Starting phenix.real_space_refine on Fri Sep 11 15:39:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t7c_10393/09_2026/6t7c_10393.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t7c_10393/09_2026/6t7c_10393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t7c_10393/09_2026/6t7c_10393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t7c_10393/09_2026/6t7c_10393.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t7c_10393/09_2026/6t7c_10393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t7c_10393/09_2026/6t7c_10393.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.022 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 190 5.49 5 S 10 5.16 5 C 6021 2.51 5 N 2026 2.21 5 O 2359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10606 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1936 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "J" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1959 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "K" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 307 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 74, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'HIS:plan': 3, 'ARG:plan': 10, 'ASN:plan1': 2, 'PHE:plan': 2, 'TRP:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 178 Chain: "L" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 288 Classifications: {'peptide': 72} Incomplete info: {'backbone_only': 70} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 473 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'HIS:plan': 3, 'ARG:plan': 8, 'ASN:plan1': 2, 'PHE:plan': 2, 'TRP:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 160 Time building chain proxies: 2.92, per 1000 atoms: 0.28 Number of scatterers: 10606 At special positions: 0 Unit cell: (89.25, 115.5, 142.8, 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 190 15.00 O 2359 8.00 N 2026 7.00 C 6021 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 249.3 milliseconds 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1434 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 9 sheets defined 69.2% alpha, 2.0% beta 94 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.966A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.530A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.765A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 4.286A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.129A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.862A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.127A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.535A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.507A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.576A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.227A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.637A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 31 through 41 removed outlier: 4.059A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.352A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.838A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.127A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.535A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.507A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.576A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.226A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 71 removed outlier: 3.615A pdb=" N VAL K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 90 Processing helix chain 'K' and resid 91 through 94 Processing helix chain 'K' and resid 95 through 113 Processing helix chain 'L' and resid 54 through 71 removed outlier: 3.603A pdb=" N VAL L 58 " --> pdb=" O ASN L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 90 Processing helix chain 'L' and resid 91 through 94 Processing helix chain 'L' and resid 95 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.879A pdb=" N ARG A 83 " --> 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 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.313A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.427A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.480A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.313A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 451 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 218 hydrogen bonds 436 hydrogen bond angles 0 basepair planarities 94 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.25 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: 2624 1.33 - 1.45: 2884 1.45 - 1.57: 5253 1.57 - 1.69: 378 1.69 - 1.81: 20 Bond restraints: 11159 Sorted by residual: bond pdb=" C3' DT J 90 " pdb=" C2' DT J 90 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.76e+01 bond pdb=" C3' DA J 89 " pdb=" O3' DA J 89 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.42e+01 bond pdb=" C3' DT I 91 " pdb=" C2' DT I 91 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT I 51 " pdb=" O3' DT I 51 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" C3' DC I 116 " pdb=" C2' DC I 116 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.52e+00 ... (remaining 11154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.73: 15780 5.73 - 11.46: 12 11.46 - 17.20: 2 17.20 - 22.93: 0 22.93 - 28.66: 2 Bond angle restraints: 15796 Sorted by residual: angle pdb=" CD LYS H 31 " pdb=" CE LYS H 31 " pdb=" NZ LYS H 31 " ideal model delta sigma weight residual 111.90 83.24 28.66 3.20e+00 9.77e-02 8.02e+01 angle pdb=" CD LYS D 31 " pdb=" CE LYS D 31 " pdb=" NZ LYS D 31 " ideal model delta sigma weight residual 111.90 83.26 28.64 3.20e+00 9.77e-02 8.01e+01 angle pdb=" CB LYS G 95 " pdb=" CG LYS G 95 " pdb=" CD LYS G 95 " ideal model delta sigma weight residual 111.30 125.49 -14.19 2.30e+00 1.89e-01 3.81e+01 angle pdb=" CB LYS C 95 " pdb=" CG LYS C 95 " pdb=" CD LYS C 95 " ideal model delta sigma weight residual 111.30 125.38 -14.08 2.30e+00 1.89e-01 3.75e+01 angle pdb=" O4' DT I 92 " pdb=" C4' DT I 92 " pdb=" C3' DT I 92 " ideal model delta sigma weight residual 106.00 102.45 3.55 6.00e-01 2.78e+00 3.50e+01 ... (remaining 15791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.65: 4370 19.65 - 39.29: 916 39.29 - 58.94: 797 58.94 - 78.58: 50 78.58 - 98.23: 18 Dihedral angle restraints: 6151 sinusoidal: 3780 harmonic: 2371 Sorted by residual: dihedral pdb=" CA LYS D 27 " pdb=" C LYS D 27 " pdb=" N ARG D 28 " pdb=" CA ARG D 28 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA LYS H 27 " pdb=" C LYS H 27 " pdb=" N ARG H 28 " pdb=" CA ARG H 28 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" C ASN F 25 " pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" CB ASN F 25 " ideal model delta harmonic sigma weight residual -122.60 -133.49 10.89 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 6148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1541 0.084 - 0.167: 167 0.167 - 0.251: 4 0.251 - 0.334: 0 0.334 - 0.418: 1 Chirality restraints: 1713 Sorted by residual: chirality pdb=" CA ASN F 25 " pdb=" N ASN F 25 " pdb=" C ASN F 25 " pdb=" CB ASN F 25 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" C PRO C 80 " pdb=" CB PRO C 80 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CA PRO G 80 " pdb=" N PRO G 80 " pdb=" C PRO G 80 " pdb=" CB PRO G 80 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.25e-01 ... (remaining 1710 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 114 " 0.027 2.00e-02 2.50e+03 2.87e-02 1.85e+01 pdb=" N1 DC J 114 " -0.068 2.00e-02 2.50e+03 pdb=" C2 DC J 114 " 0.043 2.00e-02 2.50e+03 pdb=" O2 DC J 114 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DC J 114 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC J 114 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC J 114 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC J 114 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DC J 114 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 32 " 0.019 2.00e-02 2.50e+03 2.62e-02 1.71e+01 pdb=" N1 DT J 32 " -0.064 2.00e-02 2.50e+03 pdb=" C2 DT J 32 " 0.046 2.00e-02 2.50e+03 pdb=" O2 DT J 32 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT J 32 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DT J 32 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT J 32 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DT J 32 " 0.005 2.00e-02 2.50e+03 pdb=" C7 DT J 32 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT J 32 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 25 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" CG ASN F 25 " -0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN F 25 " 0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN F 25 " 0.024 2.00e-02 2.50e+03 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 230 2.65 - 3.21: 9122 3.21 - 3.77: 19377 3.77 - 4.34: 24506 4.34 - 4.90: 35814 Nonbonded interactions: 89049 Sorted by model distance: nonbonded pdb=" NH1 ARG D 28 " pdb=" OP1 DC J 48 " model vdw 2.081 3.120 nonbonded pdb=" O THR A 58 " pdb=" OE1 GLN G 104 " model vdw 2.110 3.040 nonbonded pdb=" NH2 ARG D 30 " pdb=" OP1 DT I 27 " model vdw 2.208 3.120 nonbonded pdb=" O LEU A 61 " pdb=" NH2 ARG B 36 " model vdw 2.266 3.120 nonbonded pdb=" N GLU F 53 " pdb=" OE1 GLU F 53 " model vdw 2.292 3.120 ... (remaining 89044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'K' and resid 46 through 117) selection = chain 'L' } 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: 0.010 Normalize map: mean=0, sd=1: 0.280 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.140 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 0.079 11159 Z= 0.591 Angle : 0.988 28.661 15796 Z= 0.751 Chirality : 0.051 0.418 1713 Planarity : 0.006 0.052 1395 Dihedral : 26.054 98.228 4717 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.67 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.22), residues: 897 helix: -1.88 (0.16), residues: 623 sheet: None (None), residues: 0 loop : -1.71 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 92 TYR 0.016 0.003 TYR E 99 PHE 0.012 0.002 PHE A 78 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00884 / 0.59 (11159) covalent geometry : angle 0.98787 / 0.75 (15796) hydrogen bonds : bond 0.10676 / 6.65 ( 669) hydrogen bonds : angle 4.53446 / 3.19 ( 1771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.323 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 50 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8451 (mt-10) REVERT: A 76 GLN cc_start: 0.8598 (mt0) cc_final: 0.8354 (mt0) REVERT: A 81 ASP cc_start: 0.8102 (t0) cc_final: 0.7887 (t0) REVERT: A 90 MET cc_start: 0.8774 (mmm) cc_final: 0.8438 (mmm) REVERT: B 21 VAL cc_start: 0.6586 (p) cc_final: 0.6036 (m) REVERT: B 24 ASP cc_start: 0.8317 (t70) cc_final: 0.7864 (t70) REVERT: B 31 LYS cc_start: 0.8545 (tttt) cc_final: 0.8341 (ttpt) REVERT: B 59 LYS cc_start: 0.9325 (mtpt) cc_final: 0.9012 (tptp) REVERT: B 64 ASN cc_start: 0.9153 (m110) cc_final: 0.8902 (m110) REVERT: B 88 TYR cc_start: 0.7876 (m-10) cc_final: 0.7273 (m-10) REVERT: C 32 ARG cc_start: 0.9248 (ttp80) cc_final: 0.9015 (ttp-110) REVERT: C 56 GLU cc_start: 0.8415 (tt0) cc_final: 0.7878 (tt0) REVERT: C 89 ASN cc_start: 0.9065 (m-40) cc_final: 0.8653 (m110) REVERT: C 92 GLU cc_start: 0.8293 (mp0) cc_final: 0.8042 (mt-10) REVERT: C 95 LYS cc_start: 0.9350 (mttt) cc_final: 0.8910 (tppt) REVERT: C 104 GLN cc_start: 0.8463 (mm110) cc_final: 0.8226 (mm-40) REVERT: C 108 LEU cc_start: 0.9263 (tp) cc_final: 0.8797 (tp) REVERT: D 65 ASP cc_start: 0.9150 (t70) cc_final: 0.8813 (t0) REVERT: D 76 ARG cc_start: 0.8219 (ptp-170) cc_final: 0.7934 (ptm160) REVERT: D 89 ARG cc_start: 0.8452 (mtp180) cc_final: 0.8251 (mmm-85) REVERT: D 99 LEU cc_start: 0.9089 (mt) cc_final: 0.8842 (mp) REVERT: D 117 LYS cc_start: 0.9244 (tptm) cc_final: 0.8477 (tptm) REVERT: E 41 TYR cc_start: 0.8893 (m-80) cc_final: 0.7940 (m-10) REVERT: E 60 LEU cc_start: 0.8342 (mt) cc_final: 0.7524 (mt) REVERT: E 73 GLU cc_start: 0.9272 (tm-30) cc_final: 0.8777 (tm-30) REVERT: E 78 PHE cc_start: 0.8518 (m-80) cc_final: 0.7680 (m-10) REVERT: E 94 GLU cc_start: 0.8653 (tp30) cc_final: 0.8263 (mm-30) REVERT: E 117 VAL cc_start: 0.9479 (t) cc_final: 0.9254 (p) REVERT: E 125 GLN cc_start: 0.8694 (mt0) cc_final: 0.8444 (mt0) REVERT: F 68 ASP cc_start: 0.9071 (m-30) cc_final: 0.8854 (m-30) REVERT: F 88 TYR cc_start: 0.8663 (m-10) cc_final: 0.8305 (m-10) REVERT: G 39 TYR cc_start: 0.8215 (m-80) cc_final: 0.7388 (m-80) REVERT: G 64 GLU cc_start: 0.8382 (tp30) cc_final: 0.7713 (tm-30) REVERT: G 68 ASN cc_start: 0.9213 (m-40) cc_final: 0.8389 (m-40) REVERT: G 71 ARG cc_start: 0.9349 (ttp-170) cc_final: 0.9019 (ttp80) REVERT: H 32 GLU cc_start: 0.7002 (tp30) cc_final: 0.6574 (mp0) REVERT: H 68 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8569 (tp30) REVERT: H 77 LEU cc_start: 0.9065 (mt) cc_final: 0.8861 (mm) REVERT: H 80 TYR cc_start: 0.8342 (m-10) cc_final: 0.8065 (m-10) REVERT: H 90 GLU cc_start: 0.9098 (mp0) cc_final: 0.8724 (mp0) REVERT: H 103 LEU cc_start: 0.9590 (mt) cc_final: 0.9358 (mt) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.1363 time to fit residues: 59.3884 Evaluate side-chains 237 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.0040 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 overall best weight: 3.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN D 81 ASN D 92 GLN E 68 GLN E 76 GLN E 85 GLN F 64 ASN G 31 HIS H 92 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.074578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.053971 restraints weight = 39861.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055671 restraints weight = 21779.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.056792 restraints weight = 15077.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.057510 restraints weight = 12060.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057944 restraints weight = 10579.841| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11159 Z= 0.189 Angle : 0.730 8.280 15796 Z= 0.419 Chirality : 0.048 0.254 1713 Planarity : 0.005 0.045 1395 Dihedral : 29.461 88.968 3177 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.12 % Allowed : 15.76 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.26), residues: 897 helix: 0.11 (0.19), residues: 629 sheet: None (None), residues: 0 loop : -1.27 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 28 TYR 0.025 0.002 TYR B 98 PHE 0.009 0.001 PHE F 100 HIS 0.007 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 (11159) covalent geometry : angle 0.73026 / 0.42 (15796) hydrogen bonds : bond 0.05226 / 3.50 ( 669) hydrogen bonds : angle 3.58715 / 2.53 ( 1771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 274 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8260 (mt-10) REVERT: A 61 LEU cc_start: 0.8900 (mp) cc_final: 0.7812 (mt) REVERT: A 90 MET cc_start: 0.8442 (mmm) cc_final: 0.7943 (mmm) REVERT: A 93 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8231 (tp40) REVERT: B 46 ILE cc_start: 0.9147 (mm) cc_final: 0.8874 (mm) REVERT: B 59 LYS cc_start: 0.9408 (mtpt) cc_final: 0.9180 (mmmm) REVERT: B 63 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8553 (mt-10) REVERT: B 85 ASP cc_start: 0.8083 (m-30) cc_final: 0.7871 (m-30) REVERT: B 88 TYR cc_start: 0.7787 (m-10) cc_final: 0.7256 (m-10) REVERT: B 91 LYS cc_start: 0.9184 (ttmm) cc_final: 0.8723 (tmmt) REVERT: B 98 TYR cc_start: 0.8837 (m-10) cc_final: 0.8587 (m-80) REVERT: C 56 GLU cc_start: 0.8542 (tt0) cc_final: 0.7768 (tt0) REVERT: C 89 ASN cc_start: 0.9024 (m-40) cc_final: 0.8672 (m-40) REVERT: C 95 LYS cc_start: 0.9279 (tttt) cc_final: 0.8859 (tppt) REVERT: D 65 ASP cc_start: 0.9241 (t70) cc_final: 0.9005 (t0) REVERT: D 76 ARG cc_start: 0.8142 (ptp-170) cc_final: 0.7620 (ptp90) REVERT: D 117 LYS cc_start: 0.9378 (tptm) cc_final: 0.8773 (tptm) REVERT: E 90 MET cc_start: 0.8908 (tpp) cc_final: 0.8617 (tpp) REVERT: E 120 MET cc_start: 0.7766 (mtp) cc_final: 0.7408 (mtt) REVERT: F 24 ASP cc_start: 0.7547 (t0) cc_final: 0.7326 (p0) REVERT: F 68 ASP cc_start: 0.8996 (m-30) cc_final: 0.8796 (m-30) REVERT: F 88 TYR cc_start: 0.8739 (m-10) cc_final: 0.7827 (m-10) REVERT: F 98 TYR cc_start: 0.8046 (m-10) cc_final: 0.7747 (m-80) REVERT: G 35 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7815 (mtm-85) REVERT: G 39 TYR cc_start: 0.8272 (m-80) cc_final: 0.7572 (m-80) REVERT: G 56 GLU cc_start: 0.8787 (tt0) cc_final: 0.8315 (tt0) REVERT: G 61 GLU cc_start: 0.9011 (tp30) cc_final: 0.8747 (tp30) REVERT: G 64 GLU cc_start: 0.8110 (tp30) cc_final: 0.7467 (tm-30) REVERT: G 68 ASN cc_start: 0.9121 (m-40) cc_final: 0.8534 (m-40) REVERT: G 73 ASN cc_start: 0.9029 (t0) cc_final: 0.8772 (t0) REVERT: H 80 TYR cc_start: 0.8111 (m-10) cc_final: 0.7721 (m-10) outliers start: 20 outliers final: 7 residues processed: 283 average time/residue: 0.1088 time to fit residues: 42.2744 Evaluate side-chains 246 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 238 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 86 optimal weight: 50.0000 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 99 optimal weight: 50.0000 chunk 17 optimal weight: 0.0570 chunk 35 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 overall best weight: 6.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 106 HIS E 93 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.072231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.051960 restraints weight = 41017.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.053634 restraints weight = 22176.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.054732 restraints weight = 15276.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055425 restraints weight = 12192.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055843 restraints weight = 10665.042| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11159 Z= 0.230 Angle : 0.722 7.639 15796 Z= 0.416 Chirality : 0.046 0.241 1713 Planarity : 0.004 0.047 1395 Dihedral : 29.408 87.384 3177 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.06 % Allowed : 19.50 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 897 helix: 0.94 (0.20), residues: 631 sheet: None (None), residues: 0 loop : -1.05 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 134 TYR 0.022 0.002 TYR G 57 PHE 0.011 0.002 PHE F 100 HIS 0.012 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.23 (11159) covalent geometry : angle 0.72195 / 0.42 (15796) hydrogen bonds : bond 0.05410 / 3.61 ( 669) hydrogen bonds : angle 3.53883 / 2.52 ( 1771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8454 (mp0) REVERT: A 59 GLU cc_start: 0.8048 (pm20) cc_final: 0.7789 (pm20) REVERT: B 88 TYR cc_start: 0.7822 (m-10) cc_final: 0.7240 (m-10) REVERT: B 91 LYS cc_start: 0.9175 (ttmm) cc_final: 0.8797 (ttpt) REVERT: C 56 GLU cc_start: 0.8681 (tt0) cc_final: 0.7871 (tt0) REVERT: C 84 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8595 (tm-30) REVERT: C 89 ASN cc_start: 0.9180 (m-40) cc_final: 0.8935 (m-40) REVERT: C 92 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7951 (mt-10) REVERT: C 95 LYS cc_start: 0.9334 (tttt) cc_final: 0.8911 (tppt) REVERT: D 59 MET cc_start: 0.8758 (mmp) cc_final: 0.8468 (mmp) REVERT: D 65 ASP cc_start: 0.9273 (t70) cc_final: 0.9057 (t0) REVERT: D 76 ARG cc_start: 0.8279 (ptp-170) cc_final: 0.7771 (ptp90) REVERT: E 120 MET cc_start: 0.7892 (mtp) cc_final: 0.7484 (mtt) REVERT: F 53 GLU cc_start: 0.7860 (mp0) cc_final: 0.7551 (mp0) REVERT: F 68 ASP cc_start: 0.9053 (m-30) cc_final: 0.8832 (m-30) REVERT: F 88 TYR cc_start: 0.8791 (m-10) cc_final: 0.8037 (m-10) REVERT: G 39 TYR cc_start: 0.8338 (m-80) cc_final: 0.7775 (m-80) REVERT: G 64 GLU cc_start: 0.8159 (tp30) cc_final: 0.7534 (tm-30) REVERT: G 68 ASN cc_start: 0.9101 (m-40) cc_final: 0.7981 (m-40) REVERT: G 73 ASN cc_start: 0.9096 (t0) cc_final: 0.8776 (t0) REVERT: H 56 MET cc_start: 0.8686 (tpp) cc_final: 0.8332 (tpp) REVERT: H 80 TYR cc_start: 0.8217 (m-10) cc_final: 0.7876 (m-10) REVERT: H 110 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7965 (mt-10) outliers start: 26 outliers final: 20 residues processed: 257 average time/residue: 0.1139 time to fit residues: 40.2942 Evaluate side-chains 251 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 72 optimal weight: 50.0000 chunk 47 optimal weight: 0.9980 chunk 103 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 78 optimal weight: 50.0000 chunk 69 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 108 ASN H 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.073426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.053123 restraints weight = 40593.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.054847 restraints weight = 22149.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055980 restraints weight = 15284.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.056699 restraints weight = 12192.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.057132 restraints weight = 10662.125| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11159 Z= 0.162 Angle : 0.689 8.390 15796 Z= 0.395 Chirality : 0.045 0.238 1713 Planarity : 0.004 0.051 1395 Dihedral : 29.365 87.048 3177 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.52 % Allowed : 21.53 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.27), residues: 897 helix: 1.52 (0.20), residues: 615 sheet: None (None), residues: 0 loop : -1.00 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 23 TYR 0.034 0.002 TYR B 98 PHE 0.010 0.001 PHE E 78 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (11159) covalent geometry : angle 0.68918 / 0.40 (15796) hydrogen bonds : bond 0.04656 / 3.15 ( 669) hydrogen bonds : angle 3.34093 / 2.36 ( 1771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8457 (mp0) REVERT: A 90 MET cc_start: 0.8970 (mmm) cc_final: 0.8566 (mmt) REVERT: B 88 TYR cc_start: 0.7740 (m-10) cc_final: 0.7143 (m-10) REVERT: B 91 LYS cc_start: 0.9160 (ttmm) cc_final: 0.8658 (tmmt) REVERT: B 98 TYR cc_start: 0.8898 (m-80) cc_final: 0.8529 (m-80) REVERT: C 39 TYR cc_start: 0.8927 (m-80) cc_final: 0.8693 (m-80) REVERT: C 56 GLU cc_start: 0.8641 (tt0) cc_final: 0.7876 (tt0) REVERT: C 89 ASN cc_start: 0.9062 (m-40) cc_final: 0.8833 (m-40) REVERT: C 95 LYS cc_start: 0.9286 (tttt) cc_final: 0.8858 (tppt) REVERT: E 60 LEU cc_start: 0.8539 (mt) cc_final: 0.8023 (mt) REVERT: E 90 MET cc_start: 0.8943 (tpp) cc_final: 0.8616 (tpt) REVERT: E 112 ILE cc_start: 0.9536 (pt) cc_final: 0.9215 (mt) REVERT: E 120 MET cc_start: 0.7902 (mtp) cc_final: 0.7628 (mtt) REVERT: F 68 ASP cc_start: 0.8944 (m-30) cc_final: 0.8717 (m-30) REVERT: F 88 TYR cc_start: 0.8806 (m-10) cc_final: 0.8475 (m-10) REVERT: G 15 LYS cc_start: 0.8255 (ttpp) cc_final: 0.8043 (ttpp) REVERT: G 25 PHE cc_start: 0.8261 (m-80) cc_final: 0.8028 (m-80) REVERT: G 29 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8292 (tpp80) REVERT: G 39 TYR cc_start: 0.8357 (m-80) cc_final: 0.7911 (m-80) REVERT: G 40 SER cc_start: 0.9039 (p) cc_final: 0.8684 (p) REVERT: G 57 TYR cc_start: 0.9523 (t80) cc_final: 0.9203 (t80) REVERT: G 64 GLU cc_start: 0.8128 (tp30) cc_final: 0.7557 (tm-30) REVERT: G 68 ASN cc_start: 0.8894 (m-40) cc_final: 0.8238 (m-40) REVERT: G 73 ASN cc_start: 0.8926 (t0) cc_final: 0.7712 (t0) REVERT: H 56 MET cc_start: 0.8883 (tpp) cc_final: 0.8534 (tpp) REVERT: H 117 LYS cc_start: 0.9446 (mtpp) cc_final: 0.9013 (mtpt) outliers start: 29 outliers final: 20 residues processed: 270 average time/residue: 0.1081 time to fit residues: 40.2604 Evaluate side-chains 254 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 233 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 74 optimal weight: 50.0000 chunk 12 optimal weight: 0.0040 chunk 54 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 101 optimal weight: 30.0000 overall best weight: 4.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.072667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052332 restraints weight = 40781.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.054076 restraints weight = 21931.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055232 restraints weight = 14987.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.055965 restraints weight = 11869.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.056430 restraints weight = 10316.207| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11159 Z= 0.186 Angle : 0.693 7.942 15796 Z= 0.399 Chirality : 0.045 0.241 1713 Planarity : 0.004 0.040 1395 Dihedral : 29.332 86.937 3177 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.52 % Allowed : 23.87 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.28), residues: 897 helix: 1.73 (0.20), residues: 619 sheet: None (None), residues: 0 loop : -0.81 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.032 0.003 TYR H 37 PHE 0.008 0.001 PHE F 100 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 (11159) covalent geometry : angle 0.69291 / 0.40 (15796) hydrogen bonds : bond 0.04808 / 3.24 ( 669) hydrogen bonds : angle 3.34684 / 2.37 ( 1771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 0.322 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: A 50 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8487 (mp0) REVERT: A 90 MET cc_start: 0.8897 (mmm) cc_final: 0.8527 (mmm) REVERT: B 88 TYR cc_start: 0.7795 (m-10) cc_final: 0.7277 (m-10) REVERT: B 91 LYS cc_start: 0.9130 (ttmm) cc_final: 0.8764 (tmmt) REVERT: B 98 TYR cc_start: 0.8953 (m-80) cc_final: 0.8683 (m-80) REVERT: C 42 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7939 (mmm-85) REVERT: C 56 GLU cc_start: 0.8650 (tt0) cc_final: 0.7772 (tt0) REVERT: C 64 GLU cc_start: 0.8469 (tt0) cc_final: 0.7924 (tm-30) REVERT: C 84 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8571 (tm-30) REVERT: C 95 LYS cc_start: 0.9281 (tttt) cc_final: 0.8814 (tppt) REVERT: D 117 LYS cc_start: 0.9455 (tptm) cc_final: 0.8934 (tttm) REVERT: E 60 LEU cc_start: 0.8651 (mt) cc_final: 0.8270 (mt) REVERT: E 90 MET cc_start: 0.9071 (tpp) cc_final: 0.8683 (tpt) REVERT: E 112 ILE cc_start: 0.9545 (pt) cc_final: 0.9258 (mt) REVERT: E 120 MET cc_start: 0.7816 (mtp) cc_final: 0.7552 (mtt) REVERT: F 63 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8702 (mt-10) REVERT: F 68 ASP cc_start: 0.9042 (m-30) cc_final: 0.8815 (m-30) REVERT: F 88 TYR cc_start: 0.8779 (m-10) cc_final: 0.8412 (m-80) REVERT: G 25 PHE cc_start: 0.8267 (m-80) cc_final: 0.7922 (m-80) REVERT: G 29 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8370 (tpp80) REVERT: G 39 TYR cc_start: 0.8561 (m-80) cc_final: 0.7956 (m-80) REVERT: G 40 SER cc_start: 0.8949 (p) cc_final: 0.8721 (p) REVERT: G 57 TYR cc_start: 0.9550 (t80) cc_final: 0.9348 (t80) REVERT: G 64 GLU cc_start: 0.8255 (tp30) cc_final: 0.8027 (tm-30) REVERT: G 73 ASN cc_start: 0.8938 (t0) cc_final: 0.8516 (t0) REVERT: H 37 TYR cc_start: 0.9072 (m-80) cc_final: 0.8790 (m-80) REVERT: H 56 MET cc_start: 0.8835 (tpp) cc_final: 0.8473 (tpp) REVERT: H 110 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7668 (mt-10) REVERT: H 117 LYS cc_start: 0.9507 (mtpp) cc_final: 0.9137 (mtmt) outliers start: 29 outliers final: 22 residues processed: 261 average time/residue: 0.1113 time to fit residues: 40.0334 Evaluate side-chains 260 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 83 optimal weight: 50.0000 chunk 85 optimal weight: 40.0000 chunk 91 optimal weight: 6.9990 chunk 38 optimal weight: 0.0970 chunk 46 optimal weight: 7.9990 chunk 90 optimal weight: 50.0000 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 44 GLN H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.072375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.052089 restraints weight = 40907.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053770 restraints weight = 22485.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.054863 restraints weight = 15567.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.055567 restraints weight = 12465.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.055964 restraints weight = 10917.100| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11159 Z= 0.187 Angle : 0.703 8.098 15796 Z= 0.400 Chirality : 0.045 0.242 1713 Planarity : 0.004 0.039 1395 Dihedral : 29.306 86.717 3177 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.84 % Allowed : 22.93 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.27), residues: 897 helix: 1.85 (0.20), residues: 619 sheet: None (None), residues: 0 loop : -0.73 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 35 TYR 0.030 0.002 TYR H 80 PHE 0.009 0.001 PHE A 104 HIS 0.006 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (11159) covalent geometry : angle 0.70320 / 0.40 (15796) hydrogen bonds : bond 0.04745 / 3.19 ( 669) hydrogen bonds : angle 3.32564 / 2.35 ( 1771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.319 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: A 50 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8460 (mp0) REVERT: A 90 MET cc_start: 0.8829 (mmm) cc_final: 0.8465 (mmm) REVERT: B 88 TYR cc_start: 0.7803 (m-10) cc_final: 0.7266 (m-10) REVERT: B 91 LYS cc_start: 0.9148 (ttmm) cc_final: 0.8830 (tmmt) REVERT: B 98 TYR cc_start: 0.8936 (m-80) cc_final: 0.8694 (m-80) REVERT: C 42 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7893 (mmm-85) REVERT: C 56 GLU cc_start: 0.8676 (tt0) cc_final: 0.7839 (tt0) REVERT: C 64 GLU cc_start: 0.8407 (tt0) cc_final: 0.7923 (tm-30) REVERT: C 92 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7838 (mt-10) REVERT: C 95 LYS cc_start: 0.9227 (tttt) cc_final: 0.8820 (tppt) REVERT: D 56 MET cc_start: 0.8397 (tpp) cc_final: 0.8167 (tpp) REVERT: D 106 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8325 (m170) REVERT: E 60 LEU cc_start: 0.8569 (mt) cc_final: 0.8106 (mt) REVERT: E 90 MET cc_start: 0.8937 (tpp) cc_final: 0.8627 (tpt) REVERT: E 112 ILE cc_start: 0.9511 (pt) cc_final: 0.9154 (mt) REVERT: E 120 MET cc_start: 0.7921 (mtp) cc_final: 0.7677 (mtt) REVERT: F 63 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8543 (mm-30) REVERT: G 25 PHE cc_start: 0.8248 (m-80) cc_final: 0.7949 (m-80) REVERT: G 29 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8484 (tpp80) REVERT: G 35 ARG cc_start: 0.8211 (ttp-110) cc_final: 0.7881 (mtm110) REVERT: G 39 TYR cc_start: 0.8631 (m-80) cc_final: 0.7987 (m-80) REVERT: G 64 GLU cc_start: 0.8076 (tp30) cc_final: 0.7490 (tm-30) REVERT: G 68 ASN cc_start: 0.8890 (m-40) cc_final: 0.8396 (m-40) REVERT: G 75 LYS cc_start: 0.9112 (mptt) cc_final: 0.8783 (mmtp) REVERT: H 37 TYR cc_start: 0.9075 (m-80) cc_final: 0.8868 (m-80) REVERT: H 56 MET cc_start: 0.8888 (tpp) cc_final: 0.8537 (tpp) REVERT: H 117 LYS cc_start: 0.9499 (mtpp) cc_final: 0.9086 (mtmt) outliers start: 31 outliers final: 23 residues processed: 262 average time/residue: 0.1110 time to fit residues: 40.2388 Evaluate side-chains 261 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 106 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 17 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 78 optimal weight: 50.0000 chunk 100 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.073529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.052992 restraints weight = 40643.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.054730 restraints weight = 22182.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.055886 restraints weight = 15295.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.056624 restraints weight = 12200.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.057073 restraints weight = 10645.652| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11159 Z= 0.152 Angle : 0.683 8.137 15796 Z= 0.393 Chirality : 0.044 0.243 1713 Planarity : 0.004 0.036 1395 Dihedral : 29.253 86.926 3177 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.74 % Allowed : 25.43 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.28), residues: 897 helix: 1.90 (0.20), residues: 623 sheet: None (None), residues: 0 loop : -0.53 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.028 0.003 TYR G 57 PHE 0.006 0.001 PHE H 62 HIS 0.002 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (11159) covalent geometry : angle 0.68302 / 0.39 (15796) hydrogen bonds : bond 0.04378 / 2.95 ( 669) hydrogen bonds : angle 3.23860 / 2.30 ( 1771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8471 (mp0) REVERT: A 90 MET cc_start: 0.8819 (mmm) cc_final: 0.8461 (mmm) REVERT: B 63 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8699 (mt-10) REVERT: B 88 TYR cc_start: 0.7763 (m-10) cc_final: 0.7295 (m-10) REVERT: B 91 LYS cc_start: 0.9134 (ttmm) cc_final: 0.8817 (tmmt) REVERT: B 98 TYR cc_start: 0.8933 (m-80) cc_final: 0.8732 (m-80) REVERT: C 39 TYR cc_start: 0.8888 (m-80) cc_final: 0.8651 (m-80) REVERT: C 42 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.7837 (mmm-85) REVERT: C 56 GLU cc_start: 0.8684 (tt0) cc_final: 0.7907 (tt0) REVERT: C 84 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8674 (tm-30) REVERT: C 92 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7952 (mt-10) REVERT: C 95 LYS cc_start: 0.9257 (tttt) cc_final: 0.8797 (tppt) REVERT: D 56 MET cc_start: 0.8285 (tpp) cc_final: 0.7794 (tpp) REVERT: E 94 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8029 (mm-30) REVERT: E 112 ILE cc_start: 0.9498 (pt) cc_final: 0.9202 (mt) REVERT: F 63 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8552 (mt-10) REVERT: G 29 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8491 (tpp80) REVERT: G 39 TYR cc_start: 0.8509 (m-80) cc_final: 0.7994 (m-80) REVERT: G 64 GLU cc_start: 0.8232 (tp30) cc_final: 0.7615 (tm-30) REVERT: G 68 ASN cc_start: 0.8978 (m-40) cc_final: 0.8420 (m-40) REVERT: G 73 ASN cc_start: 0.8961 (t0) cc_final: 0.8677 (t0) REVERT: H 37 TYR cc_start: 0.9091 (m-80) cc_final: 0.8883 (m-80) REVERT: H 56 MET cc_start: 0.8897 (tpp) cc_final: 0.8516 (tpp) REVERT: H 117 LYS cc_start: 0.9505 (mtpp) cc_final: 0.9092 (mtmt) outliers start: 24 outliers final: 17 residues processed: 266 average time/residue: 0.1104 time to fit residues: 40.7523 Evaluate side-chains 263 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 0.1980 chunk 88 optimal weight: 50.0000 chunk 46 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 0.0170 chunk 101 optimal weight: 0.9980 chunk 83 optimal weight: 50.0000 chunk 71 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 overall best weight: 3.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.073173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052740 restraints weight = 40283.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054446 restraints weight = 22011.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.055579 restraints weight = 15200.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.056325 restraints weight = 12118.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.056740 restraints weight = 10565.025| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11159 Z= 0.168 Angle : 0.707 8.334 15796 Z= 0.403 Chirality : 0.045 0.246 1713 Planarity : 0.004 0.036 1395 Dihedral : 29.229 87.192 3177 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.74 % Allowed : 27.77 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.28), residues: 897 helix: 1.99 (0.20), residues: 614 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 35 TYR 0.053 0.003 TYR H 80 PHE 0.011 0.001 PHE B 100 HIS 0.005 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (11159) covalent geometry : angle 0.70716 / 0.40 (15796) hydrogen bonds : bond 0.04475 / 3.01 ( 669) hydrogen bonds : angle 3.32164 / 2.37 ( 1771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8477 (mp0) REVERT: A 90 MET cc_start: 0.8904 (mmm) cc_final: 0.8474 (mmm) REVERT: B 63 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8750 (mt-10) REVERT: B 88 TYR cc_start: 0.7801 (m-10) cc_final: 0.7278 (m-10) REVERT: B 91 LYS cc_start: 0.9138 (ttmm) cc_final: 0.8799 (tmmt) REVERT: C 42 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.7886 (mmm-85) REVERT: C 56 GLU cc_start: 0.8728 (tt0) cc_final: 0.8202 (tt0) REVERT: C 64 GLU cc_start: 0.8471 (tt0) cc_final: 0.7873 (tm-30) REVERT: C 84 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8621 (tm-30) REVERT: C 92 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7919 (mt-10) REVERT: C 95 LYS cc_start: 0.9272 (tttt) cc_final: 0.8801 (tppt) REVERT: D 56 MET cc_start: 0.8302 (tpp) cc_final: 0.7813 (tpp) REVERT: E 79 LYS cc_start: 0.8374 (tptp) cc_final: 0.8127 (tptp) REVERT: E 90 MET cc_start: 0.9094 (mmm) cc_final: 0.8857 (tpt) REVERT: E 112 ILE cc_start: 0.9489 (pt) cc_final: 0.9212 (mt) REVERT: E 120 MET cc_start: 0.7826 (mtp) cc_final: 0.7585 (mtt) REVERT: F 63 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8501 (mm-30) REVERT: G 39 TYR cc_start: 0.8549 (m-80) cc_final: 0.7942 (m-80) REVERT: G 64 GLU cc_start: 0.8260 (tp30) cc_final: 0.7646 (tm-30) REVERT: G 68 ASN cc_start: 0.9037 (m-40) cc_final: 0.8495 (m-40) REVERT: G 75 LYS cc_start: 0.9202 (mptt) cc_final: 0.8853 (mmtp) REVERT: H 37 TYR cc_start: 0.9101 (m-80) cc_final: 0.8896 (m-80) REVERT: H 56 MET cc_start: 0.8853 (tpp) cc_final: 0.8482 (tpp) REVERT: H 117 LYS cc_start: 0.9512 (mtpp) cc_final: 0.9120 (mtpt) outliers start: 24 outliers final: 19 residues processed: 256 average time/residue: 0.1102 time to fit residues: 39.1538 Evaluate side-chains 259 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 106 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 67 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 72 optimal weight: 50.0000 chunk 8 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 87 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS G 31 HIS G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.072115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.052439 restraints weight = 41301.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.054039 restraints weight = 23054.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055120 restraints weight = 16083.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.055803 restraints weight = 12900.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.056223 restraints weight = 11292.592| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11159 Z= 0.210 Angle : 0.730 8.469 15796 Z= 0.414 Chirality : 0.045 0.244 1713 Planarity : 0.005 0.081 1395 Dihedral : 29.227 87.032 3177 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.06 % Allowed : 27.61 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.28), residues: 897 helix: 1.92 (0.20), residues: 617 sheet: None (None), residues: 0 loop : -0.30 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG G 35 TYR 0.052 0.004 TYR H 80 PHE 0.011 0.001 PHE G 25 HIS 0.008 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (11159) covalent geometry : angle 0.72990 / 0.41 (15796) hydrogen bonds : bond 0.04873 / 3.25 ( 669) hydrogen bonds : angle 3.47021 / 2.47 ( 1771) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.290 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: A 50 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8462 (mp0) REVERT: B 88 TYR cc_start: 0.7810 (m-10) cc_final: 0.7229 (m-10) REVERT: B 91 LYS cc_start: 0.9123 (ttmm) cc_final: 0.8869 (tmmt) REVERT: C 42 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7844 (mmm-85) REVERT: C 56 GLU cc_start: 0.8745 (tt0) cc_final: 0.8227 (tt0) REVERT: C 64 GLU cc_start: 0.8400 (tt0) cc_final: 0.7938 (tm-30) REVERT: C 84 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8705 (tm-30) REVERT: C 92 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8038 (mt-10) REVERT: C 95 LYS cc_start: 0.9276 (tttt) cc_final: 0.8846 (tppt) REVERT: D 56 MET cc_start: 0.8401 (tpp) cc_final: 0.7882 (tpp) REVERT: D 106 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.8213 (m170) REVERT: G 39 TYR cc_start: 0.8574 (m-80) cc_final: 0.7924 (m-80) REVERT: G 64 GLU cc_start: 0.8048 (tp30) cc_final: 0.7431 (tm-30) REVERT: G 68 ASN cc_start: 0.8939 (m-40) cc_final: 0.8383 (m-40) REVERT: H 56 MET cc_start: 0.8882 (tpp) cc_final: 0.8520 (tpp) REVERT: H 117 LYS cc_start: 0.9484 (mtpp) cc_final: 0.9103 (mtpt) outliers start: 26 outliers final: 21 residues processed: 247 average time/residue: 0.1095 time to fit residues: 37.7020 Evaluate side-chains 256 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 106 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 50.0000 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.072825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.053077 restraints weight = 40808.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.054708 restraints weight = 22818.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055806 restraints weight = 15910.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056513 restraints weight = 12732.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.056938 restraints weight = 11120.416| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11159 Z= 0.170 Angle : 0.730 9.012 15796 Z= 0.412 Chirality : 0.045 0.246 1713 Planarity : 0.004 0.062 1395 Dihedral : 29.199 86.984 3177 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.28 % Allowed : 30.11 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.28), residues: 897 helix: 1.94 (0.20), residues: 617 sheet: None (None), residues: 0 loop : -0.27 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG G 35 TYR 0.053 0.003 TYR H 80 PHE 0.011 0.001 PHE B 100 HIS 0.011 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (11159) covalent geometry : angle 0.72951 / 0.41 (15796) hydrogen bonds : bond 0.04512 / 3.03 ( 669) hydrogen bonds : angle 3.41484 / 2.43 ( 1771) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 0.321 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: A 50 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8448 (mp0) REVERT: A 90 MET cc_start: 0.8839 (mmm) cc_final: 0.8413 (mmm) REVERT: B 88 TYR cc_start: 0.7777 (m-10) cc_final: 0.7248 (m-10) REVERT: B 91 LYS cc_start: 0.9099 (ttmm) cc_final: 0.8800 (tmmt) REVERT: C 42 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7757 (mmm-85) REVERT: C 56 GLU cc_start: 0.8703 (tt0) cc_final: 0.8203 (tt0) REVERT: C 64 GLU cc_start: 0.8374 (tt0) cc_final: 0.7856 (tm-30) REVERT: C 84 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8655 (tm-30) REVERT: C 92 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8050 (mt-10) REVERT: C 95 LYS cc_start: 0.9272 (tttt) cc_final: 0.8821 (tppt) REVERT: D 56 MET cc_start: 0.8426 (tpp) cc_final: 0.7970 (tpp) REVERT: D 99 LEU cc_start: 0.9295 (mp) cc_final: 0.9071 (mp) REVERT: D 106 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.7981 (m170) REVERT: E 112 ILE cc_start: 0.9514 (pt) cc_final: 0.9237 (mt) REVERT: G 39 TYR cc_start: 0.8533 (m-80) cc_final: 0.7840 (m-80) REVERT: G 57 TYR cc_start: 0.9281 (t80) cc_final: 0.8952 (t80) REVERT: G 68 ASN cc_start: 0.8944 (m-40) cc_final: 0.8660 (m-40) REVERT: H 56 MET cc_start: 0.8884 (tpp) cc_final: 0.8540 (tpp) REVERT: H 110 GLU cc_start: 0.8339 (pt0) cc_final: 0.7793 (pm20) REVERT: H 117 LYS cc_start: 0.9494 (mtpp) cc_final: 0.9124 (ttpp) outliers start: 21 outliers final: 18 residues processed: 248 average time/residue: 0.1069 time to fit residues: 36.8530 Evaluate side-chains 253 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 106 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 72 optimal weight: 50.0000 chunk 61 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 40.0000 chunk 54 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.072020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052287 restraints weight = 41466.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.053916 restraints weight = 23164.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.054981 restraints weight = 16161.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.055661 restraints weight = 12980.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.056092 restraints weight = 11365.497| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11159 Z= 0.200 Angle : 0.742 9.266 15796 Z= 0.418 Chirality : 0.045 0.245 1713 Planarity : 0.005 0.064 1395 Dihedral : 29.198 88.954 3177 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.74 % Allowed : 29.49 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.28), residues: 897 helix: 1.94 (0.20), residues: 617 sheet: None (None), residues: 0 loop : -0.28 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 35 TYR 0.060 0.003 TYR H 80 PHE 0.008 0.001 PHE F 100 HIS 0.009 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (11159) covalent geometry : angle 0.74181 / 0.42 (15796) hydrogen bonds : bond 0.04805 / 3.20 ( 669) hydrogen bonds : angle 3.52265 / 2.52 ( 1771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1758.75 seconds wall clock time: 31 minutes 2.44 seconds (1862.44 seconds total)