Starting phenix.real_space_refine on Fri Jul 3 22:05:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qky_53223/07_2026/9qky_53223.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qky_53223/07_2026/9qky_53223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qky_53223/07_2026/9qky_53223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qky_53223/07_2026/9qky_53223.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qky_53223/07_2026/9qky_53223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qky_53223/07_2026/9qky_53223.map" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 248 5.49 5 S 64 5.16 5 C 9608 2.51 5 N 2948 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16276 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "B" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "C" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "E" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "F" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "G" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "H" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "I" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "J" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "K" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "L" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "M" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "N" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "O" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "P" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 774 SG CYS A 103 74.888 57.070 29.449 1.00 82.54 S ATOM 1203 SG CYS A 156 75.204 57.421 33.243 1.00 91.55 S ATOM 1242 SG CYS A 162 72.008 58.720 31.557 1.00 78.34 S ATOM 2172 SG CYS B 103 54.378 70.897 76.630 1.00 62.60 S ATOM 2601 SG CYS B 156 54.531 71.503 72.843 1.00 72.51 S ATOM 2640 SG CYS B 162 56.949 69.030 74.464 1.00 55.51 S ATOM 4841 SG CYS E 103 39.773 59.670 74.057 1.00 66.50 S ATOM 5270 SG CYS E 156 39.304 59.578 77.850 1.00 72.72 S ATOM 5309 SG CYS E 162 41.061 56.610 76.163 1.00 52.59 S ATOM 6239 SG CYS F 103 47.650 36.186 121.220 1.00 60.97 S ATOM 6668 SG CYS F 156 47.166 35.801 117.432 1.00 61.72 S ATOM 6707 SG CYS F 162 46.739 39.232 119.056 1.00 49.69 S ATOM 8908 SG CYS I 103 66.192 36.343 118.672 1.00 65.10 S ATOM 9337 SG CYS I 156 66.618 36.134 122.465 1.00 65.94 S ATOM 9376 SG CYS I 162 67.012 39.560 120.778 1.00 52.06 S ATOM 10306 SG CYS J 103 74.064 59.823 165.838 1.00 63.98 S ATOM 10735 SG CYS J 156 74.685 59.837 162.050 1.00 69.95 S ATOM 10774 SG CYS J 162 72.952 56.845 163.673 1.00 52.33 S ATOM 12975 SG CYS M 103 59.288 70.905 163.282 1.00 65.40 S ATOM 13404 SG CYS M 156 59.077 71.333 167.075 1.00 70.43 S ATOM 13443 SG CYS M 162 56.686 68.845 165.391 1.00 56.24 S ATOM 14373 SG CYS N 103 38.810 57.038 210.465 1.00 85.28 S ATOM 14802 SG CYS N 156 38.307 57.400 206.678 1.00 84.77 S ATOM 14841 SG CYS N 162 41.499 58.731 208.299 1.00 79.47 S Time building chain proxies: 3.16, per 1000 atoms: 0.19 Number of scatterers: 16276 At special positions: 0 Unit cell: (114.681, 112.014, 240.919, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 64 16.00 P 248 15.00 O 3400 8.00 N 2948 7.00 C 9608 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: 1.11 Conformation dependent library (CDL) restraints added in 380.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" ND1 HIS A 167 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 156 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 103 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 162 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 167 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 156 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 162 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 103 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 167 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 156 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 103 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 162 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 167 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 162 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 156 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 103 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 167 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 156 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 162 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 167 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 162 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 156 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 103 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" ND1 HIS M 167 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 156 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 103 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 162 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" ND1 HIS N 167 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 156 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 162 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 103 " Number of angles added : 24 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 57.1% alpha, 3.0% beta 116 base pairs and 220 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 14 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 26 through 45 removed outlier: 3.527A pdb=" N GLN A 34 " --> pdb=" O TRP A 30 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 62 removed outlier: 3.559A pdb=" N GLY A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 83 removed outlier: 3.657A pdb=" N LYS A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 97 removed outlier: 3.764A pdb=" N VAL A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 139 removed outlier: 3.565A pdb=" N GLY A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'B' and resid 14 through 20 Processing helix chain 'B' and resid 26 through 45 removed outlier: 4.186A pdb=" N ARG B 38 " --> pdb=" O GLN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 61 Processing helix chain 'B' and resid 64 through 83 removed outlier: 3.828A pdb=" N LYS B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 87 through 97 Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.676A pdb=" N ILE B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 173 through 180 removed outlier: 3.585A pdb=" N ALA B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 20 Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 26 through 45 removed outlier: 3.527A pdb=" N GLN E 34 " --> pdb=" O TRP E 30 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 62 removed outlier: 3.559A pdb=" N GLY E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 83 removed outlier: 3.657A pdb=" N LYS E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 97 removed outlier: 3.764A pdb=" N VAL E 92 " --> pdb=" O ARG E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 139 removed outlier: 3.565A pdb=" N GLY E 139 " --> pdb=" O ILE E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 166 No H-bonds generated for 'chain 'E' and resid 164 through 166' Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'F' and resid 14 through 20 Processing helix chain 'F' and resid 26 through 45 removed outlier: 4.186A pdb=" N ARG F 38 " --> pdb=" O GLN F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 61 Processing helix chain 'F' and resid 64 through 83 removed outlier: 3.828A pdb=" N LYS F 68 " --> pdb=" O LYS F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 87 through 97 Processing helix chain 'F' and resid 129 through 139 removed outlier: 3.676A pdb=" N ILE F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 166 No H-bonds generated for 'chain 'F' and resid 164 through 166' Processing helix chain 'F' and resid 173 through 180 removed outlier: 3.585A pdb=" N ALA F 180 " --> pdb=" O ASP F 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 20 Processing helix chain 'I' and resid 21 through 23 No H-bonds generated for 'chain 'I' and resid 21 through 23' Processing helix chain 'I' and resid 26 through 45 removed outlier: 3.527A pdb=" N GLN I 34 " --> pdb=" O TRP I 30 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA I 35 " --> pdb=" O PHE I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 62 removed outlier: 3.558A pdb=" N GLY I 62 " --> pdb=" O ASP I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 83 removed outlier: 3.657A pdb=" N LYS I 68 " --> pdb=" O LYS I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 97 removed outlier: 3.763A pdb=" N VAL I 92 " --> pdb=" O ARG I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 139 removed outlier: 3.565A pdb=" N GLY I 139 " --> pdb=" O ILE I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 166 No H-bonds generated for 'chain 'I' and resid 164 through 166' Processing helix chain 'I' and resid 173 through 180 Processing helix chain 'J' and resid 14 through 20 Processing helix chain 'J' and resid 26 through 45 removed outlier: 4.185A pdb=" N ARG J 38 " --> pdb=" O GLN J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 61 Processing helix chain 'J' and resid 64 through 83 removed outlier: 3.828A pdb=" N LYS J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 86 No H-bonds generated for 'chain 'J' and resid 84 through 86' Processing helix chain 'J' and resid 87 through 97 Processing helix chain 'J' and resid 129 through 139 removed outlier: 3.676A pdb=" N ILE J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 166 No H-bonds generated for 'chain 'J' and resid 164 through 166' Processing helix chain 'J' and resid 173 through 180 removed outlier: 3.586A pdb=" N ALA J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 20 Processing helix chain 'M' and resid 21 through 23 No H-bonds generated for 'chain 'M' and resid 21 through 23' Processing helix chain 'M' and resid 26 through 45 removed outlier: 3.527A pdb=" N GLN M 34 " --> pdb=" O TRP M 30 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA M 35 " --> pdb=" O PHE M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.559A pdb=" N GLY M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 83 removed outlier: 3.658A pdb=" N LYS M 68 " --> pdb=" O LYS M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 97 removed outlier: 3.764A pdb=" N VAL M 92 " --> pdb=" O ARG M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 139 removed outlier: 3.565A pdb=" N GLY M 139 " --> pdb=" O ILE M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 166 No H-bonds generated for 'chain 'M' and resid 164 through 166' Processing helix chain 'M' and resid 173 through 180 Processing helix chain 'N' and resid 14 through 20 Processing helix chain 'N' and resid 26 through 45 removed outlier: 4.185A pdb=" N ARG N 38 " --> pdb=" O GLN N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 61 Processing helix chain 'N' and resid 64 through 83 removed outlier: 3.829A pdb=" N LYS N 68 " --> pdb=" O LYS N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 86 No H-bonds generated for 'chain 'N' and resid 84 through 86' Processing helix chain 'N' and resid 87 through 97 Processing helix chain 'N' and resid 129 through 139 removed outlier: 3.676A pdb=" N ILE N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 166 No H-bonds generated for 'chain 'N' and resid 164 through 166' Processing helix chain 'N' and resid 173 through 180 removed outlier: 3.586A pdb=" N ALA N 180 " --> pdb=" O ASP N 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 Processing sheet with id=AA2, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AA3, first strand: chain 'B' and resid 150 through 152 Processing sheet with id=AA4, first strand: chain 'E' and resid 150 through 152 Processing sheet with id=AA5, first strand: chain 'F' and resid 116 through 117 Processing sheet with id=AA6, first strand: chain 'F' and resid 150 through 152 Processing sheet with id=AA7, first strand: chain 'I' and resid 150 through 152 Processing sheet with id=AA8, first strand: chain 'J' and resid 116 through 117 Processing sheet with id=AA9, first strand: chain 'J' and resid 150 through 152 Processing sheet with id=AB1, first strand: chain 'M' and resid 150 through 152 Processing sheet with id=AB2, first strand: chain 'N' and resid 116 through 117 Processing sheet with id=AB3, first strand: chain 'N' and resid 150 through 152 484 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 300 hydrogen bonds 600 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 220 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3932 1.34 - 1.45: 4292 1.45 - 1.57: 8336 1.57 - 1.69: 488 1.69 - 1.81: 88 Bond restraints: 17136 Sorted by residual: bond pdb=" C3' DA P -9 " pdb=" C2' DA P -9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT H -14 " pdb=" C2' DT H -14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA D -9 " pdb=" C2' DA D -9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA H -9 " pdb=" C2' DA H -9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT L -14 " pdb=" C2' DT L -14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.88e+00 ... (remaining 17131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 22228 1.18 - 2.35: 1465 2.35 - 3.53: 371 3.53 - 4.70: 56 4.70 - 5.88: 28 Bond angle restraints: 24148 Sorted by residual: angle pdb=" N3 DT D -14 " pdb=" C4 DT D -14 " pdb=" O4 DT D -14 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT C 8 " pdb=" C4 DT C 8 " pdb=" O4 DT C 8 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" O5' DG D -28 " pdb=" C5' DG D -28 " pdb=" C4' DG D -28 " ideal model delta sigma weight residual 109.40 112.82 -3.42 8.00e-01 1.56e+00 1.82e+01 angle pdb=" O5' DG P -28 " pdb=" C5' DG P -28 " pdb=" C4' DG P -28 " ideal model delta sigma weight residual 109.40 112.81 -3.41 8.00e-01 1.56e+00 1.82e+01 angle pdb=" O5' DG H -28 " pdb=" C5' DG H -28 " pdb=" C4' DG H -28 " ideal model delta sigma weight residual 109.40 112.81 -3.41 8.00e-01 1.56e+00 1.82e+01 ... (remaining 24143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 6953 17.43 - 34.85: 1499 34.85 - 52.28: 1072 52.28 - 69.70: 276 69.70 - 87.13: 8 Dihedral angle restraints: 9808 sinusoidal: 5832 harmonic: 3976 Sorted by residual: dihedral pdb=" CG LYS A 152 " pdb=" CD LYS A 152 " pdb=" CE LYS A 152 " pdb=" NZ LYS A 152 " ideal model delta sinusoidal sigma weight residual -60.00 -116.51 56.51 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CG LYS E 152 " pdb=" CD LYS E 152 " pdb=" CE LYS E 152 " pdb=" NZ LYS E 152 " ideal model delta sinusoidal sigma weight residual -60.00 -116.51 56.51 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CG LYS M 152 " pdb=" CD LYS M 152 " pdb=" CE LYS M 152 " pdb=" NZ LYS M 152 " ideal model delta sinusoidal sigma weight residual -60.00 -116.50 56.50 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2425 0.087 - 0.174: 211 0.174 - 0.261: 0 0.261 - 0.348: 0 0.348 - 0.434: 4 Chirality restraints: 2640 Sorted by residual: chirality pdb=" P DT L -29 " pdb=" OP1 DT L -29 " pdb=" OP2 DT L -29 " pdb=" O5' DT L -29 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" P DT H -29 " pdb=" OP1 DT H -29 " pdb=" OP2 DT H -29 " pdb=" O5' DT H -29 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" P DT P -29 " pdb=" OP1 DT P -29 " pdb=" OP2 DT P -29 " pdb=" O5' DT P -29 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.43 2.00e-01 2.50e+01 4.66e+00 ... (remaining 2637 not shown) Planarity restraints: 2192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT H -14 " 0.024 2.00e-02 2.50e+03 1.61e-02 6.51e+00 pdb=" N1 DT H -14 " -0.041 2.00e-02 2.50e+03 pdb=" C2 DT H -14 " 0.016 2.00e-02 2.50e+03 pdb=" O2 DT H -14 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT H -14 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT H -14 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT H -14 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT H -14 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT H -14 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT H -14 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT P -14 " 0.024 2.00e-02 2.50e+03 1.61e-02 6.49e+00 pdb=" N1 DT P -14 " -0.041 2.00e-02 2.50e+03 pdb=" C2 DT P -14 " 0.016 2.00e-02 2.50e+03 pdb=" O2 DT P -14 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT P -14 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT P -14 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT P -14 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT P -14 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT P -14 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT P -14 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT L -14 " 0.024 2.00e-02 2.50e+03 1.61e-02 6.48e+00 pdb=" N1 DT L -14 " -0.040 2.00e-02 2.50e+03 pdb=" C2 DT L -14 " 0.016 2.00e-02 2.50e+03 pdb=" O2 DT L -14 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT L -14 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT L -14 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT L -14 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT L -14 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT L -14 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT L -14 " 0.000 2.00e-02 2.50e+03 ... (remaining 2189 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2567 2.77 - 3.30: 13570 3.30 - 3.84: 28356 3.84 - 4.37: 31374 4.37 - 4.90: 48803 Nonbonded interactions: 124670 Sorted by model distance: nonbonded pdb=" N3 DT D -31 " pdb=" O6 DG K 1 " model vdw 2.239 3.120 nonbonded pdb=" N3 DT H -31 " pdb=" O6 DG O 1 " model vdw 2.309 3.120 nonbonded pdb=" O4' DT D -31 " pdb=" N4 DC L -1 " model vdw 2.427 3.120 nonbonded pdb=" N SER I 49 " pdb=" OE1 GLU I 52 " model vdw 2.448 3.120 nonbonded pdb=" N SER E 49 " pdb=" OE1 GLU E 52 " model vdw 2.448 3.120 ... (remaining 124665 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } 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: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 18.000 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.005 0.038 17168 Z= 0.420 Angle : 0.688 5.877 24172 Z= 0.541 Chirality : 0.048 0.434 2640 Planarity : 0.004 0.044 2192 Dihedral : 24.337 87.125 7216 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.65 % Allowed : 29.22 % Favored : 70.13 % 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: 1.30 (0.25), residues: 1336 helix: 1.94 (0.21), residues: 672 sheet: 0.02 (0.62), residues: 80 loop : -0.25 (0.30), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 121 TYR 0.011 0.001 TYR I 181 PHE 0.008 0.001 PHE N 15 TRP 0.003 0.000 TRP A 71 HIS 0.006 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.42 (17136) covalent geometry : angle 0.68611 / 0.54 (24148) hydrogen bonds : bond 0.10895 / 6.68 ( 784) hydrogen bonds : angle 5.37522 / 3.66 ( 2040) metal coordination : bond 0.00653 / 0.41 ( 32) metal coordination : angle 1.63855 / 0.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 240 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8034 (t70) cc_final: 0.7833 (t70) REVERT: F 59 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7731 (tm-30) REVERT: J 17 GLU cc_start: 0.8306 (tp30) cc_final: 0.7855 (tp30) REVERT: J 48 MET cc_start: 0.7287 (mmt) cc_final: 0.7066 (tpp) REVERT: J 69 GLN cc_start: 0.8254 (tm-30) cc_final: 0.8013 (mm-40) REVERT: N 47 ARG cc_start: 0.7628 (mmm160) cc_final: 0.7211 (mmm-85) outliers start: 8 outliers final: 0 residues processed: 244 average time/residue: 0.1460 time to fit residues: 51.5570 Evaluate side-chains 132 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 40.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 HIS A 158 ASN E 164 GLN ** I 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.117881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.078495 restraints weight = 34957.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.080839 restraints weight = 24167.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.081488 restraints weight = 16256.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081943 restraints weight = 15203.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082172 restraints weight = 14288.469| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17168 Z= 0.229 Angle : 0.619 6.313 24172 Z= 0.346 Chirality : 0.044 0.158 2640 Planarity : 0.005 0.054 2192 Dihedral : 26.532 65.698 4160 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.60 % Allowed : 26.22 % Favored : 71.19 % 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: 1.01 (0.25), residues: 1336 helix: 1.77 (0.21), residues: 680 sheet: 0.02 (0.62), residues: 80 loop : -0.56 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 74 TYR 0.015 0.002 TYR I 40 PHE 0.014 0.002 PHE I 91 TRP 0.010 0.002 TRP B 30 HIS 0.006 0.001 HIS J 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (17136) covalent geometry : angle 0.61829 / 0.35 (24148) hydrogen bonds : bond 0.05058 / 3.26 ( 784) hydrogen bonds : angle 4.27257 / 2.93 ( 2040) metal coordination : bond 0.00684 / 0.36 ( 32) metal coordination : angle 1.34340 / 0.86 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: E 89 GLU cc_start: 0.8031 (pm20) cc_final: 0.7810 (pm20) REVERT: F 32 ASN cc_start: 0.8972 (m-40) cc_final: 0.8570 (m-40) REVERT: I 40 TYR cc_start: 0.8748 (t80) cc_final: 0.8536 (t80) REVERT: N 51 ASP cc_start: 0.8098 (p0) cc_final: 0.7874 (p0) outliers start: 32 outliers final: 24 residues processed: 175 average time/residue: 0.1023 time to fit residues: 27.9984 Evaluate side-chains 152 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 135 ILE Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 177 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 43 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 37 optimal weight: 30.0000 chunk 50 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 119 optimal weight: 0.0070 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN E 164 GLN ** I 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN M 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.118712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.079865 restraints weight = 34551.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.081741 restraints weight = 26463.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.082207 restraints weight = 18160.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.082742 restraints weight = 17183.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.082973 restraints weight = 15848.437| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17168 Z= 0.124 Angle : 0.497 5.390 24172 Z= 0.296 Chirality : 0.038 0.141 2640 Planarity : 0.004 0.059 2192 Dihedral : 26.538 65.592 4160 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.17 % Allowed : 25.73 % Favored : 71.10 % 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: 1.26 (0.25), residues: 1336 helix: 2.05 (0.21), residues: 680 sheet: 0.11 (0.62), residues: 80 loop : -0.52 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 47 TYR 0.011 0.001 TYR A 40 PHE 0.010 0.001 PHE J 15 TRP 0.007 0.001 TRP B 30 HIS 0.004 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (17136) covalent geometry : angle 0.49547 / 0.30 (24148) hydrogen bonds : bond 0.03786 / 2.42 ( 784) hydrogen bonds : angle 4.04673 / 2.77 ( 2040) metal coordination : bond 0.00669 / 0.31 ( 32) metal coordination : angle 1.44050 / 0.87 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7669 (mtm110) REVERT: E 164 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: F 32 ASN cc_start: 0.8967 (m-40) cc_final: 0.8585 (m-40) REVERT: I 40 TYR cc_start: 0.8727 (t80) cc_final: 0.8519 (t80) REVERT: I 133 MET cc_start: 0.8562 (tpp) cc_final: 0.8026 (tpp) REVERT: N 51 ASP cc_start: 0.8163 (p0) cc_final: 0.7927 (p0) outliers start: 39 outliers final: 32 residues processed: 170 average time/residue: 0.1064 time to fit residues: 28.5772 Evaluate side-chains 166 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 164 GLN Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 177 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 116 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 32 optimal weight: 50.0000 chunk 120 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 164 GLN I 44 HIS I 122 GLN M 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.115834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076499 restraints weight = 34495.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.078285 restraints weight = 24325.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.079241 restraints weight = 17659.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.079531 restraints weight = 16298.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079783 restraints weight = 15393.875| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17168 Z= 0.182 Angle : 0.559 7.205 24172 Z= 0.318 Chirality : 0.040 0.160 2640 Planarity : 0.004 0.058 2192 Dihedral : 26.727 65.575 4160 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.06 % Allowed : 25.73 % Favored : 70.21 % 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 are not related in a simple way. whole: 1.04 (0.25), residues: 1336 helix: 1.89 (0.21), residues: 680 sheet: -0.01 (0.61), residues: 80 loop : -0.68 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 88 TYR 0.010 0.001 TYR A 40 PHE 0.011 0.001 PHE J 15 TRP 0.008 0.001 TRP B 30 HIS 0.004 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (17136) covalent geometry : angle 0.55597 / 0.32 (24148) hydrogen bonds : bond 0.04428 / 2.84 ( 784) hydrogen bonds : angle 4.04734 / 2.79 ( 2040) metal coordination : bond 0.00827 / 0.56 ( 32) metal coordination : angle 1.97270 / 1.24 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7545 (mtm-85) REVERT: F 32 ASN cc_start: 0.8997 (m-40) cc_final: 0.8593 (m-40) REVERT: I 40 TYR cc_start: 0.8794 (t80) cc_final: 0.8443 (t80) REVERT: I 76 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8932 (mm) REVERT: I 133 MET cc_start: 0.8693 (tpp) cc_final: 0.8359 (tpp) REVERT: N 51 ASP cc_start: 0.8154 (p0) cc_final: 0.7898 (p0) outliers start: 50 outliers final: 40 residues processed: 171 average time/residue: 0.1164 time to fit residues: 31.2812 Evaluate side-chains 170 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 26 PHE Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 119 CYS Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain N residue 179 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 112 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 0.0040 chunk 136 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 44 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 = 0.3771 r_free = 0.3771 target = 0.117712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.078561 restraints weight = 34537.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.080563 restraints weight = 24569.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081157 restraints weight = 17220.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.081506 restraints weight = 16442.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.081693 restraints weight = 15331.072| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17168 Z= 0.116 Angle : 0.488 5.515 24172 Z= 0.288 Chirality : 0.038 0.147 2640 Planarity : 0.004 0.058 2192 Dihedral : 26.710 64.860 4160 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.08 % Allowed : 26.46 % Favored : 70.45 % 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: 1.21 (0.25), residues: 1336 helix: 2.06 (0.21), residues: 680 sheet: 0.10 (0.63), residues: 80 loop : -0.63 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 54 TYR 0.010 0.001 TYR M 40 PHE 0.010 0.001 PHE F 15 TRP 0.006 0.001 TRP B 30 HIS 0.004 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.12 (17136) covalent geometry : angle 0.48538 / 0.29 (24148) hydrogen bonds : bond 0.03476 / 2.22 ( 784) hydrogen bonds : angle 3.87833 / 2.66 ( 2040) metal coordination : bond 0.00657 / 0.45 ( 32) metal coordination : angle 1.53860 / 0.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7632 (mtm-85) REVERT: F 76 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8930 (mm) REVERT: I 40 TYR cc_start: 0.8771 (t80) cc_final: 0.8396 (t80) REVERT: I 133 MET cc_start: 0.8529 (tpp) cc_final: 0.8246 (tpp) REVERT: J 133 MET cc_start: 0.7996 (tpp) cc_final: 0.7595 (tpp) REVERT: M 114 ILE cc_start: 0.8747 (tp) cc_final: 0.8514 (tt) REVERT: N 51 ASP cc_start: 0.8131 (p0) cc_final: 0.7862 (p0) REVERT: N 64 LYS cc_start: 0.8370 (tptp) cc_final: 0.8131 (tptp) outliers start: 38 outliers final: 33 residues processed: 171 average time/residue: 0.1144 time to fit residues: 30.9388 Evaluate side-chains 166 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 111 LYS Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 177 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 141 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN B 158 ASN F 158 ASN I 164 GLN J 158 ASN ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.115111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.075615 restraints weight = 34632.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.077546 restraints weight = 24468.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.078246 restraints weight = 17294.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.078642 restraints weight = 15922.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.078776 restraints weight = 15190.433| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17168 Z= 0.167 Angle : 0.543 5.440 24172 Z= 0.309 Chirality : 0.040 0.161 2640 Planarity : 0.004 0.055 2192 Dihedral : 26.867 64.779 4160 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.73 % Allowed : 26.79 % Favored : 69.48 % 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: 1.10 (0.25), residues: 1336 helix: 2.02 (0.21), residues: 680 sheet: 0.05 (0.63), residues: 80 loop : -0.76 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 88 TYR 0.014 0.001 TYR M 40 PHE 0.011 0.001 PHE F 15 TRP 0.008 0.001 TRP B 30 HIS 0.006 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (17136) covalent geometry : angle 0.54110 / 0.31 (24148) hydrogen bonds : bond 0.04287 / 2.74 ( 784) hydrogen bonds : angle 3.96473 / 2.73 ( 2040) metal coordination : bond 0.00642 / 0.41 ( 32) metal coordination : angle 1.61075 / 0.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: B 54 ARG cc_start: 0.8017 (mtm-85) cc_final: 0.7810 (mtm110) REVERT: F 76 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8948 (mm) REVERT: I 40 TYR cc_start: 0.8786 (t80) cc_final: 0.8365 (t80) REVERT: I 76 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8912 (mm) REVERT: M 40 TYR cc_start: 0.8765 (t80) cc_final: 0.8464 (t80) REVERT: M 114 ILE cc_start: 0.8830 (tp) cc_final: 0.8612 (tt) REVERT: N 51 ASP cc_start: 0.8148 (p0) cc_final: 0.7875 (p0) REVERT: N 172 ILE cc_start: 0.9208 (mp) cc_final: 0.9008 (mt) outliers start: 46 outliers final: 42 residues processed: 167 average time/residue: 0.1045 time to fit residues: 27.4359 Evaluate side-chains 171 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 26 PHE Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain N residue 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 9.9990 chunk 70 optimal weight: 30.0000 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 34 optimal weight: 20.0000 chunk 43 optimal weight: 0.0570 chunk 133 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN A 164 GLN ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.117051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.077873 restraints weight = 34322.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.079781 restraints weight = 24155.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.080645 restraints weight = 17385.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.080733 restraints weight = 16242.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.080920 restraints weight = 15338.339| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17168 Z= 0.113 Angle : 0.483 5.639 24172 Z= 0.286 Chirality : 0.038 0.147 2640 Planarity : 0.004 0.056 2192 Dihedral : 26.820 64.038 4160 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.25 % Allowed : 27.52 % Favored : 69.24 % 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: 1.26 (0.25), residues: 1336 helix: 2.16 (0.21), residues: 680 sheet: 0.12 (0.63), residues: 80 loop : -0.71 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 54 TYR 0.010 0.001 TYR M 40 PHE 0.010 0.001 PHE F 15 TRP 0.006 0.001 TRP B 30 HIS 0.005 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (17136) covalent geometry : angle 0.48147 / 0.29 (24148) hydrogen bonds : bond 0.03388 / 2.16 ( 784) hydrogen bonds : angle 3.82153 / 2.62 ( 2040) metal coordination : bond 0.00625 / 0.44 ( 32) metal coordination : angle 1.44679 / 0.90 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: F 76 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8930 (mm) REVERT: I 40 TYR cc_start: 0.8749 (t80) cc_final: 0.8541 (t80) REVERT: I 76 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8921 (mm) REVERT: J 133 MET cc_start: 0.7980 (tpp) cc_final: 0.7599 (tpp) REVERT: M 114 ILE cc_start: 0.8823 (tp) cc_final: 0.8611 (tt) REVERT: M 176 ASP cc_start: 0.8300 (m-30) cc_final: 0.8019 (m-30) REVERT: N 51 ASP cc_start: 0.8148 (p0) cc_final: 0.7892 (p0) REVERT: N 130 ASP cc_start: 0.8164 (m-30) cc_final: 0.7866 (m-30) REVERT: N 179 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8774 (tp) outliers start: 40 outliers final: 32 residues processed: 173 average time/residue: 0.0962 time to fit residues: 26.4092 Evaluate side-chains 168 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain N residue 179 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.4980 chunk 128 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 40.0000 chunk 131 optimal weight: 0.5980 chunk 139 optimal weight: 7.9990 chunk 111 optimal weight: 30.0000 chunk 16 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.114164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.074518 restraints weight = 34383.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.076425 restraints weight = 24458.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.077102 restraints weight = 17310.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.077589 restraints weight = 15918.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.077746 restraints weight = 15060.755| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17168 Z= 0.180 Angle : 0.565 5.295 24172 Z= 0.318 Chirality : 0.041 0.163 2640 Planarity : 0.004 0.057 2192 Dihedral : 26.956 64.479 4160 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.73 % Allowed : 27.60 % Favored : 68.67 % 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: 1.09 (0.25), residues: 1336 helix: 2.05 (0.21), residues: 680 sheet: 0.10 (0.63), residues: 80 loop : -0.84 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG B 54 TYR 0.014 0.002 TYR M 40 PHE 0.012 0.001 PHE F 15 TRP 0.007 0.001 TRP B 30 HIS 0.006 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (17136) covalent geometry : angle 0.56233 / 0.32 (24148) hydrogen bonds : bond 0.04475 / 2.87 ( 784) hydrogen bonds : angle 3.97304 / 2.74 ( 2040) metal coordination : bond 0.00655 / 0.41 ( 32) metal coordination : angle 1.69140 / 1.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: B 16 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8345 (mt) REVERT: F 76 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8960 (mm) REVERT: I 40 TYR cc_start: 0.8794 (t80) cc_final: 0.8472 (t80) REVERT: I 76 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8906 (mm) REVERT: I 109 ASP cc_start: 0.7810 (p0) cc_final: 0.7432 (p0) REVERT: M 40 TYR cc_start: 0.8761 (t80) cc_final: 0.8431 (t80) REVERT: M 114 ILE cc_start: 0.8829 (tp) cc_final: 0.8614 (tt) REVERT: N 51 ASP cc_start: 0.8134 (p0) cc_final: 0.7862 (p0) REVERT: N 172 ILE cc_start: 0.9218 (mp) cc_final: 0.9012 (mt) outliers start: 46 outliers final: 39 residues processed: 169 average time/residue: 0.1078 time to fit residues: 28.5157 Evaluate side-chains 172 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 111 LYS Chi-restraints excluded: chain M residue 119 CYS Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain N residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 0.0570 chunk 126 optimal weight: 0.0170 chunk 88 optimal weight: 0.0030 chunk 64 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.3546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN F 44 HIS ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.117123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.077439 restraints weight = 34563.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.079940 restraints weight = 20741.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.080856 restraints weight = 15075.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.080940 restraints weight = 12909.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.081120 restraints weight = 13196.879| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 17168 Z= 0.116 Angle : 0.503 8.591 24172 Z= 0.295 Chirality : 0.038 0.146 2640 Planarity : 0.004 0.043 2192 Dihedral : 26.869 63.766 4160 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.84 % Allowed : 28.33 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1336 helix: 2.21 (0.20), residues: 680 sheet: 0.16 (0.63), residues: 80 loop : -0.74 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 54 TYR 0.012 0.001 TYR M 40 PHE 0.011 0.001 PHE F 15 TRP 0.007 0.001 TRP A 71 HIS 0.008 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.12 (17136) covalent geometry : angle 0.50117 / 0.29 (24148) hydrogen bonds : bond 0.03377 / 2.16 ( 784) hydrogen bonds : angle 3.81726 / 2.62 ( 2040) metal coordination : bond 0.00615 / 0.41 ( 32) metal coordination : angle 1.30675 / 0.82 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.8683 (mmt) cc_final: 0.8217 (mmm) REVERT: F 32 ASN cc_start: 0.8891 (m-40) cc_final: 0.8506 (m-40) REVERT: F 76 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8870 (mm) REVERT: I 40 TYR cc_start: 0.8709 (t80) cc_final: 0.8458 (t80) REVERT: I 109 ASP cc_start: 0.7671 (p0) cc_final: 0.7224 (p0) REVERT: J 133 MET cc_start: 0.8193 (tpp) cc_final: 0.7768 (tpp) REVERT: M 114 ILE cc_start: 0.8834 (tp) cc_final: 0.8633 (tt) REVERT: M 176 ASP cc_start: 0.8338 (m-30) cc_final: 0.8093 (m-30) REVERT: N 51 ASP cc_start: 0.8180 (p0) cc_final: 0.7914 (p0) REVERT: N 64 LYS cc_start: 0.8552 (tptp) cc_final: 0.8282 (tptp) REVERT: N 130 ASP cc_start: 0.8137 (m-30) cc_final: 0.7853 (m-30) REVERT: N 179 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8758 (tp) outliers start: 35 outliers final: 31 residues processed: 163 average time/residue: 0.1072 time to fit residues: 27.9117 Evaluate side-chains 163 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 86 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 44 HIS I 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.117711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.079106 restraints weight = 34862.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081503 restraints weight = 21650.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.082457 restraints weight = 15742.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.082573 restraints weight = 13621.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082706 restraints weight = 13655.633| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17168 Z= 0.119 Angle : 0.511 8.216 24172 Z= 0.295 Chirality : 0.038 0.144 2640 Planarity : 0.004 0.047 2192 Dihedral : 26.905 63.407 4160 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.84 % Allowed : 28.33 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.25), residues: 1336 helix: 2.26 (0.20), residues: 680 sheet: 0.19 (0.63), residues: 80 loop : -0.72 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 54 TYR 0.014 0.001 TYR M 40 PHE 0.011 0.001 PHE F 15 TRP 0.006 0.001 TRP A 71 HIS 0.008 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (17136) covalent geometry : angle 0.51008 / 0.29 (24148) hydrogen bonds : bond 0.03445 / 2.20 ( 784) hydrogen bonds : angle 3.79657 / 2.60 ( 2040) metal coordination : bond 0.00584 / 0.43 ( 32) metal coordination : angle 1.30327 / 0.80 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.8624 (mmt) cc_final: 0.8157 (mmm) REVERT: B 124 ASP cc_start: 0.7779 (p0) cc_final: 0.7505 (p0) REVERT: F 32 ASN cc_start: 0.8927 (m-40) cc_final: 0.8569 (m-40) REVERT: F 76 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8893 (mm) REVERT: I 40 TYR cc_start: 0.8738 (t80) cc_final: 0.8382 (t80) REVERT: I 76 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8864 (mm) REVERT: I 109 ASP cc_start: 0.7646 (p0) cc_final: 0.7197 (p0) REVERT: J 48 MET cc_start: 0.7770 (mmm) cc_final: 0.7537 (mtt) REVERT: J 133 MET cc_start: 0.8262 (tpp) cc_final: 0.7823 (tpp) REVERT: M 40 TYR cc_start: 0.8737 (t80) cc_final: 0.8407 (t80) REVERT: M 114 ILE cc_start: 0.8823 (tp) cc_final: 0.8610 (tt) REVERT: M 176 ASP cc_start: 0.8345 (m-30) cc_final: 0.8085 (m-30) REVERT: N 51 ASP cc_start: 0.8151 (p0) cc_final: 0.7874 (p0) REVERT: N 64 LYS cc_start: 0.8513 (tptp) cc_final: 0.8266 (tptp) REVERT: N 130 ASP cc_start: 0.8146 (m-30) cc_final: 0.7847 (m-30) REVERT: N 179 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8748 (tp) outliers start: 35 outliers final: 30 residues processed: 161 average time/residue: 0.1093 time to fit residues: 27.7712 Evaluate side-chains 165 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 50 optimal weight: 0.0060 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.117996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.078309 restraints weight = 34602.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.080954 restraints weight = 21672.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081962 restraints weight = 15356.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082000 restraints weight = 13458.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.082140 restraints weight = 13501.874| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17168 Z= 0.115 Angle : 0.501 7.981 24172 Z= 0.289 Chirality : 0.038 0.138 2640 Planarity : 0.004 0.049 2192 Dihedral : 26.910 63.464 4160 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.84 % Allowed : 28.33 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1336 helix: 2.30 (0.20), residues: 680 sheet: 0.21 (0.63), residues: 80 loop : -0.71 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.012 0.001 TYR M 40 PHE 0.010 0.001 PHE F 15 TRP 0.006 0.001 TRP A 71 HIS 0.007 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (17136) covalent geometry : angle 0.49892 / 0.29 (24148) hydrogen bonds : bond 0.03333 / 2.13 ( 784) hydrogen bonds : angle 3.76490 / 2.58 ( 2040) metal coordination : bond 0.00597 / 0.46 ( 32) metal coordination : angle 1.42210 / 0.90 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2479.51 seconds wall clock time: 43 minutes 36.03 seconds (2616.03 seconds total)