Starting phenix.real_space_refine on Sun Sep 13 06:05:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xaq_33097/09_2026/7xaq_33097.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xaq_33097/09_2026/7xaq_33097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xaq_33097/09_2026/7xaq_33097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xaq_33097/09_2026/7xaq_33097.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xaq_33097/09_2026/7xaq_33097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xaq_33097/09_2026/7xaq_33097.map" } resolution = 3.59 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= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9808 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 172 5.49 5 S 42 5.16 5 C 8005 2.51 5 N 2379 2.21 5 O 2798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13396 Number of models: 1 Model: "" Number of chains: 10 Chain: "F" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 880 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "J" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 883 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "E" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 880 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 883 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "B" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1658 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 194} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1626 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 192} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1667 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 194} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1626 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 192} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1667 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 194} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1626 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 192} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 2.78, per 1000 atoms: 0.21 Number of scatterers: 13396 At special positions: 0 Unit cell: (249.05, 156.4, 96.05, 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 42 16.00 P 172 15.00 O 2798 8.00 N 2379 7.00 C 8005 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: 1.08 Conformation dependent library (CDL) restraints added in 384.5 milliseconds 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2286 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 0 sheets defined 79.5% alpha, 0.0% beta 72 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'B' and resid 6 through 27 removed outlier: 3.579A pdb=" N LEU B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 42 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 57 through 77 removed outlier: 4.627A pdb=" N ARG B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 97 Processing helix chain 'B' and resid 100 through 113 Processing helix chain 'B' and resid 119 through 148 removed outlier: 4.899A pdb=" N GLU B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 173 removed outlier: 4.180A pdb=" N HIS B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.749A pdb=" N ASP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 198 removed outlier: 4.014A pdb=" N HIS B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 29 Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 59 through 76 removed outlier: 5.675A pdb=" N MET A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 99 through 114 removed outlier: 4.041A pdb=" N TYR A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 147 Processing helix chain 'A' and resid 155 through 175 removed outlier: 3.658A pdb=" N ALA A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 171 " --> pdb=" O HIS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 198 Processing helix chain 'G' and resid 5 through 29 removed outlier: 4.121A pdb=" N LYS G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 44 removed outlier: 3.795A pdb=" N GLY G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 52 removed outlier: 3.814A pdb=" N ILE G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 77 removed outlier: 3.520A pdb=" N ILE G 60 " --> pdb=" O SER G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 83 Processing helix chain 'G' and resid 84 through 98 removed outlier: 3.810A pdb=" N LEU G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 114 removed outlier: 3.593A pdb=" N GLU G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 148 Processing helix chain 'G' and resid 154 through 173 removed outlier: 4.309A pdb=" N HIS G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 183 Processing helix chain 'G' and resid 185 through 198 Processing helix chain 'C' and resid 8 through 29 Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.931A pdb=" N ILE C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 56 through 76 Processing helix chain 'C' and resid 85 through 98 Processing helix chain 'C' and resid 99 through 114 removed outlier: 3.864A pdb=" N GLU C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 148 removed outlier: 3.725A pdb=" N VAL C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY C 148 " --> pdb=" O ARG C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 173 removed outlier: 3.987A pdb=" N HIS C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.741A pdb=" N VAL C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 198 Processing helix chain 'H' and resid 5 through 29 Processing helix chain 'H' and resid 35 through 44 removed outlier: 3.568A pdb=" N ILE H 39 " --> pdb=" O THR H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 51 Processing helix chain 'H' and resid 56 through 76 removed outlier: 3.833A pdb=" N ILE H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 83 Processing helix chain 'H' and resid 84 through 97 removed outlier: 4.270A pdb=" N LEU H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 116 removed outlier: 3.646A pdb=" N THR H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 146 Processing helix chain 'H' and resid 154 through 175 removed outlier: 3.995A pdb=" N HIS H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 183 Processing helix chain 'H' and resid 185 through 198 removed outlier: 3.624A pdb=" N PHE H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 30 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 57 through 76 removed outlier: 3.822A pdb=" N TYR D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 Processing helix chain 'D' and resid 99 through 114 Processing helix chain 'D' and resid 119 through 147 removed outlier: 3.636A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 173 removed outlier: 4.100A pdb=" N HIS D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 185 through 198 676 hydrogen bonds defined for protein. 2013 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 182 hydrogen bonds 364 hydrogen bond angles 0 basepair planarities 72 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1929 1.32 - 1.44: 4660 1.44 - 1.57: 7033 1.57 - 1.69: 341 1.69 - 1.82: 78 Bond restraints: 14041 Sorted by residual: bond pdb=" N ASP B 99 " pdb=" CA ASP B 99 " ideal model delta sigma weight residual 1.460 1.417 0.044 7.10e-03 1.98e+04 3.79e+01 bond pdb=" CA ASP B 99 " pdb=" C ASP B 99 " ideal model delta sigma weight residual 1.534 1.477 0.057 9.50e-03 1.11e+04 3.59e+01 bond pdb=" O3' DA F 42 " pdb=" P DA F 43 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.20e-02 6.94e+03 2.53e+01 bond pdb=" C1' DT F 36 " pdb=" N1 DT F 36 " ideal model delta sigma weight residual 1.468 1.538 -0.070 1.40e-02 5.10e+03 2.47e+01 bond pdb=" C1' DT E 36 " pdb=" N1 DT E 36 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.46e+01 ... (remaining 14036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 19272 3.15 - 6.30: 351 6.30 - 9.45: 29 9.45 - 12.60: 5 12.60 - 15.75: 2 Bond angle restraints: 19659 Sorted by residual: angle pdb=" N THR A 49 " pdb=" CA THR A 49 " pdb=" C THR A 49 " ideal model delta sigma weight residual 111.82 100.25 11.57 1.16e+00 7.43e-01 9.95e+01 angle pdb=" N ASP B 71 " pdb=" CA ASP B 71 " pdb=" C ASP B 71 " ideal model delta sigma weight residual 112.38 102.44 9.94 1.22e+00 6.72e-01 6.63e+01 angle pdb=" N GLU A 183 " pdb=" CA GLU A 183 " pdb=" C GLU A 183 " ideal model delta sigma weight residual 113.41 103.49 9.92 1.22e+00 6.72e-01 6.61e+01 angle pdb=" N GLN B 101 " pdb=" CA GLN B 101 " pdb=" C GLN B 101 " ideal model delta sigma weight residual 110.80 95.05 15.75 2.13e+00 2.20e-01 5.47e+01 angle pdb=" N VAL A 34 " pdb=" CA VAL A 34 " pdb=" C VAL A 34 " ideal model delta sigma weight residual 110.21 101.91 8.30 1.13e+00 7.83e-01 5.39e+01 ... (remaining 19654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.29: 6964 31.29 - 62.57: 974 62.57 - 93.86: 45 93.86 - 125.14: 0 125.14 - 156.43: 2 Dihedral angle restraints: 7985 sinusoidal: 4460 harmonic: 3525 Sorted by residual: dihedral pdb=" CA TYR A 61 " pdb=" C TYR A 61 " pdb=" N LEU A 62 " pdb=" CA LEU A 62 " ideal model delta harmonic sigma weight residual 180.00 150.28 29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA TYR A 51 " pdb=" C TYR A 51 " pdb=" N LYS A 52 " pdb=" CA LYS A 52 " ideal model delta harmonic sigma weight residual 180.00 150.32 29.68 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLY D 48 " pdb=" C GLY D 48 " pdb=" N THR D 49 " pdb=" CA THR D 49 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 7982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1867 0.091 - 0.182: 220 0.182 - 0.272: 18 0.272 - 0.363: 6 0.363 - 0.454: 4 Chirality restraints: 2115 Sorted by residual: chirality pdb=" CA PRO G 5 " pdb=" N PRO G 5 " pdb=" C PRO G 5 " pdb=" CB PRO G 5 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" C3' DT J 2 " pdb=" C4' DT J 2 " pdb=" O3' DT J 2 " pdb=" C2' DT J 2 " both_signs ideal model delta sigma weight residual False -2.73 -2.31 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CA GLU A 183 " pdb=" N GLU A 183 " pdb=" C GLU A 183 " pdb=" CB GLU A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 2112 not shown) Planarity restraints: 1934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 98 " 0.021 2.00e-02 2.50e+03 4.41e-02 1.94e+01 pdb=" C ARG B 98 " -0.076 2.00e-02 2.50e+03 pdb=" O ARG B 98 " 0.030 2.00e-02 2.50e+03 pdb=" N ASP B 99 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS G 77 " -0.019 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C HIS G 77 " 0.069 2.00e-02 2.50e+03 pdb=" O HIS G 77 " -0.027 2.00e-02 2.50e+03 pdb=" N SER G 78 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 32 " 0.042 2.00e-02 2.50e+03 2.48e-02 1.54e+01 pdb=" N1 DT I 32 " -0.063 2.00e-02 2.50e+03 pdb=" C2 DT I 32 " -0.009 2.00e-02 2.50e+03 pdb=" O2 DT I 32 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT I 32 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DT I 32 " 0.009 2.00e-02 2.50e+03 pdb=" O4 DT I 32 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DT I 32 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 32 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DT I 32 " 0.005 2.00e-02 2.50e+03 ... (remaining 1931 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 58 2.42 - 3.04: 8276 3.04 - 3.66: 23566 3.66 - 4.28: 34081 4.28 - 4.90: 50703 Nonbonded interactions: 116684 Sorted by model distance: nonbonded pdb=" O HIS G 77 " pdb=" OE2 GLU G 79 " model vdw 1.800 3.040 nonbonded pdb=" C PRO B 100 " pdb=" N ARG B 102 " model vdw 1.932 3.350 nonbonded pdb=" O ILE D 45 " pdb=" OG1 THR D 49 " model vdw 1.980 3.040 nonbonded pdb=" O GLU B 17 " pdb=" OG1 THR B 21 " model vdw 2.004 3.040 nonbonded pdb=" O PHE D 134 " pdb=" OG1 THR D 138 " model vdw 2.045 3.040 ... (remaining 116679 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 7 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 204)) selection = (chain 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 77 or (resid 78 through 83 and (name N or name CA or name C \ or name O or name CB )) or resid 84 through 202 or (resid 203 through 204 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 7 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 204)) selection = (chain 'D' and (resid 7 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 204)) selection = (chain 'G' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 77 or (resid 78 through 83 and (name N or name CA or name C \ or name O or name CB )) or resid 84 through 202 or (resid 203 through 204 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 77 or (resid 78 through 83 and (name N or name CA or name C \ or name O or name CB )) or resid 84 through 202 or (resid 203 through 204 and ( \ name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.600 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5290 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 : 0.007 0.073 14041 Z= 0.561 Angle : 1.078 15.751 19659 Z= 0.766 Chirality : 0.062 0.454 2115 Planarity : 0.006 0.054 1934 Dihedral : 23.456 156.429 5699 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.81 % Favored : 87.93 % Rotamer: Outliers : 2.87 % Allowed : 4.35 % Favored : 92.78 % Cbeta Deviations : 0.09 % 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: -4.12 (0.21), residues: 1185 helix: -2.39 (0.14), residues: 866 sheet: None (None), residues: 0 loop : -3.15 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 102 TYR 0.025 0.003 TYR B 159 PHE 0.034 0.003 PHE A 26 TRP 0.010 0.002 TRP C 163 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.56 (14041) covalent geometry : angle 1.07833 / 0.77 (19659) hydrogen bonds : bond 0.12099 / 12.70 ( 858) hydrogen bonds : angle 6.50930 / 8.56 ( 2377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.289 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: B 20 ASP cc_start: 0.6144 (m-30) cc_final: 0.5900 (t0) REVERT: B 66 LEU cc_start: 0.8897 (mt) cc_final: 0.8354 (mt) REVERT: B 85 LYS cc_start: -0.1364 (OUTLIER) cc_final: -0.1692 (mmtt) REVERT: B 101 GLN cc_start: 0.4956 (OUTLIER) cc_final: 0.4635 (tm-30) REVERT: B 126 LEU cc_start: 0.5024 (mp) cc_final: 0.4569 (tt) REVERT: B 191 PHE cc_start: 0.5872 (t80) cc_final: 0.5494 (t80) REVERT: B 198 ARG cc_start: 0.6576 (mtm110) cc_final: 0.6069 (mmm-85) REVERT: A 97 MET cc_start: 0.7757 (mtm) cc_final: 0.7287 (ttp) REVERT: A 167 HIS cc_start: 0.5832 (t-90) cc_final: 0.5614 (t-90) REVERT: A 177 PHE cc_start: 0.5628 (OUTLIER) cc_final: 0.4935 (t80) REVERT: G 38 MET cc_start: 0.8025 (ttm) cc_final: 0.7621 (mtp) REVERT: G 127 HIS cc_start: 0.9041 (m-70) cc_final: 0.8749 (m-70) REVERT: G 128 LYS cc_start: 0.9262 (ptmt) cc_final: 0.9061 (ptpp) REVERT: G 199 MET cc_start: 0.1008 (ppp) cc_final: 0.0010 (ppp) REVERT: C 199 MET cc_start: 0.2544 (mtm) cc_final: 0.0258 (mmm) REVERT: H 65 MET cc_start: 0.8568 (mmp) cc_final: 0.8202 (mmp) REVERT: H 79 GLU cc_start: 0.0825 (OUTLIER) cc_final: -0.0880 (mm-30) REVERT: D 92 TYR cc_start: 0.8051 (t80) cc_final: 0.7806 (t80) REVERT: D 130 ARG cc_start: 0.8887 (tmm160) cc_final: 0.8651 (ttp80) outliers start: 29 outliers final: 9 residues processed: 191 average time/residue: 0.1413 time to fit residues: 36.1931 Evaluate side-chains 115 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 81 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 GLN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN H 139 GLN D 167 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.158681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.142939 restraints weight = 106373.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.143414 restraints weight = 66794.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.143560 restraints weight = 49216.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.143938 restraints weight = 41238.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.144115 restraints weight = 34766.685| |-----------------------------------------------------------------------------| r_work (final): 0.4790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5158 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 14041 Z= 0.316 Angle : 0.947 12.117 19659 Z= 0.529 Chirality : 0.052 0.363 2115 Planarity : 0.008 0.068 1934 Dihedral : 25.486 151.955 3268 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.70 % Favored : 90.13 % Rotamer: Outliers : 4.35 % Allowed : 12.36 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.89 (0.22), residues: 1185 helix: -1.49 (0.15), residues: 864 sheet: None (None), residues: 0 loop : -2.71 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 136 TYR 0.026 0.003 TYR A 51 PHE 0.031 0.003 PHE A 54 TRP 0.018 0.002 TRP A 178 HIS 0.019 0.002 HIS H 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.32 (14041) covalent geometry : angle 0.94689 / 0.53 (19659) hydrogen bonds : bond 0.08407 / 9.30 ( 858) hydrogen bonds : angle 5.97717 / 7.66 ( 2377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 118 time to evaluate : 0.395 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 13 ARG cc_start: 0.6808 (mmp-170) cc_final: 0.6451 (mmp80) REVERT: A 177 PHE cc_start: 0.4967 (OUTLIER) cc_final: 0.3069 (t80) REVERT: G 38 MET cc_start: 0.7765 (ttm) cc_final: 0.7318 (mtp) REVERT: H 68 TYR cc_start: 0.9610 (t80) cc_final: 0.9299 (t80) outliers start: 44 outliers final: 24 residues processed: 152 average time/residue: 0.1181 time to fit residues: 25.5956 Evaluate side-chains 119 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 123 optimal weight: 8.9990 chunk 78 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 50.0000 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 14 optimal weight: 40.0000 chunk 46 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 HIS H 152 ASN ** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.158289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.139656 restraints weight = 108357.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.140296 restraints weight = 64814.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.141372 restraints weight = 42391.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.143138 restraints weight = 32592.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.142939 restraints weight = 25346.346| |-----------------------------------------------------------------------------| r_work (final): 0.4789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 14041 Z= 0.265 Angle : 0.876 13.926 19659 Z= 0.485 Chirality : 0.050 0.349 2115 Planarity : 0.006 0.055 1934 Dihedral : 25.506 152.012 3250 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.55 % Favored : 89.37 % Rotamer: Outliers : 3.66 % Allowed : 17.21 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.49 (0.23), residues: 1185 helix: -1.20 (0.16), residues: 872 sheet: None (None), residues: 0 loop : -2.57 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 90 TYR 0.031 0.003 TYR A 51 PHE 0.029 0.003 PHE A 93 TRP 0.020 0.002 TRP A 178 HIS 0.017 0.002 HIS H 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.26 (14041) covalent geometry : angle 0.87582 / 0.48 (19659) hydrogen bonds : bond 0.07608 / 8.43 ( 858) hydrogen bonds : angle 5.79772 / 7.42 ( 2377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.432 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: G 38 MET cc_start: 0.7960 (ttm) cc_final: 0.7390 (mtp) REVERT: D 124 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8558 (mp0) outliers start: 37 outliers final: 22 residues processed: 132 average time/residue: 0.1173 time to fit residues: 22.6825 Evaluate side-chains 113 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 199 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 40.0000 chunk 97 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.160281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.142621 restraints weight = 107649.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.143342 restraints weight = 66541.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.144212 restraints weight = 43822.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.144712 restraints weight = 32301.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.146006 restraints weight = 26660.179| |-----------------------------------------------------------------------------| r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5250 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 14041 Z= 0.195 Angle : 0.788 14.782 19659 Z= 0.440 Chirality : 0.047 0.359 2115 Planarity : 0.005 0.064 1934 Dihedral : 25.400 151.152 3246 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.45 % Favored : 90.46 % Rotamer: Outliers : 4.15 % Allowed : 17.61 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.01 (0.23), residues: 1185 helix: -0.81 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -2.57 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 96 TYR 0.030 0.003 TYR A 51 PHE 0.031 0.002 PHE A 93 TRP 0.016 0.001 TRP A 178 HIS 0.019 0.001 HIS H 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.19 (14041) covalent geometry : angle 0.78791 / 0.44 (19659) hydrogen bonds : bond 0.06333 / 6.97 ( 858) hydrogen bonds : angle 5.48979 / 7.05 ( 2377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.398 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 191 PHE cc_start: 0.4468 (OUTLIER) cc_final: 0.3047 (t80) REVERT: G 38 MET cc_start: 0.7977 (ttm) cc_final: 0.7296 (mtp) REVERT: D 127 HIS cc_start: 0.9078 (OUTLIER) cc_final: 0.8779 (t-90) outliers start: 42 outliers final: 26 residues processed: 136 average time/residue: 0.1119 time to fit residues: 22.3711 Evaluate side-chains 121 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 92 TYR Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 199 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 96 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 25 optimal weight: 0.0970 chunk 91 optimal weight: 5.9990 chunk 7 optimal weight: 50.0000 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.159541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.141639 restraints weight = 106871.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.142565 restraints weight = 68875.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.143081 restraints weight = 45731.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.143319 restraints weight = 33788.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.143286 restraints weight = 29809.501| |-----------------------------------------------------------------------------| r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5397 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14041 Z= 0.209 Angle : 0.781 13.273 19659 Z= 0.440 Chirality : 0.047 0.357 2115 Planarity : 0.005 0.057 1934 Dihedral : 25.411 151.379 3246 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.62 % Favored : 90.30 % Rotamer: Outliers : 4.45 % Allowed : 19.19 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.67 (0.24), residues: 1185 helix: -0.57 (0.16), residues: 884 sheet: None (None), residues: 0 loop : -2.40 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 130 TYR 0.032 0.003 TYR A 51 PHE 0.021 0.002 PHE B 106 TRP 0.015 0.001 TRP A 178 HIS 0.007 0.001 HIS H 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.21 (14041) covalent geometry : angle 0.78059 / 0.44 (19659) hydrogen bonds : bond 0.06583 / 7.28 ( 858) hydrogen bonds : angle 5.43775 / 6.95 ( 2377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 98 time to evaluate : 0.431 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: B 101 GLN cc_start: 0.3538 (OUTLIER) cc_final: 0.2546 (tp-100) REVERT: A 182 LEU cc_start: 0.2518 (OUTLIER) cc_final: 0.2010 (mt) REVERT: A 191 PHE cc_start: 0.4675 (OUTLIER) cc_final: 0.3155 (t80) REVERT: G 38 MET cc_start: 0.7857 (ttm) cc_final: 0.7175 (mtp) REVERT: G 105 LEU cc_start: 0.5995 (OUTLIER) cc_final: 0.5647 (tp) REVERT: D 127 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8465 (t-90) outliers start: 45 outliers final: 31 residues processed: 134 average time/residue: 0.1143 time to fit residues: 22.7126 Evaluate side-chains 125 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 92 TYR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 199 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.9990 chunk 85 optimal weight: 0.1980 chunk 1 optimal weight: 50.0000 chunk 16 optimal weight: 0.1980 chunk 11 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 139 GLN ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.161581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.143484 restraints weight = 106226.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.143935 restraints weight = 65682.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.144739 restraints weight = 42563.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.146790 restraints weight = 31514.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.146999 restraints weight = 24024.189| |-----------------------------------------------------------------------------| r_work (final): 0.4835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5333 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14041 Z= 0.171 Angle : 0.748 11.218 19659 Z= 0.418 Chirality : 0.045 0.362 2115 Planarity : 0.005 0.053 1934 Dihedral : 25.385 150.398 3246 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.52 % Favored : 91.39 % Rotamer: Outliers : 3.26 % Allowed : 21.07 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.44 (0.24), residues: 1185 helix: -0.36 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -2.50 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 96 TYR 0.028 0.002 TYR A 51 PHE 0.017 0.002 PHE A 26 TRP 0.011 0.001 TRP A 178 HIS 0.005 0.001 HIS H 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 (14041) covalent geometry : angle 0.74773 / 0.42 (19659) hydrogen bonds : bond 0.05686 / 6.25 ( 858) hydrogen bonds : angle 5.23504 / 6.69 ( 2377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.432 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: B 101 GLN cc_start: 0.3412 (OUTLIER) cc_final: 0.2751 (tp40) REVERT: A 182 LEU cc_start: 0.2246 (OUTLIER) cc_final: 0.1729 (mt) REVERT: A 191 PHE cc_start: 0.4453 (t80) cc_final: 0.3065 (t80) REVERT: G 174 HIS cc_start: 0.0275 (OUTLIER) cc_final: -0.0766 (t70) REVERT: D 127 HIS cc_start: 0.9128 (OUTLIER) cc_final: 0.8885 (t-90) outliers start: 33 outliers final: 25 residues processed: 127 average time/residue: 0.1108 time to fit residues: 20.9474 Evaluate side-chains 121 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 92 TYR Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 111 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5076 r_free = 0.5076 target = 0.160795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.143482 restraints weight = 106446.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.144310 restraints weight = 68235.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.145974 restraints weight = 43236.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.145900 restraints weight = 30529.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.145837 restraints weight = 27897.835| |-----------------------------------------------------------------------------| r_work (final): 0.4808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5208 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14041 Z= 0.179 Angle : 0.747 11.551 19659 Z= 0.419 Chirality : 0.045 0.363 2115 Planarity : 0.005 0.061 1934 Dihedral : 25.379 150.295 3246 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.37 % Favored : 90.55 % Rotamer: Outliers : 3.56 % Allowed : 22.95 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.24), residues: 1185 helix: -0.28 (0.17), residues: 889 sheet: None (None), residues: 0 loop : -2.43 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 96 TYR 0.029 0.002 TYR A 51 PHE 0.030 0.002 PHE G 76 TRP 0.011 0.001 TRP A 178 HIS 0.005 0.001 HIS H 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.18 (14041) covalent geometry : angle 0.74694 / 0.42 (19659) hydrogen bonds : bond 0.05924 / 6.54 ( 858) hydrogen bonds : angle 5.18983 / 6.63 ( 2377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.447 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: B 97 MET cc_start: 0.6309 (tmm) cc_final: 0.6039 (tmm) REVERT: B 101 GLN cc_start: 0.3696 (OUTLIER) cc_final: 0.2828 (tp40) REVERT: A 182 LEU cc_start: 0.2237 (OUTLIER) cc_final: 0.1723 (mt) REVERT: A 191 PHE cc_start: 0.4666 (OUTLIER) cc_final: 0.3259 (t80) REVERT: G 38 MET cc_start: 0.7808 (ttm) cc_final: 0.7386 (ptp) REVERT: G 84 ASP cc_start: 0.9010 (p0) cc_final: 0.8545 (t0) REVERT: G 174 HIS cc_start: 0.0238 (OUTLIER) cc_final: -0.1029 (t70) REVERT: D 127 HIS cc_start: 0.8865 (OUTLIER) cc_final: 0.8544 (t-90) outliers start: 36 outliers final: 29 residues processed: 125 average time/residue: 0.1172 time to fit residues: 21.6547 Evaluate side-chains 127 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 92 TYR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 115 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 75 optimal weight: 0.2980 chunk 107 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.158833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.143053 restraints weight = 105512.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.143226 restraints weight = 67555.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.143965 restraints weight = 48562.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.143882 restraints weight = 34711.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.144025 restraints weight = 33954.617| |-----------------------------------------------------------------------------| r_work (final): 0.4765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5129 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 14041 Z= 0.234 Angle : 0.811 11.841 19659 Z= 0.451 Chirality : 0.047 0.358 2115 Planarity : 0.006 0.063 1934 Dihedral : 25.485 150.417 3246 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.62 % Favored : 90.30 % Rotamer: Outliers : 4.85 % Allowed : 21.96 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.44 (0.23), residues: 1185 helix: -0.37 (0.17), residues: 887 sheet: None (None), residues: 0 loop : -2.45 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 83 TYR 0.029 0.003 TYR A 51 PHE 0.020 0.002 PHE A 93 TRP 0.018 0.002 TRP A 178 HIS 0.009 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 (14041) covalent geometry : angle 0.81103 / 0.45 (19659) hydrogen bonds : bond 0.06653 / 7.33 ( 858) hydrogen bonds : angle 5.37437 / 6.85 ( 2377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 91 time to evaluate : 0.477 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: B 101 GLN cc_start: 0.3725 (OUTLIER) cc_final: 0.2705 (tp40) REVERT: A 182 LEU cc_start: 0.2501 (OUTLIER) cc_final: 0.2048 (mt) REVERT: A 191 PHE cc_start: 0.4838 (OUTLIER) cc_final: 0.3445 (t80) REVERT: G 84 ASP cc_start: 0.8845 (p0) cc_final: 0.8265 (t0) REVERT: G 174 HIS cc_start: 0.0407 (OUTLIER) cc_final: -0.1579 (t70) REVERT: C 97 MET cc_start: 0.7633 (mmt) cc_final: 0.7236 (mmt) REVERT: D 14 ARG cc_start: 0.2733 (OUTLIER) cc_final: 0.1298 (mtp85) REVERT: D 127 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8265 (t-90) outliers start: 49 outliers final: 32 residues processed: 131 average time/residue: 0.1125 time to fit residues: 22.3247 Evaluate side-chains 128 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 92 TYR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 15 optimal weight: 50.0000 chunk 129 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 50.0000 chunk 60 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5076 r_free = 0.5076 target = 0.160768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.146202 restraints weight = 106343.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.146026 restraints weight = 73957.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.146427 restraints weight = 52527.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.146622 restraints weight = 38900.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.146768 restraints weight = 32937.492| |-----------------------------------------------------------------------------| r_work (final): 0.4810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4949 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14041 Z= 0.171 Angle : 0.759 15.480 19659 Z= 0.420 Chirality : 0.046 0.363 2115 Planarity : 0.005 0.055 1934 Dihedral : 25.482 149.436 3246 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.44 % Favored : 91.48 % Rotamer: Outliers : 3.76 % Allowed : 23.44 % Favored : 72.80 % 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: -1.22 (0.23), residues: 1185 helix: -0.20 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -2.37 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 130 TYR 0.024 0.002 TYR A 51 PHE 0.024 0.002 PHE A 26 TRP 0.013 0.001 TRP A 178 HIS 0.004 0.001 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (14041) covalent geometry : angle 0.75859 / 0.42 (19659) hydrogen bonds : bond 0.05739 / 6.35 ( 858) hydrogen bonds : angle 5.22026 / 6.66 ( 2377) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.445 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: B 97 MET cc_start: 0.6408 (tmm) cc_final: 0.6086 (tmm) REVERT: A 182 LEU cc_start: 0.2714 (OUTLIER) cc_final: 0.2194 (mt) REVERT: A 191 PHE cc_start: 0.4687 (OUTLIER) cc_final: 0.3335 (t80) REVERT: G 84 ASP cc_start: 0.8835 (p0) cc_final: 0.8243 (t0) REVERT: G 174 HIS cc_start: 0.0394 (OUTLIER) cc_final: -0.1581 (t70) REVERT: C 97 MET cc_start: 0.7470 (mmt) cc_final: 0.7075 (mmt) REVERT: D 127 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.8156 (t-90) outliers start: 38 outliers final: 27 residues processed: 130 average time/residue: 0.1093 time to fit residues: 21.2680 Evaluate side-chains 127 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 92 TYR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 51 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 89 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 118 optimal weight: 0.0870 chunk 65 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 50.0000 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 GLN D 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.161843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.146809 restraints weight = 106090.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.146889 restraints weight = 67399.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.147494 restraints weight = 49590.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.147572 restraints weight = 34621.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.147653 restraints weight = 33743.482| |-----------------------------------------------------------------------------| r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4972 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14041 Z= 0.168 Angle : 0.777 18.502 19659 Z= 0.423 Chirality : 0.045 0.368 2115 Planarity : 0.006 0.160 1934 Dihedral : 25.444 148.613 3243 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer: Outliers : 3.07 % Allowed : 23.94 % Favored : 73.00 % 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: -1.05 (0.24), residues: 1185 helix: -0.06 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.39 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 13 TYR 0.025 0.002 TYR A 51 PHE 0.035 0.002 PHE G 157 TRP 0.012 0.001 TRP A 178 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (14041) covalent geometry : angle 0.77705 / 0.42 (19659) hydrogen bonds : bond 0.05543 / 6.15 ( 858) hydrogen bonds : angle 5.14986 / 6.62 ( 2377) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.445 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: B 97 MET cc_start: 0.6448 (tmm) cc_final: 0.6202 (tmm) REVERT: A 182 LEU cc_start: 0.2635 (OUTLIER) cc_final: 0.2115 (mt) REVERT: A 191 PHE cc_start: 0.4750 (OUTLIER) cc_final: 0.3292 (t80) REVERT: G 38 MET cc_start: 0.7779 (ptp) cc_final: 0.7519 (tmm) REVERT: G 69 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7736 (mt-10) REVERT: G 84 ASP cc_start: 0.8911 (p0) cc_final: 0.8312 (t0) REVERT: G 174 HIS cc_start: 0.0266 (OUTLIER) cc_final: -0.1079 (t70) REVERT: C 97 MET cc_start: 0.7488 (mmt) cc_final: 0.7110 (mmt) REVERT: D 127 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.8232 (t-90) outliers start: 31 outliers final: 26 residues processed: 121 average time/residue: 0.1221 time to fit residues: 21.6566 Evaluate side-chains 121 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 92 TYR Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 15 optimal weight: 50.0000 chunk 116 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN D 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5082 r_free = 0.5082 target = 0.161425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.145811 restraints weight = 105433.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.145872 restraints weight = 69416.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.146418 restraints weight = 50105.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.146682 restraints weight = 35248.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.146547 restraints weight = 32573.141| |-----------------------------------------------------------------------------| r_work (final): 0.4795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5118 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14041 Z= 0.177 Angle : 0.788 17.806 19659 Z= 0.428 Chirality : 0.046 0.368 2115 Planarity : 0.005 0.096 1934 Dihedral : 25.443 148.239 3243 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.86 % Favored : 91.05 % Rotamer: Outliers : 3.36 % Allowed : 24.23 % Favored : 72.40 % 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: -1.04 (0.24), residues: 1185 helix: -0.05 (0.17), residues: 883 sheet: None (None), residues: 0 loop : -2.39 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 14 TYR 0.024 0.002 TYR A 51 PHE 0.018 0.002 PHE A 26 TRP 0.013 0.001 TRP A 178 HIS 0.005 0.001 HIS B 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (14041) covalent geometry : angle 0.78811 / 0.43 (19659) hydrogen bonds : bond 0.05667 / 6.30 ( 858) hydrogen bonds : angle 5.14378 / 6.60 ( 2377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3776.40 seconds wall clock time: 65 minutes 38.05 seconds (3938.05 seconds total)