Starting phenix.real_space_refine on Wed Mar 4 02:18:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t7c_10393/03_2026/6t7c_10393.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t7c_10393/03_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_10393/03_2026/6t7c_10393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t7c_10393/03_2026/6t7c_10393.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t7c_10393/03_2026/6t7c_10393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t7c_10393/03_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-dev-5986/lib/python3.9/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: 2.64, per 1000 atoms: 0.25 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: 0.70 Conformation dependent library (CDL) restraints added in 365.4 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: 1.60 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: 1.79 Time building geometry restraints manager: 0.97 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=" CB LYS G 118 " pdb=" CG LYS G 118 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.52e+00 bond pdb=" CB LYS C 118 " pdb=" CG LYS C 118 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.30e+00 bond pdb=" CA ARG B 95 " pdb=" CB ARG B 95 " ideal model delta sigma weight residual 1.539 1.461 0.079 4.88e-02 4.20e+02 2.59e+00 bond pdb=" CB VAL B 81 " pdb=" CG2 VAL B 81 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" CB ILE A 130 " pdb=" CG2 ILE A 130 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.32e+00 ... (remaining 11154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.73: 15782 5.73 - 11.46: 10 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=" CA LYS H 31 " pdb=" CB LYS H 31 " pdb=" CG LYS H 31 " ideal model delta sigma weight residual 114.10 122.79 -8.69 2.00e+00 2.50e-01 1.89e+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: 1594 0.084 - 0.167: 116 0.167 - 0.251: 2 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: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.740 Find NCS groups from input model: 0.100 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 11159 Z= 0.377 Angle : 0.881 28.661 15796 Z= 0.503 Chirality : 0.046 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 covalent geometry : bond 0.00816 (11159) covalent geometry : angle 0.88144 (15796) hydrogen bonds : bond 0.10676 ( 669) hydrogen bonds : angle 4.53446 ( 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 : 0.305 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: 0.8452 (mt-10) REVERT: A 76 GLN cc_start: 0.8598 (mt0) cc_final: 0.8353 (mt0) REVERT: A 81 ASP cc_start: 0.8102 (t0) cc_final: 0.7886 (t0) REVERT: A 90 MET cc_start: 0.8774 (mmm) cc_final: 0.8438 (mmm) REVERT: A 99 TYR cc_start: 0.8615 (t80) cc_final: 0.8415 (t80) REVERT: A 118 THR cc_start: 0.9225 (m) cc_final: 0.8876 (p) 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: 0.8344 (ttpt) REVERT: B 59 LYS cc_start: 0.9325 (mtpt) cc_final: 0.9013 (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: 0.8981 (ttp-110) REVERT: C 56 GLU cc_start: 0.8415 (tt0) cc_final: 0.7870 (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: 0.8041 (mt-10) REVERT: C 95 LYS cc_start: 0.9350 (mttt) cc_final: 0.8911 (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: 0.8796 (tp) REVERT: D 34 TYR cc_start: 0.8586 (m-80) cc_final: 0.8269 (m-80) REVERT: D 65 ASP cc_start: 0.9150 (t70) cc_final: 0.8819 (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: 0.8248 (mmm-85) REVERT: D 99 LEU cc_start: 0.9089 (mt) cc_final: 0.8841 (mp) REVERT: D 117 LYS cc_start: 0.9244 (tptm) cc_final: 0.8478 (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: 0.7523 (mt) REVERT: E 73 GLU cc_start: 0.9272 (tm-30) cc_final: 0.8776 (tm-30) REVERT: E 78 PHE cc_start: 0.8518 (m-80) cc_final: 0.7676 (m-10) REVERT: E 94 GLU cc_start: 0.8653 (tp30) cc_final: 0.8263 (mm-30) REVERT: E 125 GLN cc_start: 0.8694 (mt0) cc_final: 0.8446 (mt0) REVERT: F 68 ASP cc_start: 0.9071 (m-30) cc_final: 0.8857 (m-30) REVERT: F 88 TYR cc_start: 0.8663 (m-10) cc_final: 0.8299 (m-10) REVERT: G 39 TYR cc_start: 0.8215 (m-80) cc_final: 0.7398 (m-80) REVERT: G 64 GLU cc_start: 0.8382 (tp30) cc_final: 0.7714 (tm-30) REVERT: G 68 ASN cc_start: 0.9213 (m-40) cc_final: 0.8390 (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: 0.6577 (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: 0.8862 (mm) REVERT: H 80 TYR cc_start: 0.8342 (m-10) cc_final: 0.8059 (m-10) REVERT: H 90 GLU cc_start: 0.9098 (mp0) cc_final: 0.8726 (mp0) REVERT: H 103 LEU cc_start: 0.9590 (mt) cc_final: 0.9359 (mt) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.1381 time to fit residues: 59.5491 Evaluate side-chains 241 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 5.9990 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: 7.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 79 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 68 GLN E 76 GLN E 85 GLN E 93 GLN F 64 ASN G 31 HIS G 110 ASN H 92 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.072526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052006 restraints weight = 40456.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053649 restraints weight = 22630.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054725 restraints weight = 15858.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055419 restraints weight = 12779.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.055818 restraints weight = 11225.984| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11159 Z= 0.231 Angle : 0.661 8.727 15796 Z= 0.386 Chirality : 0.038 0.133 1713 Planarity : 0.004 0.044 1395 Dihedral : 28.957 85.277 3177 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.90 % Allowed : 16.22 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.03 (0.26), residues: 897 helix: 0.57 (0.19), residues: 621 sheet: None (None), residues: 0 loop : -1.10 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 35 TYR 0.027 0.002 TYR B 98 PHE 0.010 0.002 PHE F 100 HIS 0.010 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00508 (11159) covalent geometry : angle 0.66122 (15796) hydrogen bonds : bond 0.04801 ( 669) hydrogen bonds : angle 3.31972 ( 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 301 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 0.309 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: 0.8752 (mt-10) cc_final: 0.8165 (mt-10) REVERT: B 46 ILE cc_start: 0.9252 (mm) cc_final: 0.9034 (mm) REVERT: B 98 TYR cc_start: 0.9070 (m-10) cc_final: 0.8726 (m-80) REVERT: C 29 ARG cc_start: 0.8739 (mtp180) cc_final: 0.8192 (ttt180) REVERT: C 56 GLU cc_start: 0.8657 (tt0) cc_final: 0.8281 (tt0) REVERT: C 89 ASN cc_start: 0.9096 (m-40) cc_final: 0.8794 (m-40) REVERT: C 95 LYS cc_start: 0.9287 (tttt) cc_final: 0.8819 (tppt) REVERT: D 44 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8545 (tm-30) REVERT: D 65 ASP cc_start: 0.9301 (t70) cc_final: 0.9064 (t0) REVERT: E 90 MET cc_start: 0.8974 (tpp) cc_final: 0.8708 (tpp) REVERT: F 25 ASN cc_start: 0.9187 (m-40) cc_final: 0.7983 (m-40) REVERT: F 88 TYR cc_start: 0.8788 (m-10) cc_final: 0.8417 (m-10) REVERT: G 57 TYR cc_start: 0.9605 (t80) cc_final: 0.9088 (t80) REVERT: G 58 LEU cc_start: 0.9644 (mt) cc_final: 0.9411 (mt) REVERT: G 62 ILE cc_start: 0.9329 (mm) cc_final: 0.9089 (tp) REVERT: G 64 GLU cc_start: 0.8019 (tp30) cc_final: 0.7513 (tm-30) REVERT: G 68 ASN cc_start: 0.9056 (m-40) cc_final: 0.7835 (m-40) REVERT: H 56 MET cc_start: 0.8878 (tpp) cc_final: 0.8599 (tpp) outliers start: 25 outliers final: 16 residues processed: 288 average time/residue: 0.1165 time to fit residues: 45.0827 Evaluate side-chains 247 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 89 VAL 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 G residue 33 LEU Chi-restraints excluded: chain G residue 49 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 93 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 99 optimal weight: 40.0000 chunk 17 optimal weight: 0.0370 chunk 35 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 104 GLN D 81 ASN D 106 HIS E 85 GLN E 125 GLN F 75 HIS H 92 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.072961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.052806 restraints weight = 40371.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054487 restraints weight = 22081.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.055606 restraints weight = 15279.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.056289 restraints weight = 12200.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.056741 restraints weight = 10679.311| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11159 Z= 0.169 Angle : 0.620 7.375 15796 Z= 0.365 Chirality : 0.037 0.160 1713 Planarity : 0.004 0.040 1395 Dihedral : 28.887 85.456 3177 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.43 % Allowed : 20.12 % 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: 1.20 (0.27), residues: 897 helix: 1.50 (0.20), residues: 619 sheet: None (None), residues: 0 loop : -0.78 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 20 TYR 0.020 0.002 TYR D 80 PHE 0.007 0.001 PHE F 100 HIS 0.021 0.002 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00367 (11159) covalent geometry : angle 0.61964 (15796) hydrogen bonds : bond 0.04032 ( 669) hydrogen bonds : angle 3.10635 ( 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 288 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 266 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8421 (mp0) REVERT: A 64 LYS cc_start: 0.7653 (tppt) cc_final: 0.6404 (tptt) REVERT: A 90 MET cc_start: 0.8728 (mmt) cc_final: 0.8415 (mmm) REVERT: A 105 GLU cc_start: 0.8193 (tp30) cc_final: 0.7882 (mm-30) REVERT: B 49 LEU cc_start: 0.8958 (mt) cc_final: 0.8443 (mt) REVERT: B 98 TYR cc_start: 0.9039 (m-10) cc_final: 0.8767 (m-10) REVERT: C 29 ARG cc_start: 0.8669 (mtp180) cc_final: 0.8188 (ttt180) REVERT: C 56 GLU cc_start: 0.8575 (tt0) cc_final: 0.8040 (tt0) REVERT: C 84 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8607 (tm-30) REVERT: C 89 ASN cc_start: 0.9080 (m-40) cc_final: 0.8849 (m-40) REVERT: C 95 LYS cc_start: 0.9230 (tttt) cc_final: 0.8777 (tppt) REVERT: D 44 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8590 (tm-30) REVERT: E 90 MET cc_start: 0.8917 (tpp) cc_final: 0.8687 (tpp) REVERT: F 88 TYR cc_start: 0.8671 (m-10) cc_final: 0.8096 (m-80) REVERT: G 39 TYR cc_start: 0.8371 (m-80) cc_final: 0.7816 (m-80) REVERT: G 57 TYR cc_start: 0.9549 (t80) cc_final: 0.9301 (t80) REVERT: G 62 ILE cc_start: 0.9337 (mm) cc_final: 0.9055 (tp) REVERT: G 64 GLU cc_start: 0.8108 (tp30) cc_final: 0.7606 (tm-30) REVERT: G 68 ASN cc_start: 0.8841 (m-40) cc_final: 0.8070 (m-40) REVERT: H 56 MET cc_start: 0.8915 (tpp) cc_final: 0.8568 (tpp) REVERT: H 102 GLU cc_start: 0.8497 (pm20) cc_final: 0.8269 (pm20) REVERT: H 110 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7778 (mt-10) REVERT: H 117 LYS cc_start: 0.9552 (mtpp) cc_final: 0.9149 (mtmt) outliers start: 22 outliers final: 15 residues processed: 278 average time/residue: 0.1129 time to fit residues: 42.1602 Evaluate side-chains 259 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 244 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL 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 30 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 58 ILE Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 72 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.072184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051854 restraints weight = 41834.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.053433 restraints weight = 23870.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.054483 restraints weight = 16924.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.055144 restraints weight = 13750.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.055532 restraints weight = 12161.373| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11159 Z= 0.201 Angle : 0.633 12.280 15796 Z= 0.370 Chirality : 0.037 0.142 1713 Planarity : 0.004 0.038 1395 Dihedral : 28.821 86.730 3177 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.06 % Allowed : 23.09 % Favored : 72.85 % 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: 1.84 (0.27), residues: 897 helix: 1.91 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -0.43 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 20 TYR 0.029 0.002 TYR H 80 PHE 0.014 0.001 PHE E 78 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00446 (11159) covalent geometry : angle 0.63335 (15796) hydrogen bonds : bond 0.04388 ( 669) hydrogen bonds : angle 3.22437 ( 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 276 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8406 (mp0) REVERT: A 76 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8595 (mt0) REVERT: A 90 MET cc_start: 0.8972 (mmt) cc_final: 0.8725 (mmm) REVERT: A 105 GLU cc_start: 0.8085 (tp30) cc_final: 0.7804 (mm-30) REVERT: B 98 TYR cc_start: 0.9122 (m-10) cc_final: 0.8783 (m-10) REVERT: C 42 ARG cc_start: 0.8394 (mtp180) cc_final: 0.7998 (mtp180) REVERT: C 56 GLU cc_start: 0.8716 (tt0) cc_final: 0.8155 (tt0) REVERT: C 64 GLU cc_start: 0.8350 (tt0) cc_final: 0.7883 (tm-30) REVERT: C 95 LYS cc_start: 0.9260 (tttt) cc_final: 0.8787 (tppt) REVERT: C 99 ARG cc_start: 0.7854 (mmp-170) cc_final: 0.7649 (mmm160) REVERT: D 44 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8714 (tm-30) REVERT: E 90 MET cc_start: 0.8832 (tpp) cc_final: 0.8454 (tpp) REVERT: E 112 ILE cc_start: 0.9503 (pt) cc_final: 0.9189 (mt) REVERT: F 98 TYR cc_start: 0.8314 (m-80) cc_final: 0.8079 (m-80) REVERT: G 39 TYR cc_start: 0.8600 (m-80) cc_final: 0.8156 (m-80) REVERT: G 56 GLU cc_start: 0.8873 (tt0) cc_final: 0.8613 (mt-10) REVERT: G 57 TYR cc_start: 0.9445 (t80) cc_final: 0.9220 (t80) REVERT: G 62 ILE cc_start: 0.9370 (mm) cc_final: 0.9061 (tp) REVERT: H 56 MET cc_start: 0.8943 (tpp) cc_final: 0.8640 (tpp) REVERT: H 102 GLU cc_start: 0.8471 (pm20) cc_final: 0.8102 (pm20) REVERT: H 117 LYS cc_start: 0.9545 (mtpp) cc_final: 0.9164 (mtmt) outliers start: 26 outliers final: 21 residues processed: 261 average time/residue: 0.1136 time to fit residues: 40.4335 Evaluate side-chains 252 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL 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 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 77 LEU 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: 9.9990 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 95 optimal weight: 40.0000 chunk 47 optimal weight: 3.9990 chunk 101 optimal weight: 50.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN D 79 HIS H 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.071820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.051594 restraints weight = 41205.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.053269 restraints weight = 22498.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054406 restraints weight = 15497.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.055145 restraints weight = 12309.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055415 restraints weight = 10692.029| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11159 Z= 0.197 Angle : 0.639 10.723 15796 Z= 0.371 Chirality : 0.037 0.149 1713 Planarity : 0.004 0.039 1395 Dihedral : 28.801 86.697 3177 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.84 % Allowed : 24.18 % Favored : 70.98 % 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: 2.13 (0.28), residues: 897 helix: 2.07 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.033 0.002 TYR H 80 PHE 0.010 0.001 PHE E 78 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00438 (11159) covalent geometry : angle 0.63859 (15796) hydrogen bonds : bond 0.04302 ( 669) hydrogen bonds : angle 3.19830 ( 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 280 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8471 (mp0) REVERT: A 76 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8606 (mt0) REVERT: A 81 ASP cc_start: 0.8144 (t0) cc_final: 0.7944 (t0) REVERT: A 90 MET cc_start: 0.8908 (mmt) cc_final: 0.8417 (mmm) REVERT: A 105 GLU cc_start: 0.8309 (tp30) cc_final: 0.7891 (mm-30) REVERT: B 34 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.8014 (tp) REVERT: B 91 LYS cc_start: 0.9109 (ttmm) cc_final: 0.8864 (ttpp) REVERT: B 98 TYR cc_start: 0.9082 (m-10) cc_final: 0.8825 (m-10) REVERT: C 42 ARG cc_start: 0.8434 (mtp180) cc_final: 0.7910 (mtp180) REVERT: C 56 GLU cc_start: 0.8704 (tt0) cc_final: 0.8106 (tt0) REVERT: C 64 GLU cc_start: 0.8507 (tt0) cc_final: 0.7944 (tm-30) REVERT: C 84 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8591 (tm-30) REVERT: C 95 LYS cc_start: 0.9286 (tttt) cc_final: 0.8778 (tppt) REVERT: D 44 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8964 (tm-30) REVERT: E 60 LEU cc_start: 0.8630 (mt) cc_final: 0.8112 (mt) REVERT: E 64 LYS cc_start: 0.8368 (mtmm) cc_final: 0.7873 (ttpt) REVERT: E 90 MET cc_start: 0.8958 (tpp) cc_final: 0.8694 (tpt) REVERT: F 93 GLN cc_start: 0.8514 (mp10) cc_final: 0.8103 (mp10) REVERT: G 39 TYR cc_start: 0.8731 (m-80) cc_final: 0.8351 (m-80) REVERT: G 56 GLU cc_start: 0.9079 (tt0) cc_final: 0.8824 (mt-10) REVERT: G 61 GLU cc_start: 0.9153 (tp30) cc_final: 0.8931 (tp30) REVERT: G 62 ILE cc_start: 0.9397 (mm) cc_final: 0.9082 (tp) REVERT: G 64 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7829 (tm-30) REVERT: G 68 ASN cc_start: 0.8719 (m-40) cc_final: 0.8342 (m-40) REVERT: H 56 MET cc_start: 0.8928 (tpp) cc_final: 0.8590 (tpp) REVERT: H 113 LYS cc_start: 0.9649 (ttpp) cc_final: 0.9278 (ptmm) REVERT: H 117 LYS cc_start: 0.9596 (mtpp) cc_final: 0.9292 (mttm) outliers start: 31 outliers final: 21 residues processed: 262 average time/residue: 0.1061 time to fit residues: 38.2095 Evaluate side-chains 255 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE 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 G residue 33 LEU Chi-restraints excluded: chain H residue 58 ILE 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: 20.0000 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 38 optimal weight: 0.0370 chunk 46 optimal weight: 6.9990 chunk 90 optimal weight: 40.0000 chunk 58 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.072191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051813 restraints weight = 41278.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.053524 restraints weight = 22403.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.054680 restraints weight = 15400.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.055412 restraints weight = 12248.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.055861 restraints weight = 10659.574| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11159 Z= 0.184 Angle : 0.641 13.122 15796 Z= 0.371 Chirality : 0.037 0.157 1713 Planarity : 0.004 0.038 1395 Dihedral : 28.754 86.874 3177 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.15 % Allowed : 25.12 % Favored : 69.73 % 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: 2.27 (0.28), residues: 897 helix: 2.18 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.17 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 23 TYR 0.026 0.002 TYR H 80 PHE 0.009 0.001 PHE F 100 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00411 (11159) covalent geometry : angle 0.64123 (15796) hydrogen bonds : bond 0.04137 ( 669) hydrogen bonds : angle 3.14710 ( 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 276 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8295 (mt-10) REVERT: A 76 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8718 (mt0) REVERT: A 90 MET cc_start: 0.8920 (mmt) cc_final: 0.8466 (mmm) REVERT: A 105 GLU cc_start: 0.8276 (tp30) cc_final: 0.7881 (mm-30) REVERT: B 34 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7968 (tp) REVERT: B 91 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8783 (ttpp) REVERT: B 98 TYR cc_start: 0.9107 (m-10) cc_final: 0.8773 (m-10) REVERT: C 42 ARG cc_start: 0.8419 (mtp180) cc_final: 0.8091 (mtp-110) REVERT: C 56 GLU cc_start: 0.8739 (tt0) cc_final: 0.8148 (tt0) REVERT: C 57 TYR cc_start: 0.9147 (t80) cc_final: 0.8562 (t80) REVERT: C 61 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8343 (mt-10) REVERT: C 64 GLU cc_start: 0.8502 (tt0) cc_final: 0.7919 (tm-30) REVERT: C 92 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7463 (tt0) REVERT: C 95 LYS cc_start: 0.9255 (tttt) cc_final: 0.8716 (tppt) REVERT: E 60 LEU cc_start: 0.8606 (mt) cc_final: 0.8143 (mt) REVERT: E 90 MET cc_start: 0.8932 (tpp) cc_final: 0.8553 (tpt) REVERT: F 93 GLN cc_start: 0.8527 (mp10) cc_final: 0.8157 (mp10) REVERT: G 39 TYR cc_start: 0.8711 (m-80) cc_final: 0.8504 (m-80) REVERT: G 62 ILE cc_start: 0.9394 (mm) cc_final: 0.9092 (tp) REVERT: G 64 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7899 (tm-30) REVERT: G 68 ASN cc_start: 0.8725 (m-40) cc_final: 0.8423 (m-40) REVERT: H 56 MET cc_start: 0.8939 (tpp) cc_final: 0.8611 (tpp) REVERT: H 92 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8758 (pt0) REVERT: H 110 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7682 (mt-10) REVERT: H 113 LYS cc_start: 0.9648 (ttpp) cc_final: 0.9282 (ptmm) outliers start: 33 outliers final: 25 residues processed: 256 average time/residue: 0.1078 time to fit residues: 37.4756 Evaluate side-chains 255 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE 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 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 17 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 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 = 0.3495 r_free = 0.3495 target = 0.072503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052109 restraints weight = 40876.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053807 restraints weight = 22311.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.054965 restraints weight = 15366.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.055717 restraints weight = 12205.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.056182 restraints weight = 10603.487| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11159 Z= 0.176 Angle : 0.644 12.688 15796 Z= 0.372 Chirality : 0.037 0.162 1713 Planarity : 0.004 0.041 1395 Dihedral : 28.706 89.880 3177 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.68 % Allowed : 25.90 % Favored : 69.42 % 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: 2.34 (0.28), residues: 897 helix: 2.25 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 23 TYR 0.034 0.002 TYR H 80 PHE 0.008 0.001 PHE G 25 HIS 0.002 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00395 (11159) covalent geometry : angle 0.64426 (15796) hydrogen bonds : bond 0.04045 ( 669) hydrogen bonds : angle 3.13133 ( 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 276 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.306 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: 0.8893 (mt-10) cc_final: 0.8303 (mt-10) REVERT: A 76 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8789 (mt0) REVERT: A 81 ASP cc_start: 0.7885 (t0) cc_final: 0.7585 (t70) REVERT: A 90 MET cc_start: 0.8945 (mmt) cc_final: 0.8476 (mmm) REVERT: A 105 GLU cc_start: 0.8339 (tp30) cc_final: 0.7971 (mm-30) REVERT: B 34 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7994 (tp) REVERT: B 91 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8819 (ttpp) REVERT: B 98 TYR cc_start: 0.9007 (m-10) cc_final: 0.8656 (m-10) REVERT: C 42 ARG cc_start: 0.8395 (mtp180) cc_final: 0.8036 (mtp-110) REVERT: C 56 GLU cc_start: 0.8705 (tt0) cc_final: 0.8125 (tt0) REVERT: C 57 TYR cc_start: 0.9190 (t80) cc_final: 0.8684 (t80) REVERT: C 61 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8400 (mm-30) REVERT: C 64 GLU cc_start: 0.8481 (tt0) cc_final: 0.7869 (tm-30) REVERT: C 92 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7444 (tt0) REVERT: C 95 LYS cc_start: 0.9261 (tttt) cc_final: 0.8721 (tppt) REVERT: D 38 VAL cc_start: 0.8897 (t) cc_final: 0.8691 (p) REVERT: D 43 LYS cc_start: 0.9469 (tppt) cc_final: 0.9161 (tppt) REVERT: E 60 LEU cc_start: 0.8595 (mt) cc_final: 0.7893 (mt) REVERT: E 79 LYS cc_start: 0.8249 (tptp) cc_final: 0.7974 (tptp) REVERT: E 90 MET cc_start: 0.9014 (tpp) cc_final: 0.8593 (tpt) REVERT: F 93 GLN cc_start: 0.8551 (mp10) cc_final: 0.8207 (mp10) REVERT: G 39 TYR cc_start: 0.8738 (m-80) cc_final: 0.8521 (m-80) REVERT: G 62 ILE cc_start: 0.9396 (mm) cc_final: 0.9094 (tp) REVERT: G 64 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7882 (tm-30) REVERT: G 68 ASN cc_start: 0.8649 (m-40) cc_final: 0.8299 (m-40) REVERT: H 56 MET cc_start: 0.8933 (tpp) cc_final: 0.8591 (tpp) REVERT: H 59 MET cc_start: 0.8475 (tpp) cc_final: 0.8205 (tpp) REVERT: H 92 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8708 (pt0) REVERT: H 113 LYS cc_start: 0.9667 (ttpp) cc_final: 0.9291 (ptmm) REVERT: H 117 LYS cc_start: 0.9582 (mtpp) cc_final: 0.9279 (mttm) outliers start: 30 outliers final: 27 residues processed: 255 average time/residue: 0.1084 time to fit residues: 37.6983 Evaluate side-chains 266 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL 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 A residue 124 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE 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 G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.070579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.050126 restraints weight = 41646.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.051674 restraints weight = 23864.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052751 restraints weight = 16934.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.053392 restraints weight = 13684.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053829 restraints weight = 12068.237| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11159 Z= 0.244 Angle : 0.712 16.668 15796 Z= 0.402 Chirality : 0.040 0.211 1713 Planarity : 0.004 0.041 1395 Dihedral : 28.733 88.013 3177 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.93 % Allowed : 25.59 % 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: 2.15 (0.28), residues: 897 helix: 2.09 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.23 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 23 TYR 0.058 0.003 TYR H 80 PHE 0.010 0.001 PHE B 100 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00544 (11159) covalent geometry : angle 0.71215 (15796) hydrogen bonds : bond 0.04817 ( 669) hydrogen bonds : angle 3.39391 ( 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 264 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8249 (mt-10) REVERT: A 76 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8730 (mt0) REVERT: A 81 ASP cc_start: 0.7790 (t0) cc_final: 0.7545 (t70) REVERT: B 34 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8091 (tp) REVERT: B 98 TYR cc_start: 0.9033 (m-10) cc_final: 0.8629 (m-10) REVERT: C 42 ARG cc_start: 0.8299 (mtp180) cc_final: 0.8018 (mtp180) REVERT: C 56 GLU cc_start: 0.8822 (tt0) cc_final: 0.8332 (tt0) REVERT: C 57 TYR cc_start: 0.9246 (t80) cc_final: 0.8715 (t80) REVERT: C 61 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8354 (mm-30) REVERT: C 64 GLU cc_start: 0.8454 (tt0) cc_final: 0.7933 (tm-30) REVERT: C 95 LYS cc_start: 0.9296 (tttt) cc_final: 0.8813 (tppt) REVERT: D 56 MET cc_start: 0.8513 (tpp) cc_final: 0.8124 (tpp) REVERT: E 112 ILE cc_start: 0.9523 (pt) cc_final: 0.9202 (mt) REVERT: E 120 MET cc_start: 0.8091 (mtp) cc_final: 0.7869 (mtp) REVERT: G 57 TYR cc_start: 0.9371 (t80) cc_final: 0.9005 (t80) REVERT: G 62 ILE cc_start: 0.9281 (mm) cc_final: 0.8978 (tp) REVERT: G 64 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7773 (tm-30) REVERT: G 68 ASN cc_start: 0.8484 (m-40) cc_final: 0.8012 (m-40) REVERT: H 56 MET cc_start: 0.9004 (tpp) cc_final: 0.8708 (tpp) REVERT: H 113 LYS cc_start: 0.9618 (ttpp) cc_final: 0.9244 (ptmm) REVERT: H 117 LYS cc_start: 0.9557 (mtpp) cc_final: 0.9286 (mttm) outliers start: 38 outliers final: 30 residues processed: 244 average time/residue: 0.1100 time to fit residues: 36.6814 Evaluate side-chains 246 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL 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 A residue 124 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 122 LYS 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 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 67 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN H 79 HIS H 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.070815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.050523 restraints weight = 41689.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.052115 restraints weight = 23741.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053208 restraints weight = 16722.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053892 restraints weight = 13484.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.054318 restraints weight = 11820.258| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 11159 Z= 0.217 Angle : 0.728 15.008 15796 Z= 0.405 Chirality : 0.039 0.198 1713 Planarity : 0.004 0.040 1395 Dihedral : 28.692 87.384 3177 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.84 % Allowed : 28.39 % 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: 2.11 (0.28), residues: 897 helix: 2.03 (0.20), residues: 637 sheet: None (None), residues: 0 loop : -0.12 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 32 TYR 0.060 0.003 TYR H 80 PHE 0.008 0.001 PHE A 104 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00495 (11159) covalent geometry : angle 0.72763 (15796) hydrogen bonds : bond 0.04456 ( 669) hydrogen bonds : angle 3.40616 ( 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 257 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8276 (mt-10) REVERT: A 64 LYS cc_start: 0.7248 (tppt) cc_final: 0.5870 (tptt) REVERT: A 76 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8715 (mt0) REVERT: A 81 ASP cc_start: 0.7833 (t0) cc_final: 0.7563 (t70) REVERT: A 90 MET cc_start: 0.8829 (mmt) cc_final: 0.8529 (mmm) REVERT: B 34 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8052 (tp) REVERT: B 98 TYR cc_start: 0.9000 (m-10) cc_final: 0.8689 (m-10) REVERT: C 56 GLU cc_start: 0.8789 (tt0) cc_final: 0.8304 (tt0) REVERT: C 57 TYR cc_start: 0.9258 (t80) cc_final: 0.8730 (t80) REVERT: C 61 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8391 (mm-30) REVERT: C 64 GLU cc_start: 0.8443 (tt0) cc_final: 0.7919 (tm-30) REVERT: C 95 LYS cc_start: 0.9288 (tttt) cc_final: 0.8797 (tppt) REVERT: D 30 ARG cc_start: 0.6419 (mmt180) cc_final: 0.5918 (mmp80) REVERT: D 56 MET cc_start: 0.8499 (tpp) cc_final: 0.8146 (tpp) REVERT: E 64 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7626 (ttpt) REVERT: G 62 ILE cc_start: 0.9248 (mm) cc_final: 0.8930 (tp) REVERT: G 64 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7781 (tm-30) REVERT: G 68 ASN cc_start: 0.8464 (m-40) cc_final: 0.8017 (m-40) REVERT: H 56 MET cc_start: 0.8984 (tpp) cc_final: 0.8721 (tpp) REVERT: H 92 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8720 (pt0) REVERT: H 110 GLU cc_start: 0.8435 (pt0) cc_final: 0.7941 (pt0) REVERT: H 113 LYS cc_start: 0.9601 (ttpp) cc_final: 0.9258 (ptmm) outliers start: 31 outliers final: 29 residues processed: 239 average time/residue: 0.1094 time to fit residues: 35.4282 Evaluate side-chains 251 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL 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 A residue 124 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 122 LYS 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 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 HIS H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.072032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.051727 restraints weight = 40984.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053358 restraints weight = 23118.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.054457 restraints weight = 16229.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055164 restraints weight = 13048.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.055584 restraints weight = 11430.777| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11159 Z= 0.176 Angle : 0.713 14.091 15796 Z= 0.398 Chirality : 0.038 0.169 1713 Planarity : 0.004 0.041 1395 Dihedral : 28.644 87.141 3177 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.06 % Allowed : 29.80 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.15 (0.28), residues: 897 helix: 2.03 (0.20), residues: 637 sheet: None (None), residues: 0 loop : -0.04 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 32 TYR 0.067 0.003 TYR H 80 PHE 0.008 0.001 PHE E 78 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00401 (11159) covalent geometry : angle 0.71284 (15796) hydrogen bonds : bond 0.04150 ( 669) hydrogen bonds : angle 3.33428 ( 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 263 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 0.309 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: 0.8798 (mt-10) cc_final: 0.8344 (mt-10) REVERT: A 64 LYS cc_start: 0.7184 (tppt) cc_final: 0.5718 (tptt) REVERT: A 76 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8711 (mt0) REVERT: A 81 ASP cc_start: 0.7749 (t0) cc_final: 0.7482 (t70) REVERT: A 90 MET cc_start: 0.8873 (mmt) cc_final: 0.8488 (mmm) REVERT: A 105 GLU cc_start: 0.8060 (tp30) cc_final: 0.7795 (mm-30) REVERT: B 98 TYR cc_start: 0.8977 (m-10) cc_final: 0.8682 (m-10) REVERT: C 42 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8002 (mtp-110) REVERT: C 56 GLU cc_start: 0.8741 (tt0) cc_final: 0.8192 (tt0) REVERT: C 57 TYR cc_start: 0.9242 (t80) cc_final: 0.8662 (t80) REVERT: C 61 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8334 (mm-30) REVERT: C 64 GLU cc_start: 0.8398 (tt0) cc_final: 0.7835 (tm-30) REVERT: C 92 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7945 (tt0) REVERT: C 95 LYS cc_start: 0.9265 (tttt) cc_final: 0.8761 (tppt) REVERT: D 43 LYS cc_start: 0.9404 (tppt) cc_final: 0.9125 (tppt) REVERT: D 56 MET cc_start: 0.8509 (tpp) cc_final: 0.8130 (tpp) REVERT: E 64 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7576 (ttpt) REVERT: E 73 GLU cc_start: 0.9067 (pt0) cc_final: 0.8690 (pt0) REVERT: E 89 VAL cc_start: 0.9643 (OUTLIER) cc_final: 0.9403 (p) REVERT: E 112 ILE cc_start: 0.9532 (pt) cc_final: 0.9250 (mt) REVERT: G 64 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7705 (tm-30) REVERT: G 68 ASN cc_start: 0.8471 (m-40) cc_final: 0.8081 (m-40) REVERT: H 56 MET cc_start: 0.8977 (tpp) cc_final: 0.8692 (tpp) REVERT: H 92 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8733 (pt0) REVERT: H 113 LYS cc_start: 0.9607 (ttpp) cc_final: 0.9243 (ptmm) outliers start: 26 outliers final: 22 residues processed: 246 average time/residue: 0.1016 time to fit residues: 34.3178 Evaluate side-chains 248 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 122 LYS 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 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 HIS H 92 GLN H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.071342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051095 restraints weight = 41478.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.052701 restraints weight = 23506.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.053798 restraints weight = 16533.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054475 restraints weight = 13306.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054930 restraints weight = 11663.409| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11159 Z= 0.208 Angle : 0.731 14.426 15796 Z= 0.408 Chirality : 0.039 0.174 1713 Planarity : 0.004 0.041 1395 Dihedral : 28.612 87.229 3177 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.90 % Allowed : 31.20 % Favored : 64.90 % 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: 2.09 (0.28), residues: 897 helix: 2.01 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.10 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 32 TYR 0.092 0.003 TYR H 80 PHE 0.009 0.001 PHE B 100 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00475 (11159) covalent geometry : angle 0.73088 (15796) hydrogen bonds : bond 0.04431 ( 669) hydrogen bonds : angle 3.41016 ( 1771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1691.51 seconds wall clock time: 29 minutes 48.54 seconds (1788.54 seconds total)