) REVERT: E 87 GLN cc_start: 0.8693 (mt0) cc_final: 0.7995 (mt0) REVERT: E 89 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8374 (pm20) REVERT: E 95 GLN cc_start: 0.9160 (tt0) cc_final: 0.8931 (tt0) REVERT: E 104 HIS cc_start: 0.9414 (m-70) cc_final: 0.9120 (m90) REVERT: E 127 GLN cc_start: 0.9386 (tp-100) cc_final: 0.8844 (tm-30) REVERT: F 35 ARG cc_start: 0.8873 (ttp-110) cc_final: 0.8473 (ttp-110) REVERT: F 39 ARG cc_start: 0.8440 (mmt90) cc_final: 0.7739 (mmt180) REVERT: F 64 ASN cc_start: 0.9248 (t0) cc_final: 0.8331 (m-40) REVERT: F 67 ARG cc_start: 0.9361 (ttm170) cc_final: 0.9121 (tmm-80) REVERT: F 68 ASP cc_start: 0.8965 (m-30) cc_final: 0.7263 (m-30) REVERT: F 70 VAL cc_start: 0.8761 (p) cc_final: 0.8005 (p) REVERT: F 71 THR cc_start: 0.8773 (p) cc_final: 0.8116 (p) REVERT: F 81 VAL cc_start: 0.9554 (t) cc_final: 0.9170 (t) REVERT: F 88 TYR cc_start: 0.9087 (m-10) cc_final: 0.8529 (m-80) REVERT: F 90 LEU cc_start: 0.9782 (mt) cc_final: 0.9579 (mp) REVERT: F 97 LEU cc_start: 0.9178 (mm) cc_final: 0.8969 (mm) REVERT: G 25 PHE cc_start: 0.8319 (m-80) cc_final: 0.7978 (m-80) REVERT: G 36 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8667 (mmmt) REVERT: G 56 GLU cc_start: 0.9539 (tm-30) cc_final: 0.9254 (tm-30) REVERT: G 87 ILE cc_start: 0.9037 (mm) cc_final: 0.8678 (mm) REVERT: G 89 ASN cc_start: 0.8546 (m-40) cc_final: 0.8330 (m110) REVERT: G 94 ASN cc_start: 0.9313 (t0) cc_final: 0.9069 (m-40) REVERT: H 68 ASP cc_start: 0.8998 (t70) cc_final: 0.8785 (t0) REVERT: H 71 GLU cc_start: 0.8888 (tp30) cc_final: 0.8622 (tm-30) REVERT: H 106 LEU cc_start: 0.9371 (mt) cc_final: 0.8884 (mt) REVERT: H 120 LYS cc_start: 0.9518 (tttt) cc_final: 0.9124 (tttm) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.3389 time to fit residues: 132.0791 Evaluate side-chains 211 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN G 31 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12761 Z= 0.285 Angle : 0.672 9.623 18476 Z= 0.390 Chirality : 0.037 0.204 2091 Planarity : 0.004 0.029 1328 Dihedral : 31.086 176.370 4002 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.32 % Allowed : 4.80 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.29), residues: 738 helix: 0.87 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.88 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 47 HIS 0.005 0.001 HIS B 75 PHE 0.011 0.001 PHE B 100 TYR 0.019 0.002 TYR E 110 ARG 0.005 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 268 time to evaluate : 0.894 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 49 LYS cc_start: 0.9277 (mmtm) cc_final: 0.8951 (pttm) REVERT: A 64 LYS cc_start: 0.9169 (mppt) cc_final: 0.8956 (mmtm) REVERT: A 67 PHE cc_start: 0.9299 (t80) cc_final: 0.9058 (t80) REVERT: A 83 ASP cc_start: 0.6797 (t70) cc_final: 0.6493 (t0) REVERT: A 86 TRP cc_start: 0.9009 (m100) cc_final: 0.8730 (m100) REVERT: A 95 GLN cc_start: 0.9257 (tt0) cc_final: 0.8717 (tt0) REVERT: A 96 GLU cc_start: 0.8593 (tp30) cc_final: 0.8245 (tp30) REVERT: A 99 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 104 HIS cc_start: 0.8874 (m-70) cc_final: 0.8581 (t-170) REVERT: A 107 GLU cc_start: 0.8535 (pp20) cc_final: 0.8164 (pp20) REVERT: A 110 TYR cc_start: 0.8623 (t80) cc_final: 0.8195 (t80) REVERT: A 130 ARG cc_start: 0.8943 (mtp180) cc_final: 0.8446 (ttt-90) REVERT: B 27 GLN cc_start: 0.8512 (pt0) cc_final: 0.7933 (pm20) REVERT: B 63 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8706 (tm-30) REVERT: B 79 LYS cc_start: 0.9329 (mttp) cc_final: 0.8981 (mtmt) REVERT: C 95 LYS cc_start: 0.9546 (tttm) cc_final: 0.9155 (mttm) REVERT: D 39 TYR cc_start: 0.8829 (t80) cc_final: 0.8315 (t80) REVERT: D 43 LYS cc_start: 0.9097 (tttt) cc_final: 0.8701 (tppt) REVERT: D 65 ASP cc_start: 0.9293 (t0) cc_final: 0.9074 (t0) REVERT: D 68 GLU cc_start: 0.9060 (tt0) cc_final: 0.8355 (tm-30) REVERT: D 77 LEU cc_start: 0.9599 (tt) cc_final: 0.9329 (tt) REVERT: D 110 GLU cc_start: 0.8929 (tt0) cc_final: 0.8527 (tt0) REVERT: E 55 GLN cc_start: 0.9249 (mt0) cc_final: 0.9026 (mt0) REVERT: E 58 THR cc_start: 0.9147 (p) cc_final: 0.8791 (t) REVERT: E 87 GLN cc_start: 0.8749 (mt0) cc_final: 0.7624 (mt0) REVERT: E 89 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8382 (pm20) REVERT: E 95 GLN cc_start: 0.9123 (tt0) cc_final: 0.8869 (tt0) REVERT: E 104 HIS cc_start: 0.9328 (m-70) cc_final: 0.9099 (m90) REVERT: E 108 ASP cc_start: 0.8862 (m-30) cc_final: 0.8423 (m-30) REVERT: E 127 GLN cc_start: 0.9340 (tp40) cc_final: 0.9023 (tm-30) REVERT: F 44 LYS cc_start: 0.8527 (tptp) cc_final: 0.7692 (tptt) REVERT: F 64 ASN cc_start: 0.9073 (t0) cc_final: 0.7958 (m-40) REVERT: F 68 ASP cc_start: 0.8700 (m-30) cc_final: 0.8049 (m-30) REVERT: F 70 VAL cc_start: 0.8736 (p) cc_final: 0.8088 (p) REVERT: F 71 THR cc_start: 0.8716 (p) cc_final: 0.8236 (p) REVERT: F 74 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8738 (mt-10) REVERT: F 81 VAL cc_start: 0.9486 (t) cc_final: 0.8877 (t) REVERT: G 36 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8738 (mmmt) REVERT: G 56 GLU cc_start: 0.9549 (tm-30) cc_final: 0.9326 (tm-30) REVERT: G 68 ASN cc_start: 0.8964 (m-40) cc_final: 0.8706 (m-40) REVERT: G 89 ASN cc_start: 0.8469 (m-40) cc_final: 0.8194 (m110) REVERT: G 94 ASN cc_start: 0.9352 (t0) cc_final: 0.9034 (m110) REVERT: H 43 LYS cc_start: 0.9604 (mtpp) cc_final: 0.9380 (ptpp) REVERT: H 47 GLN cc_start: 0.9292 (tm-30) cc_final: 0.9080 (tm-30) REVERT: H 62 MET cc_start: 0.9334 (mmm) cc_final: 0.9004 (mmm) REVERT: H 106 LEU cc_start: 0.9331 (mt) cc_final: 0.9127 (mt) REVERT: H 116 LYS cc_start: 0.9393 (ptmt) cc_final: 0.9147 (pttm) REVERT: H 120 LYS cc_start: 0.9530 (tttt) cc_final: 0.9228 (tttp) outliers start: 2 outliers final: 1 residues processed: 268 average time/residue: 0.3233 time to fit residues: 112.7581 Evaluate side-chains 213 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN B 93 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12761 Z= 0.289 Angle : 0.654 9.845 18476 Z= 0.383 Chirality : 0.037 0.163 2091 Planarity : 0.004 0.035 1328 Dihedral : 31.070 175.602 4002 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.16 % Allowed : 3.68 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.30), residues: 738 helix: 1.20 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.89 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 531 HIS 0.005 0.001 HIS F 75 PHE 0.010 0.002 PHE A 78 TYR 0.029 0.002 TYR H 83 ARG 0.006 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9283 (mmtm) cc_final: 0.8991 (pttp) REVERT: A 67 PHE cc_start: 0.9243 (t80) cc_final: 0.9026 (t80) REVERT: A 83 ASP cc_start: 0.6883 (t70) cc_final: 0.6609 (t0) REVERT: A 86 TRP cc_start: 0.8966 (m100) cc_final: 0.8702 (m100) REVERT: A 95 GLN cc_start: 0.9297 (tt0) cc_final: 0.8548 (tt0) REVERT: A 96 GLU cc_start: 0.8679 (tp30) cc_final: 0.8271 (tp30) REVERT: A 99 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 104 HIS cc_start: 0.8807 (m-70) cc_final: 0.8537 (t70) REVERT: A 107 GLU cc_start: 0.8515 (pp20) cc_final: 0.8155 (pp20) REVERT: A 110 TYR cc_start: 0.8683 (t80) cc_final: 0.8394 (t80) REVERT: A 130 ARG cc_start: 0.9033 (mtp180) cc_final: 0.8562 (ttt-90) REVERT: B 27 GLN cc_start: 0.8654 (pt0) cc_final: 0.7905 (pm20) REVERT: B 63 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8781 (tm-30) REVERT: B 74 GLU cc_start: 0.9372 (tt0) cc_final: 0.8901 (pt0) REVERT: B 79 LYS cc_start: 0.9305 (mttp) cc_final: 0.8884 (mtmt) REVERT: B 98 TYR cc_start: 0.8472 (m-80) cc_final: 0.7922 (m-80) REVERT: C 84 GLN cc_start: 0.9334 (tp40) cc_final: 0.8900 (mt0) REVERT: C 95 LYS cc_start: 0.9670 (tttm) cc_final: 0.9233 (mttm) REVERT: C 104 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8076 (tp-100) REVERT: D 39 TYR cc_start: 0.8809 (t80) cc_final: 0.8437 (t80) REVERT: D 43 LYS cc_start: 0.9097 (tttt) cc_final: 0.8708 (tppt) REVERT: D 65 ASP cc_start: 0.9355 (t0) cc_final: 0.9117 (t0) REVERT: D 68 GLU cc_start: 0.9059 (tt0) cc_final: 0.8334 (tm-30) REVERT: D 69 ARG cc_start: 0.9010 (ptp-170) cc_final: 0.8746 (ptm160) REVERT: D 77 LEU cc_start: 0.9561 (tt) cc_final: 0.9116 (tt) REVERT: D 90 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8335 (mm-30) REVERT: E 79 THR cc_start: 0.8267 (p) cc_final: 0.7949 (p) REVERT: E 87 GLN cc_start: 0.8637 (mt0) cc_final: 0.7285 (mt0) REVERT: E 89 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8403 (pm20) REVERT: E 104 HIS cc_start: 0.9309 (m-70) cc_final: 0.9080 (m90) REVERT: E 108 ASP cc_start: 0.8896 (m-30) cc_final: 0.8657 (m-30) REVERT: F 64 ASN cc_start: 0.8918 (t0) cc_final: 0.8065 (m-40) REVERT: F 67 ARG cc_start: 0.9011 (tmm-80) cc_final: 0.8694 (tmm-80) REVERT: F 68 ASP cc_start: 0.8944 (m-30) cc_final: 0.8648 (m-30) REVERT: F 70 VAL cc_start: 0.8806 (p) cc_final: 0.8232 (p) REVERT: F 71 THR cc_start: 0.8650 (p) cc_final: 0.8189 (p) REVERT: F 81 VAL cc_start: 0.9515 (t) cc_final: 0.8871 (t) REVERT: G 25 PHE cc_start: 0.8551 (m-80) cc_final: 0.8165 (m-80) REVERT: G 36 LYS cc_start: 0.9237 (mtpt) cc_final: 0.8806 (mmmt) REVERT: G 56 GLU cc_start: 0.9542 (tm-30) cc_final: 0.9315 (tm-30) REVERT: G 89 ASN cc_start: 0.8506 (m-40) cc_final: 0.8271 (m110) REVERT: G 94 ASN cc_start: 0.9401 (t0) cc_final: 0.9057 (m-40) REVERT: H 43 LYS cc_start: 0.9548 (mtpp) cc_final: 0.9322 (ttpp) REVERT: H 62 MET cc_start: 0.9373 (mmm) cc_final: 0.9061 (mmm) REVERT: H 116 LYS cc_start: 0.9393 (ptmt) cc_final: 0.9121 (pttm) REVERT: H 120 LYS cc_start: 0.9564 (tttt) cc_final: 0.9240 (tttm) outliers start: 1 outliers final: 1 residues processed: 250 average time/residue: 0.3261 time to fit residues: 106.0190 Evaluate side-chains 198 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12761 Z= 0.203 Angle : 0.608 10.055 18476 Z= 0.356 Chirality : 0.035 0.153 2091 Planarity : 0.003 0.029 1328 Dihedral : 30.886 173.487 4002 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.16 % Allowed : 1.76 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.30), residues: 738 helix: 1.50 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.73 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 531 HIS 0.003 0.001 HIS H 109 PHE 0.015 0.001 PHE B 100 TYR 0.012 0.001 TYR E 110 ARG 0.004 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 0.956 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: A 49 LYS cc_start: 0.9262 (mmtm) cc_final: 0.8936 (pttp) REVERT: A 50 GLU cc_start: 0.9267 (mp0) cc_final: 0.9001 (mp0) REVERT: A 67 PHE cc_start: 0.9148 (t80) cc_final: 0.8844 (t80) REVERT: A 83 ASP cc_start: 0.6736 (t70) cc_final: 0.6401 (t0) REVERT: A 86 TRP cc_start: 0.8852 (m100) cc_final: 0.8498 (m100) REVERT: A 95 GLN cc_start: 0.9289 (tt0) cc_final: 0.8683 (tt0) REVERT: A 96 GLU cc_start: 0.8637 (tp30) cc_final: 0.8231 (tp30) REVERT: A 99 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8011 (mt-10) REVERT: A 104 HIS cc_start: 0.8891 (m-70) cc_final: 0.8578 (t70) REVERT: A 107 GLU cc_start: 0.8461 (pp20) cc_final: 0.8094 (pp20) REVERT: A 110 TYR cc_start: 0.8520 (t80) cc_final: 0.8304 (t80) REVERT: A 130 ARG cc_start: 0.8984 (mtp180) cc_final: 0.8637 (ttt-90) REVERT: B 63 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8669 (tm-30) REVERT: B 74 GLU cc_start: 0.9360 (tt0) cc_final: 0.8876 (pt0) REVERT: B 79 LYS cc_start: 0.9356 (mttp) cc_final: 0.8892 (mtmt) REVERT: C 84 GLN cc_start: 0.9292 (tp40) cc_final: 0.8790 (mt0) REVERT: C 95 LYS cc_start: 0.9616 (tttm) cc_final: 0.9057 (mttm) REVERT: C 104 GLN cc_start: 0.8595 (tp-100) cc_final: 0.8158 (tp-100) REVERT: D 39 TYR cc_start: 0.8743 (t80) cc_final: 0.8418 (t80) REVERT: D 43 LYS cc_start: 0.9082 (tttt) cc_final: 0.8680 (tppt) REVERT: D 65 ASP cc_start: 0.9340 (t0) cc_final: 0.9046 (t0) REVERT: D 68 GLU cc_start: 0.8994 (tt0) cc_final: 0.8256 (tm-30) REVERT: D 69 ARG cc_start: 0.8961 (ptp-170) cc_final: 0.8412 (ptm160) REVERT: E 87 GLN cc_start: 0.8616 (mt0) cc_final: 0.7402 (mt0) REVERT: E 89 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8407 (pm20) REVERT: E 124 LYS cc_start: 0.9116 (mppt) cc_final: 0.8865 (tmmt) REVERT: F 44 LYS cc_start: 0.8363 (tptp) cc_final: 0.8033 (tptt) REVERT: F 63 GLU cc_start: 0.9093 (tp30) cc_final: 0.8874 (tp30) REVERT: F 68 ASP cc_start: 0.9207 (m-30) cc_final: 0.8868 (m-30) REVERT: F 70 VAL cc_start: 0.8807 (p) cc_final: 0.7513 (p) REVERT: F 71 THR cc_start: 0.8625 (p) cc_final: 0.7942 (p) REVERT: F 81 VAL cc_start: 0.9491 (t) cc_final: 0.8982 (t) REVERT: F 88 TYR cc_start: 0.8927 (m-10) cc_final: 0.8681 (m-80) REVERT: G 25 PHE cc_start: 0.8612 (m-80) cc_final: 0.8123 (m-80) REVERT: G 36 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8806 (mmmt) REVERT: G 56 GLU cc_start: 0.9480 (tm-30) cc_final: 0.9220 (tm-30) REVERT: G 87 ILE cc_start: 0.9047 (mm) cc_final: 0.8560 (pt) REVERT: G 89 ASN cc_start: 0.8518 (m-40) cc_final: 0.8268 (m110) REVERT: G 94 ASN cc_start: 0.9332 (t0) cc_final: 0.9057 (m110) REVERT: H 59 MET cc_start: 0.8479 (tpp) cc_final: 0.8202 (tpp) REVERT: H 62 MET cc_start: 0.9363 (mmm) cc_final: 0.9034 (mmm) REVERT: H 76 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8881 (mm-30) REVERT: H 79 ARG cc_start: 0.9178 (ptp90) cc_final: 0.8529 (ptp90) REVERT: H 116 LYS cc_start: 0.9344 (ptmt) cc_final: 0.9106 (pttm) REVERT: H 120 LYS cc_start: 0.9530 (tttt) cc_final: 0.9263 (tttp) outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.3234 time to fit residues: 105.9120 Evaluate side-chains 202 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 81 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12761 Z= 0.233 Angle : 0.618 10.111 18476 Z= 0.361 Chirality : 0.035 0.146 2091 Planarity : 0.003 0.031 1328 Dihedral : 30.859 171.445 4002 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.31), residues: 738 helix: 1.54 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.68 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 531 HIS 0.003 0.001 HIS H 109 PHE 0.017 0.001 PHE B 100 TYR 0.015 0.002 TYR E 110 ARG 0.004 0.000 ARG E 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 0.984 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: A 49 LYS cc_start: 0.9257 (mmtm) cc_final: 0.8917 (pttp) REVERT: A 50 GLU cc_start: 0.9272 (mp0) cc_final: 0.9001 (mp0) REVERT: A 67 PHE cc_start: 0.9140 (t80) cc_final: 0.8848 (t80) REVERT: A 83 ASP cc_start: 0.6780 (t70) cc_final: 0.6519 (t0) REVERT: A 86 TRP cc_start: 0.8883 (m100) cc_final: 0.8501 (m100) REVERT: A 95 GLN cc_start: 0.9346 (tt0) cc_final: 0.8775 (tt0) REVERT: A 96 GLU cc_start: 0.8651 (tp30) cc_final: 0.8417 (tp30) REVERT: A 99 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8114 (mt-10) REVERT: A 104 HIS cc_start: 0.8649 (m-70) cc_final: 0.8310 (t-90) REVERT: A 107 GLU cc_start: 0.8545 (pp20) cc_final: 0.8188 (pp20) REVERT: A 110 TYR cc_start: 0.8515 (t80) cc_final: 0.8291 (t80) REVERT: A 111 LEU cc_start: 0.9249 (mm) cc_final: 0.8931 (mm) REVERT: A 130 ARG cc_start: 0.8996 (mtp180) cc_final: 0.8582 (ttt-90) REVERT: B 31 LYS cc_start: 0.9516 (mtmt) cc_final: 0.9299 (mtmm) REVERT: B 63 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8705 (tm-30) REVERT: B 74 GLU cc_start: 0.9376 (tt0) cc_final: 0.8910 (pt0) REVERT: B 79 LYS cc_start: 0.9389 (mttp) cc_final: 0.8925 (mtmt) REVERT: B 88 TYR cc_start: 0.9048 (m-10) cc_final: 0.8830 (m-80) REVERT: B 98 TYR cc_start: 0.8375 (m-80) cc_final: 0.7620 (m-80) REVERT: C 84 GLN cc_start: 0.9315 (tp40) cc_final: 0.8815 (mt0) REVERT: C 95 LYS cc_start: 0.9660 (tttm) cc_final: 0.9106 (mttm) REVERT: C 104 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8163 (tp-100) REVERT: C 107 VAL cc_start: 0.8751 (t) cc_final: 0.8545 (t) REVERT: D 39 TYR cc_start: 0.8717 (t80) cc_final: 0.8442 (t80) REVERT: D 43 LYS cc_start: 0.9042 (tttt) cc_final: 0.8687 (tppt) REVERT: D 65 ASP cc_start: 0.9358 (t0) cc_final: 0.9074 (t0) REVERT: D 68 GLU cc_start: 0.9005 (tt0) cc_final: 0.8368 (tm-30) REVERT: D 69 ARG cc_start: 0.8988 (ptp-170) cc_final: 0.8437 (ptm160) REVERT: D 110 GLU cc_start: 0.9147 (tt0) cc_final: 0.8726 (tt0) REVERT: E 87 GLN cc_start: 0.8568 (mt0) cc_final: 0.7298 (mt0) REVERT: E 89 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8366 (pm20) REVERT: E 108 ASP cc_start: 0.8929 (m-30) cc_final: 0.8514 (m-30) REVERT: E 110 TYR cc_start: 0.8587 (t80) cc_final: 0.8205 (t80) REVERT: E 124 LYS cc_start: 0.9095 (mppt) cc_final: 0.8841 (tmmt) REVERT: E 125 ASP cc_start: 0.8737 (m-30) cc_final: 0.8332 (m-30) REVERT: E 127 GLN cc_start: 0.9396 (tm-30) cc_final: 0.9057 (tm-30) REVERT: E 133 ARG cc_start: 0.8690 (ttt180) cc_final: 0.8317 (ttm170) REVERT: F 31 LYS cc_start: 0.9240 (tttm) cc_final: 0.8888 (tttm) REVERT: F 63 GLU cc_start: 0.9133 (tp30) cc_final: 0.8854 (tp30) REVERT: F 67 ARG cc_start: 0.9101 (tmm-80) cc_final: 0.8828 (ttp80) REVERT: F 68 ASP cc_start: 0.9064 (m-30) cc_final: 0.7666 (m-30) REVERT: F 70 VAL cc_start: 0.8546 (p) cc_final: 0.7983 (p) REVERT: F 73 THR cc_start: 0.9202 (p) cc_final: 0.8984 (p) REVERT: F 74 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8194 (mp0) REVERT: F 81 VAL cc_start: 0.9497 (t) cc_final: 0.9034 (t) REVERT: F 88 TYR cc_start: 0.9067 (m-10) cc_final: 0.8638 (m-80) REVERT: G 36 LYS cc_start: 0.9195 (mtpt) cc_final: 0.8827 (mmmt) REVERT: G 56 GLU cc_start: 0.9508 (tm-30) cc_final: 0.9303 (tm-30) REVERT: G 87 ILE cc_start: 0.9064 (mm) cc_final: 0.8610 (pt) REVERT: G 89 ASN cc_start: 0.8482 (m-40) cc_final: 0.8262 (m110) REVERT: G 94 ASN cc_start: 0.9337 (t0) cc_final: 0.9042 (m-40) REVERT: H 62 MET cc_start: 0.9334 (mmm) cc_final: 0.9042 (mmm) REVERT: H 116 LYS cc_start: 0.9387 (ptmt) cc_final: 0.9122 (pttm) REVERT: H 120 LYS cc_start: 0.9519 (tttt) cc_final: 0.9193 (tttp) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3174 time to fit residues: 104.3668 Evaluate side-chains 203 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12761 Z= 0.276 Angle : 0.645 9.953 18476 Z= 0.374 Chirality : 0.037 0.142 2091 Planarity : 0.004 0.034 1328 Dihedral : 30.970 169.875 4002 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.16 % Allowed : 2.88 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.31), residues: 738 helix: 1.48 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.78 (0.37), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 86 HIS 0.004 0.001 HIS H 109 PHE 0.015 0.002 PHE B 100 TYR 0.023 0.002 TYR E 110 ARG 0.004 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 0.900 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 49 LYS cc_start: 0.9255 (mmtm) cc_final: 0.8943 (pttm) REVERT: A 83 ASP cc_start: 0.6979 (t70) cc_final: 0.6707 (t0) REVERT: A 86 TRP cc_start: 0.8930 (m100) cc_final: 0.8567 (m100) REVERT: A 104 HIS cc_start: 0.8836 (m-70) cc_final: 0.8500 (t-90) REVERT: A 107 GLU cc_start: 0.8501 (pp20) cc_final: 0.8107 (pp20) REVERT: A 110 TYR cc_start: 0.8545 (t80) cc_final: 0.8339 (t80) REVERT: A 130 ARG cc_start: 0.9089 (mtp180) cc_final: 0.8721 (ttt-90) REVERT: B 27 GLN cc_start: 0.8570 (pt0) cc_final: 0.7983 (pm20) REVERT: B 31 LYS cc_start: 0.9482 (mtmt) cc_final: 0.9125 (ttpt) REVERT: B 63 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8915 (tm-30) REVERT: B 74 GLU cc_start: 0.9349 (tt0) cc_final: 0.8934 (pt0) REVERT: B 79 LYS cc_start: 0.9409 (mttp) cc_final: 0.8953 (mtmt) REVERT: B 98 TYR cc_start: 0.8424 (m-80) cc_final: 0.8156 (m-80) REVERT: C 84 GLN cc_start: 0.9300 (tp40) cc_final: 0.8817 (mt0) REVERT: C 95 LYS cc_start: 0.9701 (tttm) cc_final: 0.9134 (mttm) REVERT: C 104 GLN cc_start: 0.8623 (tp-100) cc_final: 0.7994 (tp-100) REVERT: D 39 TYR cc_start: 0.8752 (t80) cc_final: 0.8490 (t80) REVERT: D 43 LYS cc_start: 0.9055 (tttt) cc_final: 0.8679 (tppt) REVERT: D 44 GLN cc_start: 0.9241 (tm-30) cc_final: 0.9036 (tm-30) REVERT: D 65 ASP cc_start: 0.9355 (t0) cc_final: 0.9048 (t0) REVERT: D 68 GLU cc_start: 0.9036 (tt0) cc_final: 0.8460 (tm-30) REVERT: D 69 ARG cc_start: 0.8959 (ptp-170) cc_final: 0.8277 (ptm160) REVERT: D 110 GLU cc_start: 0.9200 (tt0) cc_final: 0.8717 (tm-30) REVERT: E 87 GLN cc_start: 0.8718 (mt0) cc_final: 0.7443 (mt0) REVERT: E 89 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8392 (pm20) REVERT: E 125 ASP cc_start: 0.8795 (m-30) cc_final: 0.8441 (m-30) REVERT: E 127 GLN cc_start: 0.9444 (tm-30) cc_final: 0.9085 (tm-30) REVERT: F 29 ILE cc_start: 0.9509 (mm) cc_final: 0.9179 (pt) REVERT: F 46 ILE cc_start: 0.9459 (mp) cc_final: 0.9212 (pt) REVERT: F 63 GLU cc_start: 0.9092 (tp30) cc_final: 0.8886 (tp30) REVERT: F 68 ASP cc_start: 0.9079 (m-30) cc_final: 0.8816 (m-30) REVERT: F 70 VAL cc_start: 0.8712 (p) cc_final: 0.8261 (p) REVERT: F 81 VAL cc_start: 0.9445 (t) cc_final: 0.8709 (t) REVERT: F 88 TYR cc_start: 0.8934 (m-10) cc_final: 0.8491 (m-80) REVERT: G 36 LYS cc_start: 0.9204 (mtpt) cc_final: 0.8845 (mmmt) REVERT: G 50 TYR cc_start: 0.8713 (t80) cc_final: 0.7949 (t80) REVERT: G 56 GLU cc_start: 0.9520 (tm-30) cc_final: 0.9314 (tm-30) REVERT: G 87 ILE cc_start: 0.9029 (mm) cc_final: 0.8571 (pt) REVERT: G 89 ASN cc_start: 0.8471 (m-40) cc_final: 0.8257 (m110) REVERT: G 94 ASN cc_start: 0.9390 (t0) cc_final: 0.9116 (m-40) REVERT: H 95 GLN cc_start: 0.9419 (tt0) cc_final: 0.9077 (tp40) REVERT: H 120 LYS cc_start: 0.9520 (tttt) cc_final: 0.9158 (tttp) outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.3204 time to fit residues: 99.6299 Evaluate side-chains 191 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 95 GLN C 89 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12761 Z= 0.298 Angle : 0.668 9.975 18476 Z= 0.388 Chirality : 0.038 0.144 2091 Planarity : 0.004 0.032 1328 Dihedral : 31.085 168.486 4002 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.30), residues: 738 helix: 1.27 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.82 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 86 HIS 0.005 0.001 HIS G 82 PHE 0.017 0.002 PHE B 100 TYR 0.015 0.002 TYR C 50 ARG 0.006 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 0.908 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: A 49 LYS cc_start: 0.9269 (mmtm) cc_final: 0.8998 (pttp) REVERT: A 83 ASP cc_start: 0.7425 (t70) cc_final: 0.7123 (t0) REVERT: A 86 TRP cc_start: 0.8890 (m100) cc_final: 0.8471 (m100) REVERT: A 99 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8070 (mt-10) REVERT: A 104 HIS cc_start: 0.8785 (m-70) cc_final: 0.8394 (t-90) REVERT: A 107 GLU cc_start: 0.8522 (pp20) cc_final: 0.8139 (pp20) REVERT: A 130 ARG cc_start: 0.9146 (mtp180) cc_final: 0.8761 (ttt-90) REVERT: B 27 GLN cc_start: 0.8602 (pt0) cc_final: 0.7977 (pm20) REVERT: B 31 LYS cc_start: 0.9466 (mtmt) cc_final: 0.9124 (ttpt) REVERT: B 74 GLU cc_start: 0.9348 (tt0) cc_final: 0.8927 (pt0) REVERT: B 79 LYS cc_start: 0.9391 (mttp) cc_final: 0.8961 (mtmt) REVERT: B 98 TYR cc_start: 0.8517 (m-80) cc_final: 0.7898 (m-80) REVERT: C 84 GLN cc_start: 0.9303 (tp40) cc_final: 0.8857 (tp40) REVERT: C 93 LEU cc_start: 0.9562 (mt) cc_final: 0.9242 (mt) REVERT: C 95 LYS cc_start: 0.9731 (tttm) cc_final: 0.9180 (mttm) REVERT: C 104 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8162 (tp-100) REVERT: D 39 TYR cc_start: 0.8768 (t80) cc_final: 0.8403 (t80) REVERT: D 43 LYS cc_start: 0.9073 (tttt) cc_final: 0.8687 (tppt) REVERT: D 65 ASP cc_start: 0.9362 (t0) cc_final: 0.9008 (t0) REVERT: D 68 GLU cc_start: 0.9016 (tt0) cc_final: 0.8519 (tm-30) REVERT: D 69 ARG cc_start: 0.8943 (ptp-170) cc_final: 0.8263 (ptm160) REVERT: D 110 GLU cc_start: 0.9194 (tt0) cc_final: 0.8867 (tm-30) REVERT: E 55 GLN cc_start: 0.9322 (mt0) cc_final: 0.8472 (mp10) REVERT: E 84 PHE cc_start: 0.8673 (m-10) cc_final: 0.8468 (m-10) REVERT: E 87 GLN cc_start: 0.8729 (mt0) cc_final: 0.7993 (mt0) REVERT: E 125 ASP cc_start: 0.8742 (m-30) cc_final: 0.8518 (m-30) REVERT: E 127 GLN cc_start: 0.9518 (tm-30) cc_final: 0.9226 (tm-30) REVERT: F 29 ILE cc_start: 0.9538 (mm) cc_final: 0.9237 (pt) REVERT: F 44 LYS cc_start: 0.8876 (tptp) cc_final: 0.8342 (tptt) REVERT: F 63 GLU cc_start: 0.9033 (tp30) cc_final: 0.8816 (tp30) REVERT: F 68 ASP cc_start: 0.9080 (m-30) cc_final: 0.8856 (m-30) REVERT: F 70 VAL cc_start: 0.8906 (p) cc_final: 0.8152 (p) REVERT: F 71 THR cc_start: 0.8797 (p) cc_final: 0.8487 (p) REVERT: F 81 VAL cc_start: 0.9425 (t) cc_final: 0.8672 (t) REVERT: F 88 TYR cc_start: 0.9022 (m-10) cc_final: 0.8609 (m-80) REVERT: G 36 LYS cc_start: 0.9201 (mtpt) cc_final: 0.8860 (mmmt) REVERT: G 56 GLU cc_start: 0.9509 (tm-30) cc_final: 0.9263 (tm-30) REVERT: G 87 ILE cc_start: 0.9113 (mm) cc_final: 0.8579 (pt) REVERT: G 89 ASN cc_start: 0.8437 (m-40) cc_final: 0.8227 (m110) REVERT: G 94 ASN cc_start: 0.9403 (t0) cc_final: 0.9115 (m-40) REVERT: H 62 MET cc_start: 0.9286 (mmm) cc_final: 0.8874 (mmm) REVERT: H 120 LYS cc_start: 0.9512 (tttt) cc_final: 0.9101 (tttm) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.3276 time to fit residues: 95.7329 Evaluate side-chains 183 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 12761 Z= 0.314 Angle : 0.682 9.919 18476 Z= 0.394 Chirality : 0.039 0.148 2091 Planarity : 0.004 0.032 1328 Dihedral : 31.178 166.563 4002 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.30), residues: 738 helix: 1.19 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.96 (0.37), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 86 HIS 0.009 0.001 HIS D 106 PHE 0.014 0.002 PHE B 100 TYR 0.016 0.002 TYR C 50 ARG 0.005 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 0.807 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 49 LYS cc_start: 0.9279 (mmtm) cc_final: 0.9009 (pttp) REVERT: A 64 LYS cc_start: 0.9406 (mppt) cc_final: 0.9178 (mmtm) REVERT: A 86 TRP cc_start: 0.8882 (m100) cc_final: 0.8495 (m100) REVERT: A 95 GLN cc_start: 0.9192 (tt0) cc_final: 0.8581 (tt0) REVERT: A 99 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7980 (mt-10) REVERT: A 104 HIS cc_start: 0.8871 (m-70) cc_final: 0.8376 (t-90) REVERT: A 107 GLU cc_start: 0.8506 (pp20) cc_final: 0.8158 (pp20) REVERT: A 130 ARG cc_start: 0.9069 (mtp180) cc_final: 0.8683 (ttt-90) REVERT: B 27 GLN cc_start: 0.8638 (pt0) cc_final: 0.8012 (pm20) REVERT: B 31 LYS cc_start: 0.9436 (mtmt) cc_final: 0.9101 (ttpt) REVERT: B 74 GLU cc_start: 0.9353 (tt0) cc_final: 0.8930 (pt0) REVERT: B 79 LYS cc_start: 0.9375 (mttp) cc_final: 0.8920 (mtmt) REVERT: C 84 GLN cc_start: 0.9295 (tp40) cc_final: 0.8823 (tp40) REVERT: C 93 LEU cc_start: 0.9568 (mt) cc_final: 0.9294 (mt) REVERT: C 104 GLN cc_start: 0.8684 (tp-100) cc_final: 0.7987 (tp-100) REVERT: D 39 TYR cc_start: 0.8789 (t80) cc_final: 0.8415 (t80) REVERT: D 43 LYS cc_start: 0.9071 (tttt) cc_final: 0.8690 (tppt) REVERT: D 44 GLN cc_start: 0.9210 (tm-30) cc_final: 0.9008 (tm-30) REVERT: D 65 ASP cc_start: 0.9379 (t0) cc_final: 0.9003 (t0) REVERT: D 68 GLU cc_start: 0.9012 (tt0) cc_final: 0.8538 (tm-30) REVERT: D 69 ARG cc_start: 0.8924 (ptp-170) cc_final: 0.8244 (ptm160) REVERT: D 110 GLU cc_start: 0.9165 (tt0) cc_final: 0.8715 (tm-30) REVERT: E 87 GLN cc_start: 0.8687 (mt0) cc_final: 0.8011 (mt0) REVERT: E 127 GLN cc_start: 0.9516 (tm-30) cc_final: 0.9235 (tm-30) REVERT: F 29 ILE cc_start: 0.9529 (mm) cc_final: 0.9183 (pt) REVERT: F 44 LYS cc_start: 0.8889 (tptp) cc_final: 0.8338 (tptt) REVERT: F 55 ARG cc_start: 0.8296 (mtt180) cc_final: 0.7953 (mtt-85) REVERT: F 67 ARG cc_start: 0.9164 (tmm-80) cc_final: 0.8834 (ttp80) REVERT: F 81 VAL cc_start: 0.9235 (t) cc_final: 0.8605 (t) REVERT: G 36 LYS cc_start: 0.9192 (mtpt) cc_final: 0.8857 (mmmt) REVERT: G 56 GLU cc_start: 0.9465 (tm-30) cc_final: 0.9228 (tm-30) REVERT: G 87 ILE cc_start: 0.9130 (mm) cc_final: 0.8549 (pt) REVERT: G 94 ASN cc_start: 0.9407 (t0) cc_final: 0.9130 (m-40) REVERT: H 62 MET cc_start: 0.9193 (mmm) cc_final: 0.8907 (mmm) REVERT: H 120 LYS cc_start: 0.9552 (tttt) cc_final: 0.9155 (tttm) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.3169 time to fit residues: 93.6921 Evaluate side-chains 182 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12761 Z= 0.352 Angle : 0.718 11.566 18476 Z= 0.412 Chirality : 0.040 0.171 2091 Planarity : 0.004 0.031 1328 Dihedral : 31.313 165.320 4002 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.30), residues: 738 helix: 0.98 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.98 (0.37), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.011 0.002 HIS A 104 PHE 0.015 0.002 PHE H 70 TYR 0.037 0.003 TYR H 83 ARG 0.006 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.893 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 49 LYS cc_start: 0.9281 (mmtm) cc_final: 0.8976 (pttm) REVERT: A 86 TRP cc_start: 0.8854 (m100) cc_final: 0.8492 (m100) REVERT: A 95 GLN cc_start: 0.9183 (tt0) cc_final: 0.8513 (tt0) REVERT: A 99 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8018 (mt-10) REVERT: A 104 HIS cc_start: 0.8820 (m90) cc_final: 0.8423 (t-90) REVERT: A 107 GLU cc_start: 0.8521 (pp20) cc_final: 0.8109 (pp20) REVERT: A 130 ARG cc_start: 0.9142 (mtp180) cc_final: 0.8640 (ttt-90) REVERT: B 27 GLN cc_start: 0.8627 (pt0) cc_final: 0.8006 (pm20) REVERT: B 31 LYS cc_start: 0.9436 (mtmt) cc_final: 0.9061 (ttpt) REVERT: B 74 GLU cc_start: 0.9353 (tt0) cc_final: 0.8949 (pt0) REVERT: B 79 LYS cc_start: 0.9390 (mttp) cc_final: 0.8941 (mtmt) REVERT: C 84 GLN cc_start: 0.9294 (tp40) cc_final: 0.8822 (tp40) REVERT: C 93 LEU cc_start: 0.9519 (mt) cc_final: 0.9218 (mt) REVERT: C 104 GLN cc_start: 0.8712 (tp-100) cc_final: 0.7998 (tp-100) REVERT: D 39 TYR cc_start: 0.8797 (t80) cc_final: 0.8421 (t80) REVERT: D 43 LYS cc_start: 0.9096 (tttt) cc_final: 0.8698 (tppt) REVERT: D 44 GLN cc_start: 0.9227 (tm-30) cc_final: 0.9023 (tm-30) REVERT: D 65 ASP cc_start: 0.9382 (t0) cc_final: 0.9005 (t0) REVERT: D 68 GLU cc_start: 0.8998 (tt0) cc_final: 0.8564 (tm-30) REVERT: D 69 ARG cc_start: 0.8919 (ptp-170) cc_final: 0.8254 (ptm160) REVERT: D 110 GLU cc_start: 0.9101 (tt0) cc_final: 0.8714 (tm-30) REVERT: D 117 LYS cc_start: 0.9463 (ptmt) cc_final: 0.9207 (ptmm) REVERT: E 84 PHE cc_start: 0.8674 (m-10) cc_final: 0.8427 (m-10) REVERT: E 87 GLN cc_start: 0.8691 (mt0) cc_final: 0.8306 (mt0) REVERT: E 110 TYR cc_start: 0.8885 (t80) cc_final: 0.8491 (t80) REVERT: E 127 GLN cc_start: 0.9507 (tm-30) cc_final: 0.9189 (tm-30) REVERT: F 29 ILE cc_start: 0.9518 (mm) cc_final: 0.9172 (pt) REVERT: F 43 VAL cc_start: 0.9462 (t) cc_final: 0.9253 (p) REVERT: F 44 LYS cc_start: 0.8875 (tptp) cc_final: 0.8236 (tptt) REVERT: F 55 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7964 (mtt-85) REVERT: F 67 ARG cc_start: 0.9189 (tmm-80) cc_final: 0.8808 (ttp80) REVERT: F 68 ASP cc_start: 0.9119 (m-30) cc_final: 0.7812 (m-30) REVERT: F 79 LYS cc_start: 0.8354 (mtmm) cc_final: 0.7922 (mtmt) REVERT: F 81 VAL cc_start: 0.9229 (t) cc_final: 0.8871 (t) REVERT: G 36 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8880 (mmmt) REVERT: G 56 GLU cc_start: 0.9456 (tm-30) cc_final: 0.9208 (tm-30) REVERT: G 87 ILE cc_start: 0.9123 (mm) cc_final: 0.8558 (pt) REVERT: G 94 ASN cc_start: 0.9433 (t0) cc_final: 0.9151 (m-40) REVERT: H 62 MET cc_start: 0.9207 (mmm) cc_final: 0.8875 (mmm) REVERT: H 120 LYS cc_start: 0.9548 (tttt) cc_final: 0.9245 (ttpp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.3115 time to fit residues: 88.0356 Evaluate side-chains 179 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12761 Z= 0.194 Angle : 0.638 10.375 18476 Z= 0.367 Chirality : 0.036 0.173 2091 Planarity : 0.003 0.034 1328 Dihedral : 31.046 162.177 4002 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.30), residues: 738 helix: 1.33 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.90 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 531 HIS 0.003 0.001 HIS A 104 PHE 0.027 0.001 PHE A 78 TYR 0.029 0.002 TYR H 83 ARG 0.006 0.000 ARG E 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 0.938 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: A 49 LYS cc_start: 0.9236 (mmtm) cc_final: 0.8932 (pttp) REVERT: A 64 LYS cc_start: 0.9284 (mppt) cc_final: 0.9059 (mmtm) REVERT: A 86 TRP cc_start: 0.8706 (m100) cc_final: 0.8395 (m100) REVERT: A 92 LEU cc_start: 0.9110 (mm) cc_final: 0.8637 (pp) REVERT: A 95 GLN cc_start: 0.9093 (tt0) cc_final: 0.8606 (tt0) REVERT: A 99 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 107 GLU cc_start: 0.8468 (pp20) cc_final: 0.8117 (pp20) REVERT: A 130 ARG cc_start: 0.9029 (mtp180) cc_final: 0.8672 (ttt-90) REVERT: B 27 GLN cc_start: 0.8677 (pt0) cc_final: 0.8002 (pm20) REVERT: B 31 LYS cc_start: 0.9425 (mtmt) cc_final: 0.9070 (ttpt) REVERT: B 74 GLU cc_start: 0.9392 (tt0) cc_final: 0.8889 (pt0) REVERT: B 79 LYS cc_start: 0.9356 (mttp) cc_final: 0.8898 (mtmt) REVERT: C 39 TYR cc_start: 0.8889 (m-80) cc_final: 0.8685 (m-10) REVERT: C 71 ARG cc_start: 0.9137 (tmm160) cc_final: 0.8933 (ttp80) REVERT: C 84 GLN cc_start: 0.9273 (tp40) cc_final: 0.8796 (tp40) REVERT: C 89 ASN cc_start: 0.8273 (m-40) cc_final: 0.7824 (m110) REVERT: C 93 LEU cc_start: 0.9448 (mt) cc_final: 0.9179 (mt) REVERT: C 95 LYS cc_start: 0.9707 (tttm) cc_final: 0.9096 (mttm) REVERT: C 104 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8226 (tp-100) REVERT: D 39 TYR cc_start: 0.8769 (t80) cc_final: 0.8366 (t80) REVERT: D 43 LYS cc_start: 0.9017 (tttt) cc_final: 0.8699 (tppt) REVERT: D 65 ASP cc_start: 0.9345 (t0) cc_final: 0.9143 (p0) REVERT: D 68 GLU cc_start: 0.8959 (tt0) cc_final: 0.8442 (tm-30) REVERT: D 69 ARG cc_start: 0.8839 (ptp-170) cc_final: 0.8367 (ptm160) REVERT: D 82 LYS cc_start: 0.9416 (mppt) cc_final: 0.9183 (mmtm) REVERT: D 110 GLU cc_start: 0.9145 (tt0) cc_final: 0.8943 (tm-30) REVERT: E 87 GLN cc_start: 0.8726 (mt0) cc_final: 0.8090 (mt0) REVERT: E 110 TYR cc_start: 0.8844 (t80) cc_final: 0.8497 (t80) REVERT: E 127 GLN cc_start: 0.9511 (tm-30) cc_final: 0.9221 (tm-30) REVERT: F 29 ILE cc_start: 0.9515 (mm) cc_final: 0.9097 (pt) REVERT: F 55 ARG cc_start: 0.8247 (mtt180) cc_final: 0.8033 (mtt-85) REVERT: F 67 ARG cc_start: 0.9121 (tmm-80) cc_final: 0.8848 (ttp80) REVERT: F 68 ASP cc_start: 0.8975 (m-30) cc_final: 0.7718 (m-30) REVERT: F 79 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7540 (mtmt) REVERT: F 81 VAL cc_start: 0.9235 (t) cc_final: 0.8522 (t) REVERT: G 36 LYS cc_start: 0.9162 (mtpt) cc_final: 0.8796 (mmmt) REVERT: G 56 GLU cc_start: 0.9478 (tm-30) cc_final: 0.9200 (tm-30) REVERT: G 87 ILE cc_start: 0.9012 (mm) cc_final: 0.8537 (pt) REVERT: G 94 ASN cc_start: 0.9321 (t0) cc_final: 0.9114 (m-40) REVERT: H 62 MET cc_start: 0.9285 (mmm) cc_final: 0.8918 (mmm) REVERT: H 85 LYS cc_start: 0.9505 (mttt) cc_final: 0.9280 (mmmm) REVERT: H 120 LYS cc_start: 0.9482 (tttt) cc_final: 0.9029 (tttm) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3121 time to fit residues: 99.4907 Evaluate side-chains 192 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 59 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.051241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.038556 restraints weight = 88853.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.039744 restraints weight = 48151.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.040636 restraints weight = 31891.017| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12761 Z= 0.223 Angle : 0.647 10.320 18476 Z= 0.371 Chirality : 0.036 0.177 2091 Planarity : 0.003 0.034 1328 Dihedral : 30.980 159.108 4002 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.30), residues: 738 helix: 1.39 (0.23), residues: 527 sheet: None (None), residues: 0 loop : -2.02 (0.36), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 86 HIS 0.006 0.001 HIS A 104 PHE 0.017 0.002 PHE E 84 TYR 0.028 0.002 TYR H 83 ARG 0.004 0.000 ARG E 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.56 seconds wall clock time: 42 minutes 40.79 seconds (2560.79 seconds total)