Starting phenix.real_space_refine on Thu Feb 5 09:06:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qky_53223/02_2026/9qky_53223.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qky_53223/02_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_53223/02_2026/9qky_53223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qky_53223/02_2026/9qky_53223.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qky_53223/02_2026/9qky_53223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qky_53223/02_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-2.0-5952/lib/python3.9/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: 3.85, per 1000 atoms: 0.24 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: 1.31 Conformation dependent library (CDL) restraints added in 404.2 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: 2.02 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: 2.79 Time building geometry restraints manager: 1.73 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=" N ARG B 149 " pdb=" CA ARG B 149 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.26e-02 6.30e+03 7.83e+00 bond pdb=" N ARG F 149 " pdb=" CA ARG F 149 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.26e-02 6.30e+03 7.75e+00 bond pdb=" N ARG J 149 " pdb=" CA ARG J 149 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.26e-02 6.30e+03 7.74e+00 bond pdb=" N ARG N 149 " pdb=" CA ARG N 149 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.26e-02 6.30e+03 7.54e+00 bond pdb=" N ARG B 121 " pdb=" CA ARG B 121 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.35e-02 5.49e+03 6.37e+00 ... (remaining 17131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 23012 1.18 - 2.35: 836 2.35 - 3.53: 216 3.53 - 4.70: 56 4.70 - 5.88: 28 Bond angle restraints: 24148 Sorted by residual: angle pdb=" O3' DT D -30 " pdb=" P DT D -29 " pdb=" O5' DT D -29 " ideal model delta sigma weight residual 104.00 99.23 4.77 1.50e+00 4.44e-01 1.01e+01 angle pdb=" O3' DT P -30 " pdb=" P DT P -29 " pdb=" O5' DT P -29 " ideal model delta sigma weight residual 104.00 99.24 4.76 1.50e+00 4.44e-01 1.01e+01 angle pdb=" O3' DT H -30 " pdb=" P DT H -29 " pdb=" O5' DT H -29 " ideal model delta sigma weight residual 104.00 99.25 4.75 1.50e+00 4.44e-01 1.00e+01 angle pdb=" O3' DT L -30 " pdb=" P DT L -29 " pdb=" O5' DT L -29 " ideal model delta sigma weight residual 104.00 99.26 4.74 1.50e+00 4.44e-01 9.97e+00 angle pdb=" N ARG M 121 " pdb=" CA ARG M 121 " pdb=" C ARG M 121 " ideal model delta sigma weight residual 112.24 108.46 3.78 1.28e+00 6.10e-01 8.71e+00 ... (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 - 0.085: 2488 0.085 - 0.170: 148 0.170 - 0.255: 0 0.255 - 0.339: 0 0.339 - 0.424: 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 2.35 -2.77 -0.42 2.00e-01 2.50e+01 4.50e+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 2.35 -2.77 -0.42 2.00e-01 2.50e+01 4.46e+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 2.35 -2.77 -0.42 2.00e-01 2.50e+01 4.44e+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: 4.110 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.680 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.003 0.038 17168 Z= 0.179 Angle : 0.583 5.877 24172 Z= 0.351 Chirality : 0.040 0.424 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 covalent geometry : bond 0.00330 (17136) covalent geometry : angle 0.58103 (24148) hydrogen bonds : bond 0.10895 ( 784) hydrogen bonds : angle 5.37522 ( 2040) metal coordination : bond 0.00653 ( 32) metal coordination : angle 1.63855 ( 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 : 0.511 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: 0.1500 time to fit residues: 52.3839 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 : 0.476 ------------------------------------------------------------------------------- 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: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 158 ASN E 164 GLN ** I 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN ** J 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 = 0.3704 r_free = 0.3704 target = 0.113821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074536 restraints weight = 34697.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.076481 restraints weight = 22144.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.077758 restraints weight = 17061.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.078562 restraints weight = 14601.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.079009 restraints weight = 13282.849| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17168 Z= 0.243 Angle : 0.618 6.187 24172 Z= 0.347 Chirality : 0.042 0.155 2640 Planarity : 0.005 0.058 2192 Dihedral : 26.262 70.255 4160 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.46 % Allowed : 24.68 % Favored : 70.86 % 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: 1.19 (0.25), residues: 1336 helix: 1.87 (0.21), residues: 688 sheet: 0.12 (0.61), residues: 80 loop : -0.44 (0.29), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 121 TYR 0.014 0.002 TYR I 40 PHE 0.016 0.002 PHE B 15 TRP 0.013 0.002 TRP B 30 HIS 0.008 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00574 (17136) covalent geometry : angle 0.61639 (24148) hydrogen bonds : bond 0.05089 ( 784) hydrogen bonds : angle 4.29366 ( 2040) metal coordination : bond 0.00848 ( 32) metal coordination : angle 1.43752 ( 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 215 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8797 (mp) REVERT: E 89 GLU cc_start: 0.8017 (pm20) cc_final: 0.7814 (pm20) REVERT: F 32 ASN cc_start: 0.9160 (m-40) cc_final: 0.8578 (m-40) REVERT: F 69 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8237 (tm-30) REVERT: F 122 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7917 (mp10) REVERT: I 40 TYR cc_start: 0.8767 (t80) cc_final: 0.8565 (t80) REVERT: I 70 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8526 (tttm) REVERT: I 109 ASP cc_start: 0.7820 (p0) cc_final: 0.7425 (p0) REVERT: N 51 ASP cc_start: 0.8159 (p0) cc_final: 0.7936 (p0) REVERT: N 90 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8596 (t0) REVERT: N 130 ASP cc_start: 0.8339 (m-30) cc_final: 0.8000 (m-30) outliers start: 55 outliers final: 37 residues processed: 202 average time/residue: 0.1166 time to fit residues: 36.4954 Evaluate side-chains 173 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 79 LEU 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 F residue 79 LEU 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 26 PHE Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 70 LYS 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 135 ILE Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 79 LEU 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 26 PHE 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 126 VAL Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain N residue 179 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 43 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN J 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.116142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076830 restraints weight = 34494.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.078793 restraints weight = 24832.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079413 restraints weight = 17559.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079740 restraints weight = 16505.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.079930 restraints weight = 15595.245| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17168 Z= 0.133 Angle : 0.499 6.931 24172 Z= 0.287 Chirality : 0.036 0.133 2640 Planarity : 0.004 0.046 2192 Dihedral : 26.255 65.863 4160 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.17 % Allowed : 25.24 % Favored : 71.59 % 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: 1.23 (0.25), residues: 1336 helix: 2.04 (0.21), residues: 680 sheet: 0.04 (0.61), residues: 80 loop : -0.57 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 121 TYR 0.008 0.001 TYR F 178 PHE 0.011 0.001 PHE F 15 TRP 0.006 0.001 TRP A 71 HIS 0.006 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00299 (17136) covalent geometry : angle 0.49662 (24148) hydrogen bonds : bond 0.03225 ( 784) hydrogen bonds : angle 3.83973 ( 2040) metal coordination : bond 0.00573 ( 32) metal coordination : angle 1.55564 ( 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 184 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: I 76 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8873 (mm) REVERT: I 109 ASP cc_start: 0.7823 (p0) cc_final: 0.7393 (p0) REVERT: I 133 MET cc_start: 0.8735 (tpp) cc_final: 0.8425 (tpp) REVERT: M 114 ILE cc_start: 0.8839 (tp) cc_final: 0.8634 (tt) REVERT: N 51 ASP cc_start: 0.8117 (p0) cc_final: 0.7818 (p0) REVERT: N 130 ASP cc_start: 0.8144 (m-30) cc_final: 0.7863 (m-30) outliers start: 39 outliers final: 28 residues processed: 172 average time/residue: 0.1113 time to fit residues: 30.4967 Evaluate side-chains 156 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 E residue 67 ILE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 67 ILE 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 76 LEU Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 111 LYS 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 83 ILE Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 172 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 116 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 164 GLN J 158 ASN M 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.113396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.073763 restraints weight = 34441.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075632 restraints weight = 24748.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076193 restraints weight = 17559.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.076753 restraints weight = 16424.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076913 restraints weight = 15361.111| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17168 Z= 0.184 Angle : 0.538 4.593 24172 Z= 0.306 Chirality : 0.038 0.143 2640 Planarity : 0.004 0.051 2192 Dihedral : 26.381 67.094 4160 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.90 % Allowed : 26.06 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1336 helix: 2.03 (0.21), residues: 688 sheet: 0.06 (0.61), residues: 80 loop : -0.61 (0.29), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 121 TYR 0.013 0.002 TYR I 40 PHE 0.012 0.001 PHE F 15 TRP 0.006 0.001 TRP B 30 HIS 0.007 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00431 (17136) covalent geometry : angle 0.53504 (24148) hydrogen bonds : bond 0.04183 ( 784) hydrogen bonds : angle 3.96420 ( 2040) metal coordination : bond 0.00776 ( 32) metal coordination : angle 1.87216 ( 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 184 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: F 32 ASN cc_start: 0.9085 (m-40) cc_final: 0.8584 (m-40) REVERT: F 163 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8686 (t) REVERT: I 76 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8875 (mm) REVERT: I 109 ASP cc_start: 0.7952 (p0) cc_final: 0.7580 (p0) REVERT: J 48 MET cc_start: 0.7771 (mmm) cc_final: 0.7480 (mtt) REVERT: J 163 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8624 (t) REVERT: M 114 ILE cc_start: 0.8793 (tp) cc_final: 0.8585 (tt) REVERT: N 51 ASP cc_start: 0.8127 (p0) cc_final: 0.7813 (p0) REVERT: N 130 ASP cc_start: 0.8169 (m-30) cc_final: 0.7901 (m-30) outliers start: 48 outliers final: 35 residues processed: 173 average time/residue: 0.1168 time to fit residues: 31.5862 Evaluate side-chains 164 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 135 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 172 ILE Chi-restraints excluded: chain E residue 179 LEU 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 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 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 103 CYS Chi-restraints excluded: chain M residue 111 LYS Chi-restraints excluded: chain M residue 124 ASP 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 83 ILE Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 163 VAL 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: 0.9980 chunk 59 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 25 optimal weight: 0.0270 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 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 = 0.3753 r_free = 0.3753 target = 0.116413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.077380 restraints weight = 34478.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.079334 restraints weight = 26647.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.079915 restraints weight = 18273.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080207 restraints weight = 17496.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.080468 restraints weight = 16176.557| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17168 Z= 0.121 Angle : 0.484 7.280 24172 Z= 0.279 Chirality : 0.035 0.132 2640 Planarity : 0.004 0.050 2192 Dihedral : 26.265 65.519 4160 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.92 % Allowed : 27.44 % Favored : 69.64 % 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: 1.39 (0.25), residues: 1336 helix: 2.19 (0.20), residues: 688 sheet: 0.11 (0.62), residues: 80 loop : -0.55 (0.29), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.008 0.001 TYR F 178 PHE 0.010 0.001 PHE F 15 TRP 0.006 0.001 TRP I 71 HIS 0.006 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00263 (17136) covalent geometry : angle 0.48296 (24148) hydrogen bonds : bond 0.02943 ( 784) hydrogen bonds : angle 3.70118 ( 2040) metal coordination : bond 0.00410 ( 32) metal coordination : angle 1.14400 ( 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 183 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: F 32 ASN cc_start: 0.8902 (m-40) cc_final: 0.8512 (m-40) REVERT: F 69 GLN cc_start: 0.8296 (tm-30) cc_final: 0.8073 (tm-30) REVERT: I 76 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8882 (mm) REVERT: I 109 ASP cc_start: 0.7909 (p0) cc_final: 0.7522 (p0) REVERT: I 133 MET cc_start: 0.8777 (tpp) cc_final: 0.8447 (tpp) REVERT: J 19 LEU cc_start: 0.9008 (mt) cc_final: 0.8744 (mt) REVERT: J 48 MET cc_start: 0.7686 (mmm) cc_final: 0.7332 (mtt) REVERT: J 133 MET cc_start: 0.8160 (tpp) cc_final: 0.7540 (tpp) REVERT: N 51 ASP cc_start: 0.8052 (p0) cc_final: 0.7704 (p0) outliers start: 36 outliers final: 28 residues processed: 174 average time/residue: 0.1199 time to fit residues: 32.0253 Evaluate side-chains 162 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 E residue 67 ILE Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 67 ILE 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 103 CYS 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 M residue 103 CYS Chi-restraints excluded: chain M residue 111 LYS Chi-restraints excluded: chain M residue 124 ASP 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 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 136 optimal weight: 0.2980 chunk 36 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 89 optimal weight: 0.0870 chunk 8 optimal weight: 0.1980 chunk 140 optimal weight: 4.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.115893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.076201 restraints weight = 34727.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.078479 restraints weight = 22035.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.079508 restraints weight = 16152.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.079606 restraints weight = 14090.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.079762 restraints weight = 14055.316| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17168 Z= 0.143 Angle : 0.500 5.709 24172 Z= 0.286 Chirality : 0.036 0.136 2640 Planarity : 0.004 0.050 2192 Dihedral : 26.319 66.251 4160 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.41 % Allowed : 27.44 % Favored : 69.16 % 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: 1.39 (0.25), residues: 1336 helix: 2.23 (0.20), residues: 688 sheet: 0.14 (0.62), residues: 80 loop : -0.63 (0.29), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 54 TYR 0.011 0.001 TYR I 40 PHE 0.012 0.001 PHE F 15 TRP 0.005 0.001 TRP A 71 HIS 0.007 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00328 (17136) covalent geometry : angle 0.49777 (24148) hydrogen bonds : bond 0.03433 ( 784) hydrogen bonds : angle 3.77200 ( 2040) metal coordination : bond 0.00496 ( 32) metal coordination : angle 1.43071 ( 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 175 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8762 (m-30) cc_final: 0.8158 (m-30) REVERT: F 32 ASN cc_start: 0.8985 (m-40) cc_final: 0.8621 (m-40) REVERT: F 69 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8122 (tm-30) REVERT: I 48 MET cc_start: 0.8384 (mtp) cc_final: 0.8168 (mtp) REVERT: I 76 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8889 (mm) REVERT: I 109 ASP cc_start: 0.7897 (p0) cc_final: 0.7569 (p0) REVERT: J 48 MET cc_start: 0.7801 (mmm) cc_final: 0.7546 (mtt) REVERT: N 51 ASP cc_start: 0.8124 (p0) cc_final: 0.7776 (p0) REVERT: N 179 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8768 (tp) outliers start: 42 outliers final: 32 residues processed: 167 average time/residue: 0.1147 time to fit residues: 30.2571 Evaluate side-chains 160 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE 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 172 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 67 ILE 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 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 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 M residue 103 CYS Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 163 VAL 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: 6.9990 chunk 70 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 164 GLN ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.115932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.075958 restraints weight = 34669.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.077921 restraints weight = 22590.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.079215 restraints weight = 17534.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.080044 restraints weight = 15031.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.080374 restraints weight = 13663.840| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17168 Z= 0.133 Angle : 0.492 6.622 24172 Z= 0.283 Chirality : 0.036 0.134 2640 Planarity : 0.004 0.053 2192 Dihedral : 26.277 66.182 4160 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.41 % Allowed : 28.17 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.25), residues: 1336 helix: 2.29 (0.20), residues: 688 sheet: 0.15 (0.62), residues: 80 loop : -0.60 (0.29), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 121 TYR 0.010 0.001 TYR I 40 PHE 0.011 0.001 PHE F 15 TRP 0.005 0.001 TRP M 71 HIS 0.007 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00302 (17136) covalent geometry : angle 0.49126 (24148) hydrogen bonds : bond 0.03226 ( 784) hydrogen bonds : angle 3.71425 ( 2040) metal coordination : bond 0.00408 ( 32) metal coordination : angle 1.12972 ( 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 178 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 32 ASN cc_start: 0.8973 (m-40) cc_final: 0.8601 (m-40) REVERT: F 69 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8119 (tm-30) REVERT: I 76 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8864 (mm) REVERT: I 109 ASP cc_start: 0.7888 (p0) cc_final: 0.7598 (p0) REVERT: I 133 MET cc_start: 0.8798 (tpp) cc_final: 0.8388 (tpp) REVERT: J 13 MET cc_start: 0.7406 (mtp) cc_final: 0.7205 (mtt) REVERT: J 48 MET cc_start: 0.7800 (mmm) cc_final: 0.7593 (mtt) REVERT: N 51 ASP cc_start: 0.8044 (p0) cc_final: 0.7703 (p0) REVERT: N 179 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8793 (tp) outliers start: 42 outliers final: 32 residues processed: 170 average time/residue: 0.1197 time to fit residues: 31.4607 Evaluate side-chains 162 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 148 GLU Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 67 ILE 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 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 171 THR 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 M residue 103 CYS Chi-restraints excluded: chain M residue 124 ASP 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 163 VAL Chi-restraints excluded: chain N residue 172 ILE 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: 3.9990 chunk 128 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3753 r_free = 0.3753 target = 0.115382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.075881 restraints weight = 33910.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.076651 restraints weight = 28376.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.077012 restraints weight = 23782.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.077724 restraints weight = 23840.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.077856 restraints weight = 21724.764| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 17168 Z= 0.233 Angle : 0.590 9.109 24172 Z= 0.331 Chirality : 0.040 0.142 2640 Planarity : 0.004 0.050 2192 Dihedral : 26.421 69.232 4160 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.90 % Allowed : 27.60 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.24), residues: 1336 helix: 2.00 (0.20), residues: 688 sheet: 0.04 (0.62), residues: 80 loop : -0.87 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 121 TYR 0.012 0.002 TYR F 151 PHE 0.014 0.002 PHE B 15 TRP 0.006 0.001 TRP A 30 HIS 0.005 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00553 (17136) covalent geometry : angle 0.58617 (24148) hydrogen bonds : bond 0.04969 ( 784) hydrogen bonds : angle 4.11031 ( 2040) metal coordination : bond 0.00924 ( 32) metal coordination : angle 2.28615 ( 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 170 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 32 ASN cc_start: 0.9163 (m-40) cc_final: 0.8663 (m-40) REVERT: F 109 ASP cc_start: 0.7894 (p0) cc_final: 0.7516 (p0) REVERT: F 163 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8688 (t) REVERT: I 76 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8998 (mm) REVERT: I 133 MET cc_start: 0.8804 (tpp) cc_final: 0.8545 (tpp) REVERT: M 51 ASP cc_start: 0.8717 (m-30) cc_final: 0.8320 (m-30) outliers start: 48 outliers final: 41 residues processed: 159 average time/residue: 0.1192 time to fit residues: 29.6024 Evaluate side-chains 160 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 145 THR Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 120 LEU 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 172 ILE Chi-restraints excluded: chain F residue 67 ILE 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 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 126 VAL Chi-restraints excluded: chain I residue 171 THR 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 103 CYS Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 172 ILE 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: 2.9990 chunk 1 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 126 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN E 44 HIS ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3731 r_free = 0.3731 target = 0.114976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.075919 restraints weight = 34527.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.077647 restraints weight = 24518.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.078137 restraints weight = 18072.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078313 restraints weight = 17414.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.078620 restraints weight = 16499.560| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17168 Z= 0.132 Angle : 0.511 8.343 24172 Z= 0.293 Chirality : 0.036 0.136 2640 Planarity : 0.004 0.053 2192 Dihedral : 26.297 67.251 4160 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.68 % Allowed : 29.06 % Favored : 68.26 % 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: 1.33 (0.25), residues: 1336 helix: 2.24 (0.20), residues: 688 sheet: 0.01 (0.61), residues: 80 loop : -0.71 (0.29), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 121 TYR 0.008 0.001 TYR F 178 PHE 0.011 0.001 PHE F 15 TRP 0.007 0.001 TRP M 71 HIS 0.005 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00296 (17136) covalent geometry : angle 0.50962 (24148) hydrogen bonds : bond 0.03271 ( 784) hydrogen bonds : angle 3.74699 ( 2040) metal coordination : bond 0.00403 ( 32) metal coordination : angle 1.27530 ( 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 161 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 32 ASN cc_start: 0.8974 (m-40) cc_final: 0.8616 (m-40) REVERT: F 109 ASP cc_start: 0.7764 (p0) cc_final: 0.7360 (p0) REVERT: F 163 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8551 (t) REVERT: I 13 MET cc_start: 0.7083 (mtt) cc_final: 0.6727 (mtp) REVERT: I 76 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8865 (mm) REVERT: I 133 MET cc_start: 0.8733 (tpp) cc_final: 0.8428 (tpp) REVERT: M 13 MET cc_start: 0.7242 (mtp) cc_final: 0.7022 (mtm) outliers start: 33 outliers final: 28 residues processed: 154 average time/residue: 0.1183 time to fit residues: 28.6559 Evaluate side-chains 153 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 120 LEU 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 172 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 67 ILE 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 76 LEU Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain M residue 124 ASP 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 163 VAL Chi-restraints excluded: chain N residue 177 LEU 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: 3.9990 chunk 44 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 HIS ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.114928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075157 restraints weight = 34438.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.077123 restraints weight = 22530.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078417 restraints weight = 17477.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.079228 restraints weight = 14973.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.079629 restraints weight = 13596.290| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17168 Z= 0.135 Angle : 0.504 8.200 24172 Z= 0.288 Chirality : 0.036 0.154 2640 Planarity : 0.004 0.054 2192 Dihedral : 26.354 67.369 4160 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.60 % Allowed : 29.30 % Favored : 68.10 % 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: 1.41 (0.25), residues: 1336 helix: 2.29 (0.20), residues: 688 sheet: 0.08 (0.62), residues: 80 loop : -0.65 (0.29), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 121 TYR 0.011 0.001 TYR E 40 PHE 0.012 0.001 PHE F 15 TRP 0.005 0.001 TRP E 71 HIS 0.012 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00307 (17136) covalent geometry : angle 0.50230 (24148) hydrogen bonds : bond 0.03358 ( 784) hydrogen bonds : angle 3.75653 ( 2040) metal coordination : bond 0.00504 ( 32) metal coordination : angle 1.34557 ( 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 155 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 32 ASN cc_start: 0.8997 (m-40) cc_final: 0.8611 (m-40) REVERT: I 13 MET cc_start: 0.7100 (mtt) cc_final: 0.6754 (mtp) REVERT: I 76 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8866 (mm) REVERT: I 133 MET cc_start: 0.8722 (tpp) cc_final: 0.8272 (tpp) REVERT: M 176 ASP cc_start: 0.8277 (m-30) cc_final: 0.8073 (m-30) REVERT: N 56 VAL cc_start: 0.8804 (m) cc_final: 0.8567 (p) REVERT: N 179 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8798 (tp) outliers start: 32 outliers final: 27 residues processed: 149 average time/residue: 0.1187 time to fit residues: 27.6567 Evaluate side-chains 150 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 120 LEU 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 172 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 67 ILE 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 103 CYS Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain M residue 124 ASP 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 163 VAL Chi-restraints excluded: chain N residue 177 LEU 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: 0.0670 chunk 117 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 0.0270 chunk 105 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN E 44 HIS ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3745 r_free = 0.3745 target = 0.116917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.077559 restraints weight = 34864.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.079630 restraints weight = 21928.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.080987 restraints weight = 16708.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.081867 restraints weight = 14136.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.082457 restraints weight = 12747.696| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17168 Z= 0.127 Angle : 0.494 7.913 24172 Z= 0.283 Chirality : 0.035 0.135 2640 Planarity : 0.004 0.054 2192 Dihedral : 26.303 67.064 4160 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.60 % Allowed : 29.14 % Favored : 68.26 % 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: 1.48 (0.25), residues: 1336 helix: 2.34 (0.20), residues: 688 sheet: 0.10 (0.62), residues: 80 loop : -0.61 (0.29), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 121 TYR 0.007 0.001 TYR B 40 PHE 0.011 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 covalent geometry : bond 0.00286 (17136) covalent geometry : angle 0.49306 (24148) hydrogen bonds : bond 0.03128 ( 784) hydrogen bonds : angle 3.68971 ( 2040) metal coordination : bond 0.00374 ( 32) metal coordination : angle 1.12883 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2648.98 seconds wall clock time: 46 minutes 40.29 seconds (2800.29 seconds total)