Starting phenix.real_space_refine on Sun Aug 24 16:35:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xaq_33097/08_2025/7xaq_33097.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xaq_33097/08_2025/7xaq_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_33097/08_2025/7xaq_33097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xaq_33097/08_2025/7xaq_33097.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xaq_33097/08_2025/7xaq_33097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xaq_33097/08_2025/7xaq_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-2.0-5787/lib/python3.9/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: 3.34, per 1000 atoms: 0.25 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: 1.55 Conformation dependent library (CDL) restraints added in 663.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.93 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: 2.30 Time building geometry restraints manager: 1.96 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 1.50e-02 4.44e+03 1.62e+01 bond pdb=" O3' DC I 3 " pdb=" P DG I 4 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.47e+01 bond pdb=" C ARG A 179 " pdb=" O ARG A 179 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.19e-02 7.06e+03 1.31e+01 ... (remaining 14036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 19297 3.15 - 6.30: 324 6.30 - 9.45: 30 9.45 - 12.60: 6 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: 1986 0.091 - 0.182: 104 0.182 - 0.272: 15 0.272 - 0.363: 8 0.363 - 0.454: 2 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=" 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 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 -2.66 -2.31 -0.35 2.00e-01 2.50e+01 3.13e+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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.830 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5253 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= 0.349 Angle : 1.015 15.751 19659 Z= 0.606 Chirality : 0.053 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 aren 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 covalent geometry : bond 0.00670 (14041) covalent geometry : angle 1.01501 (19659) hydrogen bonds : bond 0.12099 ( 858) hydrogen bonds : angle 6.50930 ( 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 : 0.529 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 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: 0.0259 (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: 8 residues processed: 191 average time/residue: 0.1687 time to fit residues: 42.9540 Evaluate side-chains 114 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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: 10.0000 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: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN G 167 HIS C 101 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 GLN D 139 GLN D 167 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.158831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.141619 restraints weight = 106363.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.142043 restraints weight = 65929.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.142773 restraints weight = 49346.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.143037 restraints weight = 38176.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.143409 restraints weight = 29647.138| |-----------------------------------------------------------------------------| r_work (final): 0.4786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5279 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 14041 Z= 0.294 Angle : 0.879 12.092 19659 Z= 0.483 Chirality : 0.046 0.234 2115 Planarity : 0.007 0.051 1934 Dihedral : 25.466 152.668 3264 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.54 % Favored : 90.30 % Rotamer: Outliers : 4.06 % Allowed : 11.97 % Favored : 83.98 % 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 aren not related in a simple way. whole: -2.65 (0.22), residues: 1185 helix: -1.30 (0.16), residues: 875 sheet: None (None), residues: 0 loop : -2.67 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 136 TYR 0.031 0.003 TYR A 51 PHE 0.031 0.003 PHE A 54 TRP 0.027 0.002 TRP A 178 HIS 0.014 0.002 HIS B 158 Details of bonding type rmsd covalent geometry : bond 0.00627 (14041) covalent geometry : angle 0.87888 (19659) hydrogen bonds : bond 0.07545 ( 858) hydrogen bonds : angle 5.79349 ( 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 163 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.465 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 122 MET cc_start: -0.3217 (tmm) cc_final: -0.3449 (tmm) REVERT: A 177 PHE cc_start: 0.4643 (OUTLIER) cc_final: 0.2681 (t80) REVERT: G 38 MET cc_start: 0.7841 (ttm) cc_final: 0.7336 (mtp) REVERT: G 199 MET cc_start: 0.1875 (ppp) cc_final: 0.1605 (ppp) REVERT: C 199 MET cc_start: -0.2107 (mtm) cc_final: -0.2471 (mmp) REVERT: H 68 TYR cc_start: 0.9724 (t80) cc_final: 0.9485 (t80) outliers start: 41 outliers final: 20 residues processed: 152 average time/residue: 0.1298 time to fit residues: 27.5255 Evaluate side-chains 111 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 GLU 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 123 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 chunk 30 optimal weight: 0.0050 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 50 optimal weight: 0.0370 chunk 88 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 overall best weight: 1.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.160406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.143606 restraints weight = 108390.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.143958 restraints weight = 65474.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.144984 restraints weight = 43125.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.145441 restraints weight = 31544.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.146319 restraints weight = 24975.304| |-----------------------------------------------------------------------------| r_work (final): 0.4836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5081 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14041 Z= 0.204 Angle : 0.765 10.939 19659 Z= 0.420 Chirality : 0.043 0.191 2115 Planarity : 0.005 0.046 1934 Dihedral : 25.333 152.193 3248 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.11 % Favored : 90.80 % Rotamer: Outliers : 2.97 % Allowed : 15.83 % Favored : 81.21 % 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 aren not related in a simple way. whole: -2.07 (0.23), residues: 1185 helix: -0.87 (0.16), residues: 889 sheet: None (None), residues: 0 loop : -2.53 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 96 TYR 0.029 0.002 TYR A 51 PHE 0.033 0.002 PHE A 93 TRP 0.018 0.001 TRP A 178 HIS 0.007 0.001 HIS G 127 Details of bonding type rmsd covalent geometry : bond 0.00434 (14041) covalent geometry : angle 0.76457 (19659) hydrogen bonds : bond 0.06169 ( 858) hydrogen bonds : angle 5.46264 ( 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 136 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 PHE cc_start: 0.3952 (t80) cc_final: 0.3671 (t80) REVERT: A 191 PHE cc_start: 0.4539 (t80) cc_final: 0.2955 (t80) REVERT: G 38 MET cc_start: 0.7990 (ttm) cc_final: 0.7400 (mtp) outliers start: 30 outliers final: 19 residues processed: 128 average time/residue: 0.1290 time to fit residues: 23.7868 Evaluate side-chains 111 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 27 LEU 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 C residue 68 TYR Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain D residue 35 THR 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 199 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5089 r_free = 0.5089 target = 0.161502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.144082 restraints weight = 106726.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.144061 restraints weight = 65033.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.144754 restraints weight = 42439.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.146027 restraints weight = 31334.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.146232 restraints weight = 24976.523| |-----------------------------------------------------------------------------| r_work (final): 0.4836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5201 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14041 Z= 0.179 Angle : 0.733 13.659 19659 Z= 0.401 Chirality : 0.041 0.182 2115 Planarity : 0.005 0.046 1934 Dihedral : 25.179 151.836 3246 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.03 % Favored : 90.89 % Rotamer: Outliers : 3.66 % Allowed : 16.91 % Favored : 79.43 % 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 aren not related in a simple way. whole: -1.50 (0.24), residues: 1185 helix: -0.47 (0.16), residues: 891 sheet: None (None), residues: 0 loop : -2.32 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 130 TYR 0.028 0.002 TYR A 51 PHE 0.028 0.002 PHE A 93 TRP 0.015 0.001 TRP A 178 HIS 0.006 0.001 HIS G 127 Details of bonding type rmsd covalent geometry : bond 0.00376 (14041) covalent geometry : angle 0.73284 (19659) hydrogen bonds : bond 0.05575 ( 858) hydrogen bonds : angle 5.18739 ( 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 138 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.2265 (OUTLIER) cc_final: 0.1794 (mt) REVERT: G 38 MET cc_start: 0.8000 (ttm) cc_final: 0.7402 (mtp) REVERT: G 105 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5417 (tp) REVERT: G 199 MET cc_start: 0.1949 (ppp) cc_final: 0.1606 (ppp) REVERT: C 199 MET cc_start: -0.2239 (mtm) cc_final: -0.2752 (mmp) REVERT: D 124 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8458 (mp0) REVERT: D 127 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.8611 (t-90) outliers start: 37 outliers final: 20 residues processed: 133 average time/residue: 0.1257 time to fit residues: 24.3639 Evaluate side-chains 110 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 27 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 68 TYR 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 G residue 21 THR Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain H residue 126 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 96 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 121 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 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 = 0.5079 r_free = 0.5079 target = 0.160840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.143021 restraints weight = 106568.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.143080 restraints weight = 66939.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.143674 restraints weight = 43338.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.144230 restraints weight = 32961.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.145593 restraints weight = 27602.725| |-----------------------------------------------------------------------------| r_work (final): 0.4809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5260 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14041 Z= 0.188 Angle : 0.732 10.644 19659 Z= 0.400 Chirality : 0.041 0.183 2115 Planarity : 0.005 0.046 1934 Dihedral : 25.177 151.679 3246 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.69 % Favored : 91.22 % Rotamer: Outliers : 3.66 % Allowed : 18.60 % Favored : 77.74 % 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 aren not related in a simple way. whole: -1.27 (0.24), residues: 1185 helix: -0.28 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -2.34 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 13 TYR 0.029 0.002 TYR A 51 PHE 0.022 0.002 PHE B 189 TRP 0.012 0.001 TRP A 178 HIS 0.021 0.001 HIS H 174 Details of bonding type rmsd covalent geometry : bond 0.00403 (14041) covalent geometry : angle 0.73169 (19659) hydrogen bonds : bond 0.05622 ( 858) hydrogen bonds : angle 5.12707 ( 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 138 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.554 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: 0.3424 (OUTLIER) cc_final: 0.2662 (tp-100) REVERT: A 191 PHE cc_start: 0.4650 (OUTLIER) cc_final: 0.3209 (t80) REVERT: G 38 MET cc_start: 0.8058 (ttm) cc_final: 0.7383 (mtp) REVERT: G 122 MET cc_start: 0.3464 (tpt) cc_final: 0.3213 (tpt) REVERT: G 174 HIS cc_start: 0.0087 (OUTLIER) cc_final: -0.1053 (t70) REVERT: G 199 MET cc_start: 0.1982 (ppp) cc_final: 0.1572 (ppp) REVERT: C 97 MET cc_start: 0.8144 (mmt) cc_final: 0.7870 (mmt) REVERT: C 199 MET cc_start: -0.2499 (mtm) cc_final: -0.2832 (mmp) REVERT: D 127 HIS cc_start: 0.9092 (OUTLIER) cc_final: 0.8785 (t-90) outliers start: 37 outliers final: 27 residues processed: 127 average time/residue: 0.1264 time to fit residues: 23.5420 Evaluate side-chains 122 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 88 LEU 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 179 ARG Chi-restraints excluded: chain A residue 19 LEU 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 123 VAL 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 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 21 THR 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 195 ILE 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: 1.9990 chunk 1 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 103 optimal weight: 0.0670 chunk 88 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.162405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.144811 restraints weight = 106619.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.145799 restraints weight = 62728.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.146552 restraints weight = 41241.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.148088 restraints weight = 30287.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.148360 restraints weight = 24259.400| |-----------------------------------------------------------------------------| r_work (final): 0.4853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5100 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14041 Z= 0.167 Angle : 0.703 11.141 19659 Z= 0.385 Chirality : 0.040 0.190 2115 Planarity : 0.005 0.044 1934 Dihedral : 25.141 150.465 3246 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.68 % Favored : 92.24 % Rotamer: Outliers : 3.56 % Allowed : 19.29 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.24), residues: 1185 helix: -0.01 (0.17), residues: 889 sheet: None (None), residues: 0 loop : -2.33 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 13 TYR 0.025 0.002 TYR A 51 PHE 0.024 0.002 PHE D 157 TRP 0.009 0.001 TRP A 178 HIS 0.019 0.001 HIS H 174 Details of bonding type rmsd covalent geometry : bond 0.00352 (14041) covalent geometry : angle 0.70322 (19659) hydrogen bonds : bond 0.05119 ( 858) hydrogen bonds : angle 4.94278 ( 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 139 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.2067 (OUTLIER) cc_final: 0.1534 (mt) REVERT: A 191 PHE cc_start: 0.4574 (OUTLIER) cc_final: 0.3103 (t80) REVERT: G 84 ASP cc_start: 0.9163 (p0) cc_final: 0.8735 (t0) REVERT: G 174 HIS cc_start: 0.0103 (OUTLIER) cc_final: -0.1030 (t70) REVERT: C 97 MET cc_start: 0.8227 (mmt) cc_final: 0.8008 (mmt) REVERT: D 124 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: D 127 HIS cc_start: 0.9127 (OUTLIER) cc_final: 0.8597 (m90) outliers start: 36 outliers final: 21 residues processed: 131 average time/residue: 0.1387 time to fit residues: 25.7606 Evaluate side-chains 119 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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 93 PHE 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 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 110 GLU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 195 ILE 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: 0.7980 chunk 57 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 82 optimal weight: 0.0000 chunk 76 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 78 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 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 = 0.5097 r_free = 0.5097 target = 0.162560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.145061 restraints weight = 107048.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.146371 restraints weight = 60633.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.146425 restraints weight = 44852.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.146627 restraints weight = 33265.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.146445 restraints weight = 35428.615| |-----------------------------------------------------------------------------| r_work (final): 0.4814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5213 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14041 Z= 0.164 Angle : 0.712 16.727 19659 Z= 0.384 Chirality : 0.039 0.181 2115 Planarity : 0.004 0.044 1934 Dihedral : 25.109 149.643 3246 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.85 % Favored : 92.07 % Rotamer: Outliers : 3.46 % Allowed : 20.47 % Favored : 76.06 % 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 aren not related in a simple way. whole: -0.71 (0.24), residues: 1185 helix: 0.17 (0.17), residues: 883 sheet: None (None), residues: 0 loop : -2.19 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 13 TYR 0.024 0.002 TYR A 51 PHE 0.024 0.002 PHE A 26 TRP 0.008 0.001 TRP A 178 HIS 0.019 0.001 HIS H 174 Details of bonding type rmsd covalent geometry : bond 0.00348 (14041) covalent geometry : angle 0.71232 (19659) hydrogen bonds : bond 0.05119 ( 858) hydrogen bonds : angle 4.86146 ( 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 136 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.498 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 101 GLN cc_start: 0.3680 (OUTLIER) cc_final: 0.2854 (tp40) REVERT: A 182 LEU cc_start: 0.2090 (OUTLIER) cc_final: 0.1539 (mt) REVERT: A 191 PHE cc_start: 0.4598 (OUTLIER) cc_final: 0.3099 (t80) REVERT: G 84 ASP cc_start: 0.9270 (p0) cc_final: 0.8969 (t0) REVERT: G 174 HIS cc_start: -0.0216 (OUTLIER) cc_final: -0.1405 (t70) REVERT: C 97 MET cc_start: 0.8153 (mmt) cc_final: 0.7837 (mmt) outliers start: 35 outliers final: 25 residues processed: 126 average time/residue: 0.1412 time to fit residues: 25.1183 Evaluate side-chains 120 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 95 PHE 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 27 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 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 21 THR Chi-restraints excluded: chain G residue 65 MET 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 21 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.0452 > 50: distance: 3 - 24: 12.908 distance: 19 - 24: 11.886 distance: 24 - 25: 32.706 distance: 25 - 26: 46.492 distance: 25 - 28: 8.060 distance: 26 - 27: 22.365 distance: 26 - 35: 18.425 distance: 28 - 29: 29.784 distance: 29 - 30: 3.879 distance: 29 - 31: 14.217 distance: 30 - 32: 26.717 distance: 31 - 33: 16.317 distance: 32 - 34: 5.647 distance: 35 - 36: 15.343 distance: 36 - 37: 15.192 distance: 36 - 39: 17.445 distance: 37 - 38: 17.989 distance: 37 - 45: 17.098 distance: 39 - 40: 11.189 distance: 40 - 41: 9.418 distance: 40 - 42: 19.285 distance: 41 - 43: 3.132 distance: 42 - 44: 19.127 distance: 43 - 44: 14.930 distance: 45 - 46: 44.808 distance: 46 - 47: 22.712 distance: 46 - 49: 29.986 distance: 47 - 48: 25.053 distance: 47 - 50: 12.307 distance: 50 - 51: 37.853 distance: 51 - 52: 35.044 distance: 51 - 54: 24.034 distance: 52 - 53: 5.628 distance: 52 - 55: 15.179 distance: 55 - 56: 28.060 distance: 56 - 57: 29.973 distance: 56 - 59: 41.618 distance: 57 - 58: 14.800 distance: 57 - 60: 35.013 distance: 60 - 61: 20.774 distance: 61 - 62: 21.951 distance: 61 - 64: 25.379 distance: 62 - 63: 20.683 distance: 62 - 65: 31.925 distance: 65 - 66: 18.624 distance: 66 - 67: 15.493 distance: 66 - 69: 34.367 distance: 67 - 68: 21.568 distance: 67 - 70: 16.898 distance: 70 - 71: 16.088 distance: 71 - 72: 31.107 distance: 71 - 74: 18.612 distance: 72 - 73: 24.543 distance: 72 - 75: 15.449 distance: 75 - 76: 35.883 distance: 76 - 77: 25.965 distance: 76 - 79: 20.710 distance: 77 - 78: 41.658 distance: 77 - 83: 10.688 distance: 79 - 80: 33.184 distance: 80 - 81: 14.740 distance: 80 - 82: 6.382 distance: 83 - 84: 5.147 distance: 84 - 85: 10.243 distance: 84 - 87: 29.835 distance: 85 - 86: 12.191 distance: 85 - 92: 27.857 distance: 87 - 88: 18.461 distance: 88 - 89: 17.398 distance: 89 - 90: 16.524 distance: 90 - 91: 11.002