Starting phenix.real_space_refine on Thu Aug 6 17:40:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qky_53223/08_2026/9qky_53223.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qky_53223/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9qky_53223/08_2026/9qky_53223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qky_53223/08_2026/9qky_53223.map" model { file = "/net/cci-nas-00/data/ceres_data/9qky_53223/08_2026/9qky_53223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qky_53223/08_2026/9qky_53223.cif" } 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16276 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "B" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "C" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "E" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "F" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "G" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "H" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "I" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "J" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "K" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "L" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "M" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "N" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1398 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "O" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "P" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 774 SG CYS A 103 74.888 57.070 29.449 1.00 82.54 S ATOM 1203 SG CYS A 156 75.204 57.421 33.243 1.00 91.55 S ATOM 1242 SG CYS A 162 72.008 58.720 31.557 1.00 78.34 S ATOM 2172 SG CYS B 103 54.378 70.897 76.630 1.00 62.60 S ATOM 2601 SG CYS B 156 54.531 71.503 72.843 1.00 72.51 S ATOM 2640 SG CYS B 162 56.949 69.030 74.464 1.00 55.51 S ATOM 4841 SG CYS E 103 39.773 59.670 74.057 1.00 66.50 S ATOM 5270 SG CYS E 156 39.304 59.578 77.850 1.00 72.72 S ATOM 5309 SG CYS E 162 41.061 56.610 76.163 1.00 52.59 S ATOM 6239 SG CYS F 103 47.650 36.186 121.220 1.00 60.97 S ATOM 6668 SG CYS F 156 47.166 35.801 117.432 1.00 61.72 S ATOM 6707 SG CYS F 162 46.739 39.232 119.056 1.00 49.69 S ATOM 8908 SG CYS I 103 66.192 36.343 118.672 1.00 65.10 S ATOM 9337 SG CYS I 156 66.618 36.134 122.465 1.00 65.94 S ATOM 9376 SG CYS I 162 67.012 39.560 120.778 1.00 52.06 S ATOM 10306 SG CYS J 103 74.064 59.823 165.838 1.00 63.98 S ATOM 10735 SG CYS J 156 74.685 59.837 162.050 1.00 69.95 S ATOM 10774 SG CYS J 162 72.952 56.845 163.673 1.00 52.33 S ATOM 12975 SG CYS M 103 59.288 70.905 163.282 1.00 65.40 S ATOM 13404 SG CYS M 156 59.077 71.333 167.075 1.00 70.43 S ATOM 13443 SG CYS M 162 56.686 68.845 165.391 1.00 56.24 S ATOM 14373 SG CYS N 103 38.810 57.038 210.465 1.00 85.28 S ATOM 14802 SG CYS N 156 38.307 57.400 206.678 1.00 84.77 S ATOM 14841 SG CYS N 162 41.499 58.731 208.299 1.00 79.47 S Time building chain proxies: 3.06, per 1000 atoms: 0.19 Number of scatterers: 16276 At special positions: 0 Unit cell: (114.681, 112.014, 240.919, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 64 16.00 P 248 15.00 O 3400 8.00 N 2948 7.00 C 9608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 460.6 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: 2.24 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: 2.75 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3932 1.34 - 1.45: 4292 1.45 - 1.57: 8336 1.57 - 1.69: 488 1.69 - 1.81: 88 Bond restraints: 17136 Sorted by residual: bond pdb=" C3' DA P -9 " pdb=" C2' DA P -9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT H -14 " pdb=" C2' DT H -14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA D -9 " pdb=" C2' DA D -9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA H -9 " pdb=" C2' DA H -9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT L -14 " pdb=" C2' DT L -14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.88e+00 ... (remaining 17131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 22224 1.18 - 2.35: 1473 2.35 - 3.53: 367 3.53 - 4.70: 56 4.70 - 5.88: 28 Bond angle restraints: 24148 Sorted by residual: angle pdb=" N3 DT D -14 " pdb=" C4 DT D -14 " pdb=" O4 DT D -14 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT C 8 " pdb=" C4 DT C 8 " pdb=" O4 DT C 8 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" O5' DG D -28 " pdb=" C5' DG D -28 " pdb=" C4' DG D -28 " ideal model delta sigma weight residual 109.40 112.82 -3.42 8.00e-01 1.56e+00 1.82e+01 angle pdb=" O5' DG P -28 " pdb=" C5' DG P -28 " pdb=" C4' DG P -28 " ideal model delta sigma weight residual 109.40 112.81 -3.41 8.00e-01 1.56e+00 1.82e+01 angle pdb=" O5' DG H -28 " pdb=" C5' DG H -28 " pdb=" C4' DG H -28 " ideal model delta sigma weight residual 109.40 112.81 -3.41 8.00e-01 1.56e+00 1.82e+01 ... (remaining 24143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 6953 17.43 - 34.85: 1499 34.85 - 52.28: 1072 52.28 - 69.70: 276 69.70 - 87.13: 8 Dihedral angle restraints: 9808 sinusoidal: 5832 harmonic: 3976 Sorted by residual: dihedral pdb=" CG LYS A 152 " pdb=" CD LYS A 152 " pdb=" CE LYS A 152 " pdb=" NZ LYS A 152 " ideal model delta sinusoidal sigma weight residual -60.00 -116.51 56.51 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CG LYS E 152 " pdb=" CD LYS E 152 " pdb=" CE LYS E 152 " pdb=" NZ LYS E 152 " ideal model delta sinusoidal sigma weight residual -60.00 -116.51 56.51 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CG LYS M 152 " pdb=" CD LYS M 152 " pdb=" CE LYS M 152 " pdb=" NZ LYS M 152 " ideal model delta sinusoidal sigma weight residual -60.00 -116.50 56.50 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2425 0.087 - 0.174: 211 0.174 - 0.261: 0 0.261 - 0.348: 0 0.348 - 0.434: 4 Chirality restraints: 2640 Sorted by residual: chirality pdb=" P DT L -29 " pdb=" OP1 DT L -29 " pdb=" OP2 DT L -29 " pdb=" O5' DT L -29 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" P DT H -29 " pdb=" OP1 DT H -29 " pdb=" OP2 DT H -29 " pdb=" O5' DT H -29 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" P DT P -29 " pdb=" OP1 DT P -29 " pdb=" OP2 DT P -29 " pdb=" O5' DT P -29 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.43 2.00e-01 2.50e+01 4.66e+00 ... (remaining 2637 not shown) Planarity restraints: 2192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT H -14 " 0.024 2.00e-02 2.50e+03 1.61e-02 6.51e+00 pdb=" N1 DT H -14 " -0.041 2.00e-02 2.50e+03 pdb=" C2 DT H -14 " 0.016 2.00e-02 2.50e+03 pdb=" O2 DT H -14 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT H -14 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT H -14 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT H -14 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT H -14 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT H -14 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT H -14 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT P -14 " 0.024 2.00e-02 2.50e+03 1.61e-02 6.49e+00 pdb=" N1 DT P -14 " -0.041 2.00e-02 2.50e+03 pdb=" C2 DT P -14 " 0.016 2.00e-02 2.50e+03 pdb=" O2 DT P -14 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT P -14 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT P -14 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT P -14 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT P -14 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT P -14 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT P -14 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT L -14 " 0.024 2.00e-02 2.50e+03 1.61e-02 6.48e+00 pdb=" N1 DT L -14 " -0.040 2.00e-02 2.50e+03 pdb=" C2 DT L -14 " 0.016 2.00e-02 2.50e+03 pdb=" O2 DT L -14 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT L -14 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT L -14 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT L -14 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT L -14 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT L -14 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT L -14 " 0.000 2.00e-02 2.50e+03 ... (remaining 2189 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2567 2.77 - 3.30: 13570 3.30 - 3.84: 28356 3.84 - 4.37: 31374 4.37 - 4.90: 48803 Nonbonded interactions: 124670 Sorted by model distance: nonbonded pdb=" N3 DT D -31 " pdb=" O6 DG K 1 " model vdw 2.239 3.120 nonbonded pdb=" N3 DT H -31 " pdb=" O6 DG O 1 " model vdw 2.309 3.120 nonbonded pdb=" O4' DT D -31 " pdb=" N4 DC L -1 " model vdw 2.427 3.120 nonbonded pdb=" N SER I 49 " pdb=" OE1 GLU I 52 " model vdw 2.448 3.120 nonbonded pdb=" N SER E 49 " pdb=" OE1 GLU E 52 " model vdw 2.448 3.120 ... (remaining 124665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.730 Find NCS groups from input model: 0.330 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17168 Z= 0.420 Angle : 0.691 5.877 24172 Z= 0.543 Chirality : 0.048 0.434 2640 Planarity : 0.004 0.044 2192 Dihedral : 24.337 87.125 7216 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.65 % Allowed : 29.22 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1336 helix: 1.94 (0.21), residues: 672 sheet: 0.02 (0.62), residues: 80 loop : -0.25 (0.30), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 121 TYR 0.011 0.001 TYR I 181 PHE 0.008 0.001 PHE N 15 TRP 0.003 0.000 TRP A 71 HIS 0.006 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.42 (17136) covalent geometry : angle 0.68938 / 0.54 (24148) hydrogen bonds : bond 0.10895 / 6.68 ( 784) hydrogen bonds : angle 5.37522 / 3.66 ( 2040) metal coordination : bond 0.00653 / 0.41 ( 32) metal coordination : angle 1.63855 / 0.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 240 time to evaluate : 0.377 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: 0.1443 time to fit residues: 50.8739 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 : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 40.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN E 164 GLN I 44 HIS I 164 GLN ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.117566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078080 restraints weight = 34946.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.080083 restraints weight = 25132.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.081087 restraints weight = 17145.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.081282 restraints weight = 15615.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.081498 restraints weight = 14836.828| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17168 Z= 0.226 Angle : 0.636 6.208 24172 Z= 0.353 Chirality : 0.044 0.160 2640 Planarity : 0.005 0.052 2192 Dihedral : 26.524 65.855 4160 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.76 % Allowed : 25.89 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1336 helix: 1.71 (0.21), residues: 680 sheet: -0.04 (0.61), residues: 80 loop : -0.61 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 149 TYR 0.015 0.002 TYR I 40 PHE 0.014 0.002 PHE N 15 TRP 0.011 0.002 TRP B 30 HIS 0.006 0.001 HIS J 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 (17136) covalent geometry : angle 0.63422 / 0.35 (24148) hydrogen bonds : bond 0.05099 / 3.30 ( 784) hydrogen bonds : angle 4.26221 / 2.93 ( 2040) metal coordination : bond 0.00716 / 0.37 ( 32) metal coordination : angle 1.46353 / 0.93 ( 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 188 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: E 89 GLU cc_start: 0.8021 (pm20) cc_final: 0.7807 (pm20) REVERT: F 32 ASN cc_start: 0.8977 (m-40) cc_final: 0.8567 (m-40) REVERT: I 40 TYR cc_start: 0.8781 (t80) cc_final: 0.8531 (t80) REVERT: N 51 ASP cc_start: 0.8101 (p0) cc_final: 0.7873 (p0) outliers start: 34 outliers final: 23 residues processed: 178 average time/residue: 0.1141 time to fit residues: 31.7850 Evaluate side-chains 153 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 177 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 43 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 37 optimal weight: 30.0000 chunk 50 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 HIS ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 GLN ** I 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.118588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079186 restraints weight = 34849.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081338 restraints weight = 24323.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082141 restraints weight = 16555.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.082424 restraints weight = 15461.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.082636 restraints weight = 14589.159| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17168 Z= 0.135 Angle : 0.510 5.334 24172 Z= 0.300 Chirality : 0.039 0.148 2640 Planarity : 0.004 0.057 2192 Dihedral : 26.541 65.733 4160 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.08 % Allowed : 26.14 % Favored : 70.78 % 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: 1.99 (0.21), residues: 680 sheet: 0.08 (0.62), residues: 80 loop : -0.56 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 47 TYR 0.008 0.001 TYR M 40 PHE 0.011 0.001 PHE J 15 TRP 0.007 0.001 TRP B 30 HIS 0.004 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (17136) covalent geometry : angle 0.50765 / 0.30 (24148) hydrogen bonds : bond 0.03875 / 2.47 ( 784) hydrogen bonds : angle 4.05202 / 2.77 ( 2040) metal coordination : bond 0.00607 / 0.28 ( 32) metal coordination : angle 1.49232 / 0.90 ( 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 179 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7534 (mtm-85) REVERT: E 164 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: F 32 ASN cc_start: 0.8973 (m-40) cc_final: 0.8576 (m-40) REVERT: I 40 TYR cc_start: 0.8732 (t80) cc_final: 0.8482 (t80) REVERT: I 133 MET cc_start: 0.8719 (tpp) cc_final: 0.8226 (tpp) REVERT: N 51 ASP cc_start: 0.8213 (p0) cc_final: 0.7980 (p0) outliers start: 38 outliers final: 32 residues processed: 168 average time/residue: 0.1088 time to fit residues: 29.0681 Evaluate side-chains 165 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 164 GLN Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 177 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 116 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 133 optimal weight: 0.2980 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 32 optimal weight: 40.0000 chunk 120 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 158 ASN E 164 GLN I 44 HIS I 122 GLN J 158 ASN ** M 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.113578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.074123 restraints weight = 34621.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.075592 restraints weight = 27298.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.075976 restraints weight = 19536.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.076497 restraints weight = 18840.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.076630 restraints weight = 17713.293| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17168 Z= 0.224 Angle : 0.630 8.629 24172 Z= 0.347 Chirality : 0.043 0.177 2640 Planarity : 0.005 0.060 2192 Dihedral : 26.813 66.223 4160 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.95 % Allowed : 25.00 % 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: 0.80 (0.24), residues: 1336 helix: 1.72 (0.21), residues: 680 sheet: -0.20 (0.60), residues: 80 loop : -0.81 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 88 TYR 0.015 0.002 TYR M 40 PHE 0.012 0.002 PHE I 91 TRP 0.011 0.001 TRP B 30 HIS 0.005 0.001 HIS E 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (17136) covalent geometry : angle 0.62655 / 0.35 (24148) hydrogen bonds : bond 0.05257 / 3.38 ( 784) hydrogen bonds : angle 4.18147 / 2.89 ( 2040) metal coordination : bond 0.01117 / 0.75 ( 32) metal coordination : angle 2.07501 / 1.30 ( 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 193 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 132 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: B 16 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8313 (mt) REVERT: B 54 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7540 (mtm-85) REVERT: F 32 ASN cc_start: 0.9047 (m-40) cc_final: 0.8616 (m-40) REVERT: F 69 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8150 (tm-30) REVERT: F 76 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8954 (mm) REVERT: F 163 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8787 (t) REVERT: I 40 TYR cc_start: 0.8863 (t80) cc_final: 0.8549 (t80) REVERT: I 76 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8945 (mm) REVERT: I 133 MET cc_start: 0.8687 (tpp) cc_final: 0.8438 (tpp) REVERT: M 40 TYR cc_start: 0.8847 (t80) cc_final: 0.8505 (t80) REVERT: M 114 ILE cc_start: 0.8832 (tp) cc_final: 0.8609 (tt) REVERT: N 51 ASP cc_start: 0.8112 (p0) cc_final: 0.7842 (p0) outliers start: 61 outliers final: 45 residues processed: 181 average time/residue: 0.1120 time to fit residues: 31.7665 Evaluate side-chains 176 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 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 135 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 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 27 SER Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 26 PHE Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 26 PHE Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 119 CYS Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 177 LEU Chi-restraints excluded: chain N residue 179 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 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 = 0.3744 r_free = 0.3744 target = 0.115886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.076604 restraints weight = 34370.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078594 restraints weight = 24446.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079114 restraints weight = 17243.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.079471 restraints weight = 16381.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.079617 restraints weight = 15474.593| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17168 Z= 0.126 Angle : 0.512 5.672 24172 Z= 0.300 Chirality : 0.039 0.165 2640 Planarity : 0.004 0.063 2192 Dihedral : 26.735 65.406 4160 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.90 % Allowed : 26.38 % Favored : 69.72 % 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: 1.03 (0.25), residues: 1336 helix: 1.93 (0.21), residues: 680 sheet: -0.05 (0.62), residues: 80 loop : -0.74 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 54 TYR 0.009 0.001 TYR F 178 PHE 0.011 0.001 PHE F 15 TRP 0.007 0.001 TRP B 30 HIS 0.004 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (17136) covalent geometry : angle 0.51008 / 0.30 (24148) hydrogen bonds : bond 0.03800 / 2.43 ( 784) hydrogen bonds : angle 3.93458 / 2.70 ( 2040) metal coordination : bond 0.00567 / 0.40 ( 32) metal coordination : angle 1.58259 / 1.01 ( 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 189 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: B 54 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7646 (mtm-85) REVERT: I 40 TYR cc_start: 0.8786 (t80) cc_final: 0.8531 (t80) REVERT: I 76 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8885 (mm) REVERT: I 109 ASP cc_start: 0.7669 (p0) cc_final: 0.7212 (p0) REVERT: J 133 MET cc_start: 0.8040 (tpp) cc_final: 0.7717 (tpp) REVERT: M 114 ILE cc_start: 0.8800 (tp) cc_final: 0.8578 (tt) REVERT: M 176 ASP cc_start: 0.8313 (m-30) cc_final: 0.8062 (m-30) REVERT: N 51 ASP cc_start: 0.8151 (p0) cc_final: 0.7889 (p0) REVERT: N 179 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8797 (tp) outliers start: 48 outliers final: 39 residues processed: 177 average time/residue: 0.1133 time to fit residues: 31.1635 Evaluate side-chains 171 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 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 90 ASP Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 126 VAL 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 177 LEU Chi-restraints excluded: chain N residue 179 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 136 optimal weight: 0.1980 chunk 36 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 164 GLN F 158 ASN I 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.115068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.075566 restraints weight = 34595.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.077434 restraints weight = 24376.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.078001 restraints weight = 17650.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.078180 restraints weight = 16841.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.078461 restraints weight = 15949.828| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2584 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= 0.143 Angle : 0.530 5.456 24172 Z= 0.303 Chirality : 0.039 0.165 2640 Planarity : 0.004 0.057 2192 Dihedral : 26.824 64.575 4160 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.06 % Allowed : 26.46 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.25), residues: 1336 helix: 1.98 (0.21), residues: 680 sheet: 0.01 (0.62), residues: 80 loop : -0.77 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 88 TYR 0.009 0.001 TYR F 178 PHE 0.011 0.001 PHE F 15 TRP 0.007 0.001 TRP B 30 HIS 0.006 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (17136) covalent geometry : angle 0.52830 / 0.30 (24148) hydrogen bonds : bond 0.03995 / 2.55 ( 784) hydrogen bonds : angle 3.91611 / 2.69 ( 2040) metal coordination : bond 0.00618 / 0.44 ( 32) metal coordination : angle 1.45251 / 0.91 ( 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 183 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: B 54 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7813 (mtm110) REVERT: F 76 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8926 (mm) REVERT: I 40 TYR cc_start: 0.8788 (t80) cc_final: 0.8520 (t80) REVERT: I 76 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8891 (mm) REVERT: I 109 ASP cc_start: 0.7729 (p0) cc_final: 0.7274 (p0) REVERT: I 133 MET cc_start: 0.8763 (tpp) cc_final: 0.8455 (tpp) REVERT: N 51 ASP cc_start: 0.8164 (p0) cc_final: 0.7901 (p0) REVERT: N 179 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8832 (tp) outliers start: 50 outliers final: 43 residues processed: 170 average time/residue: 0.1118 time to fit residues: 29.9423 Evaluate side-chains 173 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 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 124 ASP Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 26 PHE Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 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 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 30.0000 chunk 43 optimal weight: 0.0870 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.116805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.077152 restraints weight = 34494.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079689 restraints weight = 20705.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.080513 restraints weight = 15004.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.080627 restraints weight = 12978.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.080741 restraints weight = 13194.344| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17168 Z= 0.115 Angle : 0.499 7.827 24172 Z= 0.291 Chirality : 0.038 0.153 2640 Planarity : 0.004 0.058 2192 Dihedral : 26.815 63.798 4160 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.49 % Allowed : 27.60 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1336 helix: 2.11 (0.21), residues: 680 sheet: 0.09 (0.63), residues: 80 loop : -0.70 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 54 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 0.000 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.12 (17136) covalent geometry : angle 0.49659 / 0.29 (24148) hydrogen bonds : bond 0.03397 / 2.16 ( 784) hydrogen bonds : angle 3.81236 / 2.61 ( 2040) metal coordination : bond 0.00593 / 0.43 ( 32) metal coordination : angle 1.48380 / 0.91 ( 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 183 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: B 54 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7820 (mtm110) REVERT: F 32 ASN cc_start: 0.8898 (m-40) cc_final: 0.8519 (m-40) REVERT: I 40 TYR cc_start: 0.8730 (t80) cc_final: 0.8479 (t80) REVERT: I 76 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8840 (mm) REVERT: I 109 ASP cc_start: 0.7673 (p0) cc_final: 0.7223 (p0) REVERT: I 133 MET cc_start: 0.8660 (tpp) cc_final: 0.8241 (tpp) REVERT: J 56 VAL cc_start: 0.8619 (t) cc_final: 0.8364 (p) REVERT: J 133 MET cc_start: 0.8162 (tpp) cc_final: 0.7803 (tpp) REVERT: M 176 ASP cc_start: 0.8375 (m-30) cc_final: 0.8152 (m-30) REVERT: N 51 ASP cc_start: 0.8201 (p0) cc_final: 0.7949 (p0) REVERT: N 90 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8528 (t0) REVERT: N 130 ASP cc_start: 0.8168 (m-30) cc_final: 0.7865 (m-30) REVERT: N 179 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8790 (tp) outliers start: 43 outliers final: 37 residues processed: 170 average time/residue: 0.0985 time to fit residues: 26.4169 Evaluate side-chains 172 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 119 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 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 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 90 ASP Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 90 ASP 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 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: 3.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 50.0000 chunk 131 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN I 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.113284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074026 restraints weight = 34497.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.075758 restraints weight = 26926.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.076215 restraints weight = 18866.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.076532 restraints weight = 18147.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.076783 restraints weight = 16839.396| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17168 Z= 0.190 Angle : 0.588 5.569 24172 Z= 0.326 Chirality : 0.042 0.172 2640 Planarity : 0.004 0.054 2192 Dihedral : 26.962 64.525 4160 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.22 % Allowed : 27.11 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.25), residues: 1336 helix: 2.00 (0.21), residues: 680 sheet: -0.00 (0.63), residues: 80 loop : -0.86 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 47 TYR 0.011 0.002 TYR N 178 PHE 0.012 0.002 PHE J 15 TRP 0.007 0.001 TRP B 30 HIS 0.007 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (17136) covalent geometry : angle 0.58571 / 0.33 (24148) hydrogen bonds : bond 0.04700 / 3.01 ( 784) hydrogen bonds : angle 3.99375 / 2.76 ( 2040) metal coordination : bond 0.00701 / 0.43 ( 32) metal coordination : angle 1.73944 / 1.07 ( 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 184 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: F 76 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8965 (mm) REVERT: I 40 TYR cc_start: 0.8829 (t80) cc_final: 0.8368 (t80) REVERT: I 76 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8890 (mm) REVERT: I 109 ASP cc_start: 0.7922 (p0) cc_final: 0.7543 (p0) REVERT: J 48 MET cc_start: 0.7946 (mmm) cc_final: 0.7634 (mtt) REVERT: N 51 ASP cc_start: 0.8113 (p0) cc_final: 0.7824 (p0) REVERT: N 90 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8649 (t0) outliers start: 52 outliers final: 45 residues processed: 173 average time/residue: 0.1153 time to fit residues: 31.4000 Evaluate side-chains 177 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 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 A residue 172 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 171 THR 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 76 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 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 82 ASP Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 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 119 CYS Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 90 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 0.0370 chunk 126 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 43 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN ** J 164 GLN ** 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 = 0.3740 r_free = 0.3740 target = 0.116155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076416 restraints weight = 34483.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078968 restraints weight = 20847.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.079675 restraints weight = 15154.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.079818 restraints weight = 13227.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.079936 restraints weight = 13367.174| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17168 Z= 0.116 Angle : 0.513 7.877 24172 Z= 0.298 Chirality : 0.038 0.156 2640 Planarity : 0.004 0.042 2192 Dihedral : 26.855 64.123 4160 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.08 % Allowed : 28.08 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1336 helix: 2.16 (0.20), residues: 680 sheet: 0.08 (0.63), residues: 80 loop : -0.76 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 149 TYR 0.013 0.001 TYR M 40 PHE 0.011 0.001 PHE F 15 TRP 0.007 0.001 TRP M 30 HIS 0.006 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.12 (17136) covalent geometry : angle 0.51079 / 0.30 (24148) hydrogen bonds : bond 0.03475 / 2.21 ( 784) hydrogen bonds : angle 3.82493 / 2.63 ( 2040) metal coordination : bond 0.00601 / 0.42 ( 32) metal coordination : angle 1.47113 / 0.90 ( 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 174 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 163 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8724 (t) REVERT: F 32 ASN cc_start: 0.8924 (m-40) cc_final: 0.8535 (m-40) REVERT: F 76 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8858 (mm) REVERT: I 40 TYR cc_start: 0.8752 (t80) cc_final: 0.8285 (t80) REVERT: I 109 ASP cc_start: 0.7719 (p0) cc_final: 0.7432 (p0) REVERT: I 133 MET cc_start: 0.8771 (tpp) cc_final: 0.8358 (tpp) REVERT: J 48 MET cc_start: 0.7920 (mmm) cc_final: 0.7715 (mtt) REVERT: J 56 VAL cc_start: 0.8587 (t) cc_final: 0.8377 (p) REVERT: J 133 MET cc_start: 0.8085 (tpp) cc_final: 0.7752 (tpp) REVERT: N 51 ASP cc_start: 0.8200 (p0) cc_final: 0.7933 (p0) REVERT: N 64 LYS cc_start: 0.8547 (tptp) cc_final: 0.8318 (tptp) REVERT: N 90 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8510 (t0) REVERT: N 130 ASP cc_start: 0.8159 (m-30) cc_final: 0.7865 (m-30) REVERT: N 179 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8791 (tp) outliers start: 38 outliers final: 32 residues processed: 165 average time/residue: 0.1098 time to fit residues: 28.5062 Evaluate side-chains 166 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 171 THR Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 90 ASP 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: 5.9990 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 31 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 44 HIS ** 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 = 0.115634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.075669 restraints weight = 34644.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.078248 restraints weight = 21566.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.079244 restraints weight = 15410.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.079260 restraints weight = 13350.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079397 restraints weight = 13468.881| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17168 Z= 0.127 Angle : 0.525 7.394 24172 Z= 0.300 Chirality : 0.039 0.156 2640 Planarity : 0.004 0.050 2192 Dihedral : 26.894 63.795 4160 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.17 % Allowed : 27.92 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.25), residues: 1336 helix: 2.21 (0.20), residues: 680 sheet: 0.10 (0.62), residues: 80 loop : -0.76 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 54 TYR 0.016 0.001 TYR M 40 PHE 0.012 0.001 PHE F 15 TRP 0.006 0.001 TRP A 71 HIS 0.006 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (17136) covalent geometry : angle 0.52292 / 0.30 (24148) hydrogen bonds : bond 0.03653 / 2.33 ( 784) hydrogen bonds : angle 3.82606 / 2.63 ( 2040) metal coordination : bond 0.00597 / 0.39 ( 32) metal coordination : angle 1.42024 / 0.84 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8875 (m-30) cc_final: 0.8577 (m-30) REVERT: F 32 ASN cc_start: 0.8945 (m-40) cc_final: 0.8525 (m-40) REVERT: F 69 GLN cc_start: 0.8296 (tm-30) cc_final: 0.8084 (tm-30) REVERT: F 76 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8898 (mm) REVERT: I 40 TYR cc_start: 0.8749 (t80) cc_final: 0.8203 (t80) REVERT: I 109 ASP cc_start: 0.7746 (p0) cc_final: 0.7444 (p0) REVERT: I 133 MET cc_start: 0.8766 (tpp) cc_final: 0.8435 (tpp) REVERT: J 133 MET cc_start: 0.8162 (tpp) cc_final: 0.7757 (tpp) REVERT: N 51 ASP cc_start: 0.8187 (p0) cc_final: 0.7917 (p0) REVERT: N 64 LYS cc_start: 0.8566 (tptp) cc_final: 0.8352 (tptp) REVERT: N 90 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8539 (t0) REVERT: N 130 ASP cc_start: 0.8206 (m-30) cc_final: 0.7903 (m-30) REVERT: N 179 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8808 (tp) outliers start: 39 outliers final: 35 residues processed: 159 average time/residue: 0.1095 time to fit residues: 27.4283 Evaluate side-chains 167 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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 119 CYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 119 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 179 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 90 ASP 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: 0.5980 chunk 117 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 chunk 132 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.116304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.077184 restraints weight = 34591.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079106 restraints weight = 24065.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079899 restraints weight = 17543.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.080204 restraints weight = 16472.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080389 restraints weight = 15438.103| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17168 Z= 0.116 Angle : 0.504 6.879 24172 Z= 0.291 Chirality : 0.038 0.147 2640 Planarity : 0.004 0.050 2192 Dihedral : 26.883 63.787 4160 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.92 % Allowed : 28.25 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.25), residues: 1336 helix: 2.26 (0.20), residues: 680 sheet: 0.14 (0.62), residues: 80 loop : -0.72 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 54 TYR 0.013 0.001 TYR M 40 PHE 0.011 0.001 PHE F 15 TRP 0.007 0.001 TRP A 71 HIS 0.004 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (17136) covalent geometry : angle 0.50256 / 0.29 (24148) hydrogen bonds : bond 0.03359 / 2.14 ( 784) hydrogen bonds : angle 3.77520 / 2.59 ( 2040) metal coordination : bond 0.00543 / 0.37 ( 32) metal coordination : angle 1.32465 / 0.80 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2494.88 seconds wall clock time: 43 minutes 53.63 seconds (2633.63 seconds total)