Starting phenix.real_space_refine on Wed Feb 14 08:20:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pop_17794/02_2024/8pop_17794.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pop_17794/02_2024/8pop_17794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pop_17794/02_2024/8pop_17794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pop_17794/02_2024/8pop_17794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pop_17794/02_2024/8pop_17794.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pop_17794/02_2024/8pop_17794.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.013 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 55 5.49 5 S 1 5.16 5 C 5374 2.51 5 N 1692 2.21 5 O 1807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ARG 114": "NH1" <-> "NH2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G ARG 114": "NH1" <-> "NH2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H ARG 114": "NH1" <-> "NH2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I ARG 114": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8929 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 978 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "B" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1003 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "D" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "E" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "H" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "I" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "J" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 577 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "K" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 568 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Time building chain proxies: 5.39, per 1000 atoms: 0.60 Number of scatterers: 8929 At special positions: 0 Unit cell: (96.3001, 103.433, 105.811, 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 1 16.00 P 55 15.00 O 1807 8.00 N 1692 7.00 C 5374 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: 4.17 Conformation dependent library (CDL) restraints added in 1.6 seconds 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1850 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 81.8% alpha, 0.0% beta 28 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 removed outlier: 3.555A pdb=" N ALA A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 48 through 49 No H-bonds generated for 'chain 'A' and resid 48 through 49' Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 55 through 85 removed outlier: 3.597A pdb=" N GLU A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 116 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 48 through 49 No H-bonds generated for 'chain 'B' and resid 48 through 49' Processing helix chain 'B' and resid 50 through 54 Processing helix chain 'B' and resid 55 through 85 removed outlier: 3.599A pdb=" N GLU B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 116 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 126 through 129 Processing helix chain 'B' and resid 130 through 145 removed outlier: 3.972A pdb=" N ASN B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 47 Processing helix chain 'C' and resid 48 through 49 No H-bonds generated for 'chain 'C' and resid 48 through 49' Processing helix chain 'C' and resid 50 through 54 Processing helix chain 'C' and resid 55 through 85 removed outlier: 3.597A pdb=" N GLU C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 116 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 47 Processing helix chain 'D' and resid 48 through 49 No H-bonds generated for 'chain 'D' and resid 48 through 49' Processing helix chain 'D' and resid 50 through 54 Processing helix chain 'D' and resid 55 through 85 removed outlier: 3.585A pdb=" N GLU D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 116 Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 48 through 49 No H-bonds generated for 'chain 'E' and resid 48 through 49' Processing helix chain 'E' and resid 50 through 54 Processing helix chain 'E' and resid 55 through 85 removed outlier: 3.598A pdb=" N GLU E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR E 73 " --> pdb=" O GLN E 69 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE E 85 " --> pdb=" O LYS E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 116 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 38 through 47 Processing helix chain 'F' and resid 48 through 49 No H-bonds generated for 'chain 'F' and resid 48 through 49' Processing helix chain 'F' and resid 50 through 54 Processing helix chain 'F' and resid 55 through 85 removed outlier: 3.601A pdb=" N GLU F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR F 73 " --> pdb=" O GLN F 69 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 116 Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'G' and resid 35 through 37 No H-bonds generated for 'chain 'G' and resid 35 through 37' Processing helix chain 'G' and resid 38 through 47 Processing helix chain 'G' and resid 48 through 49 No H-bonds generated for 'chain 'G' and resid 48 through 49' Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 55 through 85 removed outlier: 3.594A pdb=" N GLU G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR G 73 " --> pdb=" O GLN G 69 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE G 85 " --> pdb=" O LYS G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 116 Processing helix chain 'G' and resid 119 through 124 Processing helix chain 'H' and resid 35 through 37 No H-bonds generated for 'chain 'H' and resid 35 through 37' Processing helix chain 'H' and resid 38 through 47 Processing helix chain 'H' and resid 48 through 49 No H-bonds generated for 'chain 'H' and resid 48 through 49' Processing helix chain 'H' and resid 50 through 54 Processing helix chain 'H' and resid 55 through 85 removed outlier: 3.587A pdb=" N GLU H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR H 73 " --> pdb=" O GLN H 69 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE H 85 " --> pdb=" O LYS H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 116 Processing helix chain 'H' and resid 119 through 124 Processing helix chain 'I' and resid 35 through 37 No H-bonds generated for 'chain 'I' and resid 35 through 37' Processing helix chain 'I' and resid 38 through 47 Processing helix chain 'I' and resid 48 through 49 No H-bonds generated for 'chain 'I' and resid 48 through 49' Processing helix chain 'I' and resid 50 through 54 Processing helix chain 'I' and resid 55 through 85 removed outlier: 3.619A pdb=" N GLU I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR I 73 " --> pdb=" O GLN I 69 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE I 85 " --> pdb=" O LYS I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 116 Processing helix chain 'I' and resid 119 through 124 525 hydrogen bonds defined for protein. 1506 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1862 1.33 - 1.45: 2434 1.45 - 1.58: 4777 1.58 - 1.70: 109 1.70 - 1.82: 2 Bond restraints: 9184 Sorted by residual: bond pdb=" CE1 HIS I 119 " pdb=" NE2 HIS I 119 " ideal model delta sigma weight residual 1.321 1.288 0.033 1.00e-02 1.00e+04 1.12e+01 bond pdb=" CG HIS I 119 " pdb=" CD2 HIS I 119 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.71e+00 bond pdb=" CA SER A 48 " pdb=" CB SER A 48 " ideal model delta sigma weight residual 1.530 1.482 0.048 1.64e-02 3.72e+03 8.40e+00 bond pdb=" C ASN A 124 " pdb=" O ASN A 124 " ideal model delta sigma weight residual 1.231 1.289 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" CG HIS H 119 " pdb=" CD2 HIS H 119 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.33e+00 ... (remaining 9179 not shown) Histogram of bond angle deviations from ideal: 92.88 - 101.23: 63 101.23 - 109.58: 1628 109.58 - 117.92: 5809 117.92 - 126.27: 4867 126.27 - 134.62: 269 Bond angle restraints: 12636 Sorted by residual: angle pdb=" C4' DT K 29 " pdb=" C3' DT K 29 " pdb=" O3' DT K 29 " ideal model delta sigma weight residual 110.00 98.67 11.33 1.50e+00 4.44e-01 5.70e+01 angle pdb=" O3' DA J 22 " pdb=" P DA J 23 " pdb=" O5' DA J 23 " ideal model delta sigma weight residual 104.00 92.88 11.12 1.50e+00 4.44e-01 5.50e+01 angle pdb=" O3' DT J 16 " pdb=" P DA J 17 " pdb=" O5' DA J 17 " ideal model delta sigma weight residual 104.00 93.58 10.42 1.50e+00 4.44e-01 4.82e+01 angle pdb=" O3' DT K 24 " pdb=" C3' DT K 24 " pdb=" C2' DT K 24 " ideal model delta sigma weight residual 111.50 101.26 10.24 1.50e+00 4.44e-01 4.66e+01 angle pdb=" O3' DG K 14 " pdb=" P DC K 15 " pdb=" O5' DC K 15 " ideal model delta sigma weight residual 104.00 94.21 9.79 1.50e+00 4.44e-01 4.26e+01 ... (remaining 12631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.10: 5151 33.10 - 66.21: 422 66.21 - 99.31: 10 99.31 - 132.41: 0 132.41 - 165.51: 1 Dihedral angle restraints: 5584 sinusoidal: 2781 harmonic: 2803 Sorted by residual: dihedral pdb=" CA ALA A 22 " pdb=" C ALA A 22 " pdb=" N VAL A 23 " pdb=" CA VAL A 23 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DT K 10 " pdb=" C3' DT K 10 " pdb=" O3' DT K 10 " pdb=" P DA K 11 " ideal model delta sinusoidal sigma weight residual 220.00 54.49 165.51 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CA ASP H 24 " pdb=" C ASP H 24 " pdb=" N THR H 25 " pdb=" CA THR H 25 " ideal model delta harmonic sigma weight residual -180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1292 0.126 - 0.253: 117 0.253 - 0.379: 5 0.379 - 0.506: 0 0.506 - 0.632: 1 Chirality restraints: 1415 Sorted by residual: chirality pdb=" P DT K 10 " pdb=" OP1 DT K 10 " pdb=" OP2 DT K 10 " pdb=" O5' DT K 10 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 9.99e+00 chirality pdb=" CB VAL C 103 " pdb=" CA VAL C 103 " pdb=" CG1 VAL C 103 " pdb=" CG2 VAL C 103 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA SER A 120 " pdb=" N SER A 120 " pdb=" C SER A 120 " pdb=" CB SER A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1412 not shown) Planarity restraints: 1461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT K 26 " -0.105 2.00e-02 2.50e+03 4.69e-02 5.50e+01 pdb=" N1 DT K 26 " 0.070 2.00e-02 2.50e+03 pdb=" C2 DT K 26 " 0.026 2.00e-02 2.50e+03 pdb=" O2 DT K 26 " 0.021 2.00e-02 2.50e+03 pdb=" N3 DT K 26 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DT K 26 " -0.037 2.00e-02 2.50e+03 pdb=" O4 DT K 26 " -0.044 2.00e-02 2.50e+03 pdb=" C5 DT K 26 " 0.008 2.00e-02 2.50e+03 pdb=" C7 DT K 26 " 0.016 2.00e-02 2.50e+03 pdb=" C6 DT K 26 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT K 29 " -0.090 2.00e-02 2.50e+03 4.27e-02 4.56e+01 pdb=" N1 DT K 29 " 0.083 2.00e-02 2.50e+03 pdb=" C2 DT K 29 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DT K 29 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT K 29 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DT K 29 " -0.024 2.00e-02 2.50e+03 pdb=" O4 DT K 29 " -0.035 2.00e-02 2.50e+03 pdb=" C5 DT K 29 " 0.007 2.00e-02 2.50e+03 pdb=" C7 DT K 29 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT K 29 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT K 25 " -0.076 2.00e-02 2.50e+03 3.83e-02 3.67e+01 pdb=" N1 DT K 25 " 0.077 2.00e-02 2.50e+03 pdb=" C2 DT K 25 " 0.024 2.00e-02 2.50e+03 pdb=" O2 DT K 25 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT K 25 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DT K 25 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT K 25 " -0.045 2.00e-02 2.50e+03 pdb=" C5 DT K 25 " 0.009 2.00e-02 2.50e+03 pdb=" C7 DT K 25 " 0.014 2.00e-02 2.50e+03 pdb=" C6 DT K 25 " -0.011 2.00e-02 2.50e+03 ... (remaining 1458 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2015 2.80 - 3.33: 8523 3.33 - 3.85: 15099 3.85 - 4.38: 18959 4.38 - 4.90: 28441 Nonbonded interactions: 73037 Sorted by model distance: nonbonded pdb=" O ASN A 20 " pdb=" O VAL A 23 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR C 71 " pdb=" OE2 GLU D 83 " model vdw 2.389 2.440 nonbonded pdb=" N GLU E 89 " pdb=" OE1 GLU E 89 " model vdw 2.405 2.520 nonbonded pdb=" O ALA A 50 " pdb=" OG SER A 53 " model vdw 2.409 2.440 nonbonded pdb=" OG SER F 120 " pdb=" OD1 ASN F 124 " model vdw 2.410 2.440 ... (remaining 73032 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 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 24 through 124) selection = chain 'G' selection = (chain 'H' and resid 24 through 124) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 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: 1.010 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 30.060 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 9184 Z= 0.543 Angle : 1.443 13.313 12636 Z= 0.945 Chirality : 0.075 0.632 1415 Planarity : 0.015 0.236 1461 Dihedral : 20.033 165.513 3734 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.12 % Allowed : 1.19 % Favored : 98.69 % 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: -0.51 (0.23), residues: 935 helix: -0.39 (0.17), residues: 686 sheet: None (None), residues: 0 loop : 0.37 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.007 TRP A 42 HIS 0.024 0.005 HIS A 31 PHE 0.039 0.009 PHE H 41 TYR 0.024 0.008 TYR G 71 ARG 0.028 0.003 ARG H 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 294 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8046 (mtpt) REVERT: A 24 ASP cc_start: 0.8444 (t0) cc_final: 0.8135 (t0) REVERT: A 64 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8271 (mt-10) REVERT: A 77 LYS cc_start: 0.8046 (mttt) cc_final: 0.7680 (mptt) REVERT: A 78 ASP cc_start: 0.8275 (t0) cc_final: 0.7883 (t0) REVERT: A 82 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7874 (mp0) REVERT: A 92 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 96 LYS cc_start: 0.8329 (ttpt) cc_final: 0.8114 (ttpt) REVERT: B 47 ARG cc_start: 0.8969 (mtt90) cc_final: 0.8123 (mtp180) REVERT: B 78 ASP cc_start: 0.8375 (m-30) cc_final: 0.8140 (m-30) REVERT: B 82 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8513 (mp0) REVERT: B 96 LYS cc_start: 0.8859 (tttt) cc_final: 0.8533 (ttpp) REVERT: B 135 GLN cc_start: 0.8698 (tp40) cc_final: 0.8436 (tp40) REVERT: C 82 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8154 (mm-30) REVERT: C 121 HIS cc_start: 0.8124 (t-90) cc_final: 0.7845 (t-90) REVERT: D 47 ARG cc_start: 0.8835 (mtm110) cc_final: 0.8028 (mtt90) REVERT: D 82 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8204 (mp0) REVERT: D 97 ASP cc_start: 0.8403 (m-30) cc_final: 0.8151 (m-30) REVERT: D 100 LYS cc_start: 0.8511 (mttt) cc_final: 0.7976 (tptp) REVERT: E 77 LYS cc_start: 0.8395 (tttt) cc_final: 0.8066 (tmtt) REVERT: E 81 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7754 (tttt) REVERT: E 96 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8103 (tttp) REVERT: E 100 LYS cc_start: 0.7858 (mttt) cc_final: 0.7502 (tptp) REVERT: E 115 ASP cc_start: 0.8726 (t70) cc_final: 0.8392 (OUTLIER) REVERT: F 39 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8443 (tm-30) REVERT: F 52 ASP cc_start: 0.8196 (m-30) cc_final: 0.7867 (p0) REVERT: F 64 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8445 (mm-30) REVERT: F 83 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8090 (mt-10) REVERT: F 91 ASP cc_start: 0.7858 (t0) cc_final: 0.7416 (t0) REVERT: F 96 LYS cc_start: 0.8619 (tttt) cc_final: 0.8330 (ttpp) REVERT: G 34 LEU cc_start: 0.7714 (tp) cc_final: 0.7480 (tp) REVERT: G 82 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8006 (mp0) REVERT: G 85 ILE cc_start: 0.7764 (mt) cc_final: 0.7501 (mp) REVERT: H 77 LYS cc_start: 0.8342 (mmtm) cc_final: 0.8123 (mmmt) REVERT: H 78 ASP cc_start: 0.8058 (m-30) cc_final: 0.7822 (m-30) REVERT: I 51 LEU cc_start: 0.8593 (mt) cc_final: 0.8324 (mm) REVERT: I 85 ILE cc_start: 0.7976 (mt) cc_final: 0.7737 (mm) REVERT: I 96 LYS cc_start: 0.8573 (tttt) cc_final: 0.8271 (ttpp) REVERT: I 107 ARG cc_start: 0.8475 (mtt180) cc_final: 0.7602 (mtp85) outliers start: 1 outliers final: 1 residues processed: 295 average time/residue: 1.7563 time to fit residues: 540.5759 Evaluate side-chains 227 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 101 GLN C 69 GLN C 124 ASN D 43 HIS D 101 GLN E 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9184 Z= 0.273 Angle : 0.644 6.292 12636 Z= 0.359 Chirality : 0.040 0.130 1415 Planarity : 0.005 0.030 1461 Dihedral : 21.896 149.190 1682 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 3.23 % Allowed : 13.38 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.25), residues: 935 helix: 2.48 (0.19), residues: 656 sheet: None (None), residues: 0 loop : 0.83 (0.29), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 42 HIS 0.006 0.001 HIS F 43 PHE 0.008 0.002 PHE G 41 TYR 0.009 0.002 TYR D 71 ARG 0.005 0.001 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 236 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8257 (mtpt) cc_final: 0.8039 (mtpt) REVERT: A 18 MET cc_start: 0.7736 (tpt) cc_final: 0.7381 (mmt) REVERT: A 37 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8450 (mmmt) REVERT: A 64 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8111 (mt-10) REVERT: A 77 LYS cc_start: 0.8003 (mttt) cc_final: 0.7595 (mptt) REVERT: A 115 ASP cc_start: 0.8708 (t70) cc_final: 0.8410 (t0) REVERT: B 47 ARG cc_start: 0.9058 (mtt90) cc_final: 0.8227 (mtp-110) REVERT: B 100 LYS cc_start: 0.8235 (tptt) cc_final: 0.7967 (mmtm) REVERT: B 104 GLU cc_start: 0.8336 (tp30) cc_final: 0.8130 (mm-30) REVERT: B 145 ASN cc_start: 0.6982 (m110) cc_final: 0.6610 (m110) REVERT: C 39 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: C 64 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8111 (mm-30) REVERT: C 81 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7798 (mppt) REVERT: C 121 HIS cc_start: 0.7992 (t-90) cc_final: 0.7691 (t-90) REVERT: D 36 LYS cc_start: 0.8377 (tptt) cc_final: 0.7943 (ptpp) REVERT: D 47 ARG cc_start: 0.8738 (mtm110) cc_final: 0.8115 (mtt-85) REVERT: D 81 LYS cc_start: 0.8008 (ttmt) cc_final: 0.7671 (ttmm) REVERT: D 82 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7898 (mp0) REVERT: D 100 LYS cc_start: 0.8360 (mttt) cc_final: 0.7782 (tptp) REVERT: E 77 LYS cc_start: 0.8491 (tttt) cc_final: 0.8214 (tmtt) REVERT: E 81 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8012 (tttt) REVERT: E 100 LYS cc_start: 0.7867 (mttt) cc_final: 0.7457 (tptp) REVERT: E 115 ASP cc_start: 0.8809 (t70) cc_final: 0.8535 (t0) REVERT: E 117 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8640 (mt0) REVERT: F 39 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8215 (tm-30) REVERT: F 52 ASP cc_start: 0.8164 (m-30) cc_final: 0.7902 (p0) REVERT: F 82 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7693 (mp0) REVERT: F 91 ASP cc_start: 0.7920 (t0) cc_final: 0.7452 (t0) REVERT: F 115 ASP cc_start: 0.8256 (t70) cc_final: 0.7991 (t0) REVERT: G 44 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8270 (t0) REVERT: G 78 ASP cc_start: 0.8035 (m-30) cc_final: 0.7834 (m-30) REVERT: G 82 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7807 (mp0) REVERT: G 85 ILE cc_start: 0.7633 (mt) cc_final: 0.7286 (mp) REVERT: H 81 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7738 (tmtm) REVERT: H 84 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7379 (mpp-170) REVERT: H 121 HIS cc_start: 0.8360 (t-90) cc_final: 0.8147 (t70) REVERT: I 107 ARG cc_start: 0.8433 (mtt180) cc_final: 0.7559 (mtp85) outliers start: 27 outliers final: 7 residues processed: 242 average time/residue: 1.7451 time to fit residues: 440.8789 Evaluate side-chains 230 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 220 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain I residue 48 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 101 GLN B 135 GLN C 124 ASN D 101 GLN F 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9184 Z= 0.229 Angle : 0.573 6.684 12636 Z= 0.316 Chirality : 0.037 0.118 1415 Planarity : 0.004 0.047 1461 Dihedral : 21.901 147.911 1682 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 3.35 % Allowed : 17.68 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.25), residues: 935 helix: 2.90 (0.19), residues: 656 sheet: None (None), residues: 0 loop : 1.05 (0.30), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 42 HIS 0.004 0.001 HIS A 119 PHE 0.009 0.001 PHE G 41 TYR 0.005 0.001 TYR D 71 ARG 0.008 0.000 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 221 time to evaluate : 0.990 Fit side-chains REVERT: A 4 LYS cc_start: 0.8246 (mtpt) cc_final: 0.8017 (mtpt) REVERT: A 18 MET cc_start: 0.7749 (tpt) cc_final: 0.7355 (mmt) REVERT: A 37 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8458 (mmmt) REVERT: A 64 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8070 (mt-10) REVERT: A 77 LYS cc_start: 0.8067 (mttt) cc_final: 0.7647 (mptt) REVERT: A 115 ASP cc_start: 0.8761 (t70) cc_final: 0.8532 (t0) REVERT: B 47 ARG cc_start: 0.9033 (mtt90) cc_final: 0.8182 (mtp-110) REVERT: C 39 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: C 64 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7818 (mm-30) REVERT: C 82 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7998 (tp30) REVERT: C 84 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7531 (ptp-110) REVERT: C 121 HIS cc_start: 0.7941 (t-90) cc_final: 0.7548 (t-90) REVERT: D 24 ASP cc_start: 0.6185 (p0) cc_final: 0.5867 (p0) REVERT: D 36 LYS cc_start: 0.8389 (tptt) cc_final: 0.8171 (mmtt) REVERT: D 47 ARG cc_start: 0.8736 (mtm110) cc_final: 0.8086 (mtt-85) REVERT: D 82 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7831 (mp0) REVERT: D 100 LYS cc_start: 0.8255 (mttt) cc_final: 0.7730 (tptp) REVERT: E 35 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: E 77 LYS cc_start: 0.8535 (tttt) cc_final: 0.8243 (tmtt) REVERT: E 100 LYS cc_start: 0.7922 (mttt) cc_final: 0.7399 (tptt) REVERT: E 115 ASP cc_start: 0.8708 (t70) cc_final: 0.8452 (t0) REVERT: E 117 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8727 (mt0) REVERT: F 39 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8228 (tm-30) REVERT: F 52 ASP cc_start: 0.8189 (m-30) cc_final: 0.7927 (p0) REVERT: G 44 ASP cc_start: 0.8788 (m-30) cc_final: 0.8267 (t0) REVERT: G 85 ILE cc_start: 0.7173 (mt) cc_final: 0.6864 (mp) REVERT: G 86 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6349 (ttm170) REVERT: H 81 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7605 (tmtm) REVERT: H 121 HIS cc_start: 0.8428 (t-90) cc_final: 0.8222 (t70) REVERT: I 30 SER cc_start: 0.7697 (OUTLIER) cc_final: 0.7409 (p) REVERT: I 77 LYS cc_start: 0.7988 (tttt) cc_final: 0.7725 (tmtt) REVERT: I 107 ARG cc_start: 0.8361 (mtt180) cc_final: 0.7454 (mtp85) outliers start: 28 outliers final: 9 residues processed: 230 average time/residue: 1.7355 time to fit residues: 417.2541 Evaluate side-chains 227 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 214 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 48 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 0.4980 chunk 25 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN B 135 GLN C 124 ASN F 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9184 Z= 0.267 Angle : 0.590 7.294 12636 Z= 0.321 Chirality : 0.037 0.120 1415 Planarity : 0.005 0.032 1461 Dihedral : 21.943 146.550 1682 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 4.30 % Allowed : 18.04 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.25), residues: 935 helix: 2.89 (0.19), residues: 656 sheet: None (None), residues: 0 loop : 1.01 (0.30), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 42 HIS 0.005 0.001 HIS F 119 PHE 0.009 0.002 PHE G 41 TYR 0.006 0.002 TYR F 71 ARG 0.011 0.001 ARG F 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 222 time to evaluate : 1.332 Fit side-chains REVERT: A 4 LYS cc_start: 0.8263 (mtpt) cc_final: 0.8024 (mtpt) REVERT: A 18 MET cc_start: 0.7770 (tpt) cc_final: 0.7359 (mmt) REVERT: A 27 ASP cc_start: 0.8699 (m-30) cc_final: 0.8449 (m-30) REVERT: A 37 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8478 (mmmt) REVERT: A 64 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8082 (mt-10) REVERT: A 77 LYS cc_start: 0.8073 (mttt) cc_final: 0.7650 (mptt) REVERT: A 115 ASP cc_start: 0.8803 (t70) cc_final: 0.8545 (t0) REVERT: B 47 ARG cc_start: 0.9038 (mtt90) cc_final: 0.8213 (mtp-110) REVERT: B 81 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8000 (ttmt) REVERT: C 39 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: C 64 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7957 (mm-30) REVERT: C 82 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8119 (tp30) REVERT: C 121 HIS cc_start: 0.8044 (t-90) cc_final: 0.7649 (t-90) REVERT: D 36 LYS cc_start: 0.8394 (tptt) cc_final: 0.8169 (mmtt) REVERT: D 47 ARG cc_start: 0.8760 (mtm110) cc_final: 0.8120 (mtt-85) REVERT: D 82 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7763 (mp0) REVERT: D 100 LYS cc_start: 0.8325 (mttt) cc_final: 0.7778 (tptp) REVERT: E 35 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: E 100 LYS cc_start: 0.7975 (mttt) cc_final: 0.7479 (tptp) REVERT: E 115 ASP cc_start: 0.8534 (t70) cc_final: 0.8257 (t0) REVERT: E 117 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8741 (mt0) REVERT: F 39 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8252 (tm-30) REVERT: F 52 ASP cc_start: 0.8159 (m-30) cc_final: 0.7902 (p0) REVERT: G 44 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8342 (t0) REVERT: G 85 ILE cc_start: 0.7156 (mt) cc_final: 0.6827 (mp) REVERT: G 86 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.5814 (ttm-80) REVERT: H 81 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7600 (tmtm) REVERT: I 30 SER cc_start: 0.7827 (OUTLIER) cc_final: 0.7520 (p) REVERT: I 39 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8262 (pm20) REVERT: I 77 LYS cc_start: 0.8045 (tttt) cc_final: 0.7772 (tmtt) REVERT: I 104 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7098 (tp30) REVERT: I 107 ARG cc_start: 0.8225 (mtt180) cc_final: 0.7391 (mtp85) outliers start: 36 outliers final: 15 residues processed: 235 average time/residue: 1.6416 time to fit residues: 403.7995 Evaluate side-chains 235 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 96 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN B 135 GLN C 124 ASN F 124 ASN H 124 ASN I 69 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9184 Z= 0.244 Angle : 0.570 7.422 12636 Z= 0.310 Chirality : 0.036 0.117 1415 Planarity : 0.004 0.033 1461 Dihedral : 21.803 145.806 1682 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 4.42 % Allowed : 19.00 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.26), residues: 935 helix: 2.79 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.09 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 42 HIS 0.004 0.001 HIS A 119 PHE 0.008 0.001 PHE G 41 TYR 0.005 0.001 TYR A 71 ARG 0.006 0.000 ARG F 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 0.889 Fit side-chains REVERT: A 4 LYS cc_start: 0.8274 (mtpt) cc_final: 0.8038 (mtpt) REVERT: A 18 MET cc_start: 0.7811 (tpt) cc_final: 0.7411 (mmt) REVERT: A 27 ASP cc_start: 0.8751 (m-30) cc_final: 0.8498 (m-30) REVERT: A 37 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8463 (mmmt) REVERT: A 64 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8048 (mt-10) REVERT: A 77 LYS cc_start: 0.8065 (mttt) cc_final: 0.7636 (mptt) REVERT: A 115 ASP cc_start: 0.8762 (t70) cc_final: 0.8518 (t0) REVERT: B 47 ARG cc_start: 0.9015 (mtt90) cc_final: 0.8200 (mtp-110) REVERT: B 81 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7980 (ttmt) REVERT: C 39 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: C 64 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7918 (mm-30) REVERT: C 82 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8135 (tp30) REVERT: C 121 HIS cc_start: 0.7979 (t-90) cc_final: 0.7577 (t-90) REVERT: D 36 LYS cc_start: 0.8390 (tptt) cc_final: 0.8162 (mmtt) REVERT: D 47 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8119 (mtt-85) REVERT: D 82 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7734 (mp0) REVERT: D 100 LYS cc_start: 0.8308 (mttt) cc_final: 0.7757 (tptp) REVERT: E 71 TYR cc_start: 0.9005 (t80) cc_final: 0.8764 (t80) REVERT: E 77 LYS cc_start: 0.8612 (ttmp) cc_final: 0.8141 (tmtt) REVERT: E 84 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7412 (mtp180) REVERT: E 100 LYS cc_start: 0.7973 (mttt) cc_final: 0.7441 (tptp) REVERT: E 115 ASP cc_start: 0.8495 (t70) cc_final: 0.8223 (t0) REVERT: E 117 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8782 (mt0) REVERT: F 39 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8229 (tm-30) REVERT: F 52 ASP cc_start: 0.8164 (m-30) cc_final: 0.7911 (p0) REVERT: G 44 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8302 (t0) REVERT: G 82 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7388 (tp30) REVERT: G 86 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.5780 (ttm-80) REVERT: H 81 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7606 (tmtm) REVERT: I 30 SER cc_start: 0.7902 (OUTLIER) cc_final: 0.7614 (p) REVERT: I 77 LYS cc_start: 0.8094 (tttt) cc_final: 0.7763 (tmtt) REVERT: I 104 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7083 (tp30) outliers start: 37 outliers final: 15 residues processed: 231 average time/residue: 1.6352 time to fit residues: 395.1692 Evaluate side-chains 235 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 48 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN C 124 ASN I 69 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9184 Z= 0.261 Angle : 0.582 7.944 12636 Z= 0.317 Chirality : 0.037 0.116 1415 Planarity : 0.005 0.039 1461 Dihedral : 21.723 144.190 1682 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 3.70 % Allowed : 20.19 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.26), residues: 935 helix: 2.73 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.07 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 42 HIS 0.004 0.001 HIS F 119 PHE 0.009 0.001 PHE G 41 TYR 0.005 0.001 TYR A 71 ARG 0.008 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 0.944 Fit side-chains REVERT: A 4 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7970 (mtpt) REVERT: A 18 MET cc_start: 0.7828 (tpt) cc_final: 0.7419 (mmt) REVERT: A 27 ASP cc_start: 0.8703 (m-30) cc_final: 0.8446 (m-30) REVERT: A 37 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8437 (mmmt) REVERT: A 64 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8056 (mt-10) REVERT: A 77 LYS cc_start: 0.8082 (mttt) cc_final: 0.7651 (mptt) REVERT: A 115 ASP cc_start: 0.8782 (t70) cc_final: 0.8543 (t0) REVERT: B 47 ARG cc_start: 0.9011 (mtt90) cc_final: 0.8209 (mtp-110) REVERT: B 81 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7944 (ttmt) REVERT: C 39 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: C 64 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8003 (mm-30) REVERT: C 82 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8115 (tp30) REVERT: C 86 ARG cc_start: 0.6489 (mtt-85) cc_final: 0.6190 (mtt-85) REVERT: C 121 HIS cc_start: 0.8014 (t-90) cc_final: 0.7615 (t-90) REVERT: D 36 LYS cc_start: 0.8420 (tptt) cc_final: 0.8167 (mmtt) REVERT: D 47 ARG cc_start: 0.8733 (mtm110) cc_final: 0.8112 (mtt-85) REVERT: D 82 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7745 (mp0) REVERT: D 100 LYS cc_start: 0.8328 (mttt) cc_final: 0.7782 (tptp) REVERT: E 77 LYS cc_start: 0.8654 (ttmp) cc_final: 0.8196 (tmtt) REVERT: E 100 LYS cc_start: 0.8006 (mttt) cc_final: 0.7385 (tptt) REVERT: E 115 ASP cc_start: 0.8495 (t70) cc_final: 0.8223 (t0) REVERT: E 117 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8796 (mt0) REVERT: F 39 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8275 (tm-30) REVERT: F 52 ASP cc_start: 0.8166 (m-30) cc_final: 0.7917 (p0) REVERT: G 44 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8286 (t0) REVERT: G 82 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7435 (tp30) REVERT: G 86 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.5727 (ttm-80) REVERT: H 81 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7616 (tmtm) REVERT: H 86 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7709 (mmt90) REVERT: I 30 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7700 (p) REVERT: I 39 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8249 (pm20) REVERT: I 77 LYS cc_start: 0.8096 (tttt) cc_final: 0.7768 (tmtt) REVERT: I 104 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7118 (tm-30) outliers start: 31 outliers final: 16 residues processed: 233 average time/residue: 1.6910 time to fit residues: 412.4706 Evaluate side-chains 235 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 213 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 84 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN C 124 ASN H 124 ASN I 69 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9184 Z= 0.195 Angle : 0.539 8.510 12636 Z= 0.298 Chirality : 0.035 0.120 1415 Planarity : 0.004 0.033 1461 Dihedral : 21.639 143.796 1682 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.11 % Allowed : 21.74 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.72 (0.26), residues: 935 helix: 2.92 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.26 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 42 HIS 0.003 0.001 HIS A 119 PHE 0.007 0.001 PHE G 41 TYR 0.005 0.001 TYR E 71 ARG 0.005 0.000 ARG F 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 0.969 Fit side-chains REVERT: A 4 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7984 (mtpt) REVERT: A 18 MET cc_start: 0.7796 (tpt) cc_final: 0.7399 (mmt) REVERT: A 27 ASP cc_start: 0.8690 (m-30) cc_final: 0.8439 (m-30) REVERT: A 37 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8410 (mmmt) REVERT: A 64 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8036 (mt-10) REVERT: A 77 LYS cc_start: 0.7991 (mttt) cc_final: 0.7597 (mptt) REVERT: A 80 ARG cc_start: 0.7945 (tpp80) cc_final: 0.7588 (mpt180) REVERT: A 115 ASP cc_start: 0.8718 (t70) cc_final: 0.8506 (t0) REVERT: B 47 ARG cc_start: 0.8977 (mtt90) cc_final: 0.8170 (mtp-110) REVERT: B 81 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7963 (ttmt) REVERT: C 27 ASP cc_start: 0.8264 (m-30) cc_final: 0.7944 (m-30) REVERT: C 39 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: C 86 ARG cc_start: 0.6336 (mtt-85) cc_final: 0.6038 (mtt-85) REVERT: C 121 HIS cc_start: 0.8001 (t-90) cc_final: 0.7594 (t-90) REVERT: D 24 ASP cc_start: 0.6421 (p0) cc_final: 0.5994 (p0) REVERT: D 36 LYS cc_start: 0.8426 (tptt) cc_final: 0.8205 (mmtt) REVERT: D 47 ARG cc_start: 0.8735 (mtm110) cc_final: 0.8069 (mtt-85) REVERT: D 82 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7509 (mp0) REVERT: D 100 LYS cc_start: 0.8263 (mttt) cc_final: 0.7724 (tptp) REVERT: E 81 LYS cc_start: 0.8275 (tmtt) cc_final: 0.7845 (ttmm) REVERT: E 100 LYS cc_start: 0.7895 (mttt) cc_final: 0.7430 (mmmt) REVERT: E 115 ASP cc_start: 0.8445 (t70) cc_final: 0.8194 (t0) REVERT: F 39 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8210 (tm-30) REVERT: F 52 ASP cc_start: 0.8187 (m-30) cc_final: 0.7937 (p0) REVERT: G 44 ASP cc_start: 0.8797 (m-30) cc_final: 0.8384 (t0) REVERT: G 82 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7388 (tp30) REVERT: G 85 ILE cc_start: 0.6807 (mt) cc_final: 0.6593 (mp) REVERT: G 115 ASP cc_start: 0.9172 (t70) cc_final: 0.8864 (t70) REVERT: H 81 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7655 (tmtm) REVERT: H 86 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7679 (mmt90) REVERT: I 30 SER cc_start: 0.7972 (p) cc_final: 0.7704 (p) REVERT: I 77 LYS cc_start: 0.8090 (tttt) cc_final: 0.7774 (tmtt) REVERT: I 83 GLU cc_start: 0.7393 (tm-30) cc_final: 0.6419 (mt-10) REVERT: I 104 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7176 (tm-30) REVERT: I 107 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7484 (mtp180) REVERT: I 109 ILE cc_start: 0.8881 (mt) cc_final: 0.8662 (mt) outliers start: 26 outliers final: 12 residues processed: 230 average time/residue: 1.6703 time to fit residues: 402.3890 Evaluate side-chains 222 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 207 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain I residue 48 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 74 optimal weight: 0.0770 chunk 85 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN F 124 ASN H 124 ASN I 69 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9184 Z= 0.212 Angle : 0.545 9.185 12636 Z= 0.302 Chirality : 0.035 0.129 1415 Planarity : 0.004 0.042 1461 Dihedral : 21.608 142.207 1682 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 2.51 % Allowed : 22.70 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.26), residues: 935 helix: 2.93 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.30 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 42 HIS 0.003 0.001 HIS F 119 PHE 0.007 0.001 PHE G 41 TYR 0.008 0.001 TYR E 71 ARG 0.010 0.000 ARG F 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 215 time to evaluate : 0.993 Fit side-chains REVERT: A 4 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7986 (mtpt) REVERT: A 18 MET cc_start: 0.7794 (tpt) cc_final: 0.7395 (mmt) REVERT: A 27 ASP cc_start: 0.8683 (m-30) cc_final: 0.8435 (m-30) REVERT: A 37 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8422 (mmmt) REVERT: A 64 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8052 (mt-10) REVERT: A 77 LYS cc_start: 0.7982 (mttt) cc_final: 0.7588 (mptt) REVERT: A 80 ARG cc_start: 0.8008 (tpp80) cc_final: 0.7593 (mpt180) REVERT: A 115 ASP cc_start: 0.8728 (t70) cc_final: 0.8517 (t0) REVERT: B 47 ARG cc_start: 0.8987 (mtt90) cc_final: 0.8173 (mtp-110) REVERT: B 81 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7937 (ttmt) REVERT: C 27 ASP cc_start: 0.8261 (m-30) cc_final: 0.8015 (m-30) REVERT: C 39 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: C 86 ARG cc_start: 0.6384 (mtt-85) cc_final: 0.6080 (mtt-85) REVERT: C 121 HIS cc_start: 0.7997 (t-90) cc_final: 0.7584 (t-90) REVERT: D 24 ASP cc_start: 0.6544 (p0) cc_final: 0.6220 (p0) REVERT: D 36 LYS cc_start: 0.8470 (tptt) cc_final: 0.8234 (mmtt) REVERT: D 47 ARG cc_start: 0.8733 (mtm110) cc_final: 0.8067 (mtt-85) REVERT: D 82 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7522 (mp0) REVERT: D 100 LYS cc_start: 0.8270 (mttt) cc_final: 0.7745 (tptp) REVERT: E 64 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8375 (mm-30) REVERT: E 81 LYS cc_start: 0.8261 (tmtt) cc_final: 0.7832 (ttmm) REVERT: E 100 LYS cc_start: 0.7918 (mttt) cc_final: 0.7467 (mmmt) REVERT: E 115 ASP cc_start: 0.8432 (t70) cc_final: 0.8189 (t0) REVERT: F 39 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8211 (tm-30) REVERT: F 52 ASP cc_start: 0.8191 (m-30) cc_final: 0.7941 (p0) REVERT: G 44 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8402 (t0) REVERT: G 82 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7401 (tp30) REVERT: G 85 ILE cc_start: 0.6851 (mt) cc_final: 0.6627 (mp) REVERT: G 115 ASP cc_start: 0.9174 (t70) cc_final: 0.8860 (t70) REVERT: H 81 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7656 (tmtm) REVERT: I 30 SER cc_start: 0.7983 (OUTLIER) cc_final: 0.7715 (p) REVERT: I 77 LYS cc_start: 0.8082 (tttt) cc_final: 0.7767 (tmtt) REVERT: I 96 LYS cc_start: 0.7568 (ptpt) cc_final: 0.7271 (ptmm) REVERT: I 104 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7168 (tm-30) REVERT: I 107 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7498 (mtp180) REVERT: I 109 ILE cc_start: 0.8893 (mt) cc_final: 0.8654 (mt) outliers start: 21 outliers final: 11 residues processed: 222 average time/residue: 1.8239 time to fit residues: 424.1784 Evaluate side-chains 222 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 207 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 48 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 90 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN I 69 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9184 Z= 0.198 Angle : 0.532 9.453 12636 Z= 0.295 Chirality : 0.034 0.115 1415 Planarity : 0.004 0.048 1461 Dihedral : 21.475 141.306 1682 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.51 % Allowed : 22.58 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.26), residues: 935 helix: 3.03 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.48 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 42 HIS 0.003 0.001 HIS A 119 PHE 0.006 0.001 PHE G 41 TYR 0.006 0.001 TYR E 71 ARG 0.009 0.000 ARG F 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 1.045 Fit side-chains REVERT: A 4 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7994 (mtpt) REVERT: A 18 MET cc_start: 0.7781 (tpt) cc_final: 0.7394 (mmt) REVERT: A 27 ASP cc_start: 0.8680 (m-30) cc_final: 0.8437 (m-30) REVERT: A 37 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8404 (mmmt) REVERT: A 64 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8031 (mt-10) REVERT: A 77 LYS cc_start: 0.7988 (mttt) cc_final: 0.7598 (mptt) REVERT: A 80 ARG cc_start: 0.8050 (tpp80) cc_final: 0.7789 (mpt180) REVERT: B 47 ARG cc_start: 0.8969 (mtt90) cc_final: 0.8151 (mtp-110) REVERT: B 81 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7919 (ttmt) REVERT: C 27 ASP cc_start: 0.8287 (m-30) cc_final: 0.8068 (m-30) REVERT: C 39 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: C 86 ARG cc_start: 0.6361 (mtt-85) cc_final: 0.6055 (mtt-85) REVERT: C 121 HIS cc_start: 0.7991 (t-90) cc_final: 0.7650 (t-90) REVERT: D 36 LYS cc_start: 0.8475 (tptt) cc_final: 0.8240 (mmtt) REVERT: D 47 ARG cc_start: 0.8733 (mtm110) cc_final: 0.8093 (mtt-85) REVERT: D 82 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7432 (mp0) REVERT: D 100 LYS cc_start: 0.8232 (mttt) cc_final: 0.7709 (tptp) REVERT: E 81 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7693 (ttmm) REVERT: E 100 LYS cc_start: 0.7898 (mttt) cc_final: 0.7369 (tptp) REVERT: E 101 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8389 (mm-40) REVERT: E 115 ASP cc_start: 0.8226 (t70) cc_final: 0.7956 (t0) REVERT: F 39 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8245 (tm-30) REVERT: F 52 ASP cc_start: 0.8078 (m-30) cc_final: 0.7857 (p0) REVERT: F 114 ARG cc_start: 0.7789 (ttp80) cc_final: 0.7577 (ttp80) REVERT: G 44 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8391 (t0) REVERT: G 82 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7363 (tp30) REVERT: G 85 ILE cc_start: 0.6807 (mt) cc_final: 0.6599 (mp) REVERT: G 115 ASP cc_start: 0.9192 (t70) cc_final: 0.8876 (t70) REVERT: H 81 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7655 (tmtm) REVERT: I 30 SER cc_start: 0.8018 (OUTLIER) cc_final: 0.7752 (p) REVERT: I 77 LYS cc_start: 0.8069 (tttt) cc_final: 0.7761 (tmtt) REVERT: I 96 LYS cc_start: 0.7463 (ptpt) cc_final: 0.7186 (ptmm) REVERT: I 104 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7143 (tm-30) REVERT: I 107 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7468 (mtp180) REVERT: I 109 ILE cc_start: 0.8885 (mt) cc_final: 0.8640 (mt) outliers start: 21 outliers final: 12 residues processed: 221 average time/residue: 1.7357 time to fit residues: 400.9901 Evaluate side-chains 222 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 48 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.0060 chunk 64 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 142 ASN D 101 GLN F 124 ASN I 69 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9184 Z= 0.217 Angle : 0.555 9.828 12636 Z= 0.304 Chirality : 0.035 0.140 1415 Planarity : 0.004 0.039 1461 Dihedral : 21.429 140.061 1682 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 2.15 % Allowed : 23.30 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.26), residues: 935 helix: 2.99 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.48 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 42 HIS 0.003 0.001 HIS F 119 PHE 0.007 0.001 PHE G 41 TYR 0.009 0.001 TYR E 71 ARG 0.009 0.000 ARG F 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 212 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7997 (mtpt) REVERT: A 18 MET cc_start: 0.7789 (tpt) cc_final: 0.7384 (mmt) REVERT: A 19 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7460 (tttt) REVERT: A 27 ASP cc_start: 0.8693 (m-30) cc_final: 0.8453 (m-30) REVERT: A 37 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8411 (mmmt) REVERT: A 64 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8065 (mt-10) REVERT: A 77 LYS cc_start: 0.8030 (mttt) cc_final: 0.7627 (mptt) REVERT: B 47 ARG cc_start: 0.8976 (mtt90) cc_final: 0.8173 (mtp-110) REVERT: B 81 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7895 (ttmt) REVERT: C 86 ARG cc_start: 0.6381 (mtt-85) cc_final: 0.6076 (mtt-85) REVERT: C 121 HIS cc_start: 0.7989 (t-90) cc_final: 0.7645 (t-90) REVERT: D 24 ASP cc_start: 0.6415 (p0) cc_final: 0.6176 (p0) REVERT: D 36 LYS cc_start: 0.8494 (tptt) cc_final: 0.8243 (mmtt) REVERT: D 47 ARG cc_start: 0.8735 (mtm110) cc_final: 0.8073 (mtt-85) REVERT: D 82 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7419 (mp0) REVERT: D 100 LYS cc_start: 0.8227 (mttt) cc_final: 0.7710 (tptp) REVERT: E 81 LYS cc_start: 0.8238 (tmtt) cc_final: 0.7812 (ttmm) REVERT: E 100 LYS cc_start: 0.7908 (mttt) cc_final: 0.7371 (tptp) REVERT: E 101 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8410 (mm-40) REVERT: E 115 ASP cc_start: 0.8238 (t70) cc_final: 0.7946 (t0) REVERT: F 35 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7906 (mm-30) REVERT: F 39 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8188 (tm-30) REVERT: F 52 ASP cc_start: 0.8200 (m-30) cc_final: 0.7951 (p0) REVERT: F 114 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7716 (ttp80) REVERT: G 44 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8404 (t0) REVERT: G 82 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7356 (tp30) REVERT: G 85 ILE cc_start: 0.6804 (mt) cc_final: 0.6584 (mp) REVERT: G 115 ASP cc_start: 0.9221 (t70) cc_final: 0.8908 (t70) REVERT: H 81 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7722 (tmtm) REVERT: I 30 SER cc_start: 0.8033 (OUTLIER) cc_final: 0.7768 (p) REVERT: I 77 LYS cc_start: 0.8073 (tttt) cc_final: 0.7772 (tmtt) REVERT: I 86 ARG cc_start: 0.7361 (mmt-90) cc_final: 0.7086 (mmt180) REVERT: I 96 LYS cc_start: 0.7495 (ptpt) cc_final: 0.7214 (ptmm) REVERT: I 104 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7103 (tm-30) REVERT: I 107 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7498 (mtp180) REVERT: I 109 ILE cc_start: 0.8889 (mt) cc_final: 0.8665 (mt) outliers start: 18 outliers final: 13 residues processed: 221 average time/residue: 1.7075 time to fit residues: 394.8921 Evaluate side-chains 226 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 210 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 48 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN D 101 GLN I 69 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123563 restraints weight = 11200.600| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.40 r_work: 0.3347 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9184 Z= 0.250 Angle : 0.582 9.735 12636 Z= 0.318 Chirality : 0.036 0.113 1415 Planarity : 0.005 0.040 1461 Dihedral : 21.413 138.904 1682 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 2.27 % Allowed : 23.06 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.26), residues: 935 helix: 2.90 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.41 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 42 HIS 0.004 0.001 HIS F 119 PHE 0.008 0.001 PHE G 41 TYR 0.012 0.001 TYR E 71 ARG 0.009 0.000 ARG F 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5564.91 seconds wall clock time: 98 minutes 12.55 seconds (5892.55 seconds total)