Starting phenix.real_space_refine on Fri Mar 6 12:27:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ut1_26744/03_2026/7ut1_26744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut1_26744/03_2026/7ut1_26744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ut1_26744/03_2026/7ut1_26744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut1_26744/03_2026/7ut1_26744.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ut1_26744/03_2026/7ut1_26744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut1_26744/03_2026/7ut1_26744.map" } resolution = 3.8 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= 0.006 sd= 0.034 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 12 6.06 5 P 294 5.49 5 S 108 5.16 5 C 19070 2.51 5 N 5707 2.21 5 O 6128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31319 Number of models: 1 Model: "" Number of chains: 40 Chain: "a" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2114 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 245} Chain: "b" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1957 Classifications: {'peptide': 244} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 229} Chain breaks: 2 Chain: "c" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 385 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 42} Chain: "d" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "e" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2114 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 245} Chain: "f" Number of atoms: 1951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1951 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 228} Chain breaks: 2 Chain: "g" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1893 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 223} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "h" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1833 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 218} Chain breaks: 4 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "i" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "j" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 813 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "k" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 296 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "l" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "m" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 773 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "n" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 254 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2114 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 245} Chain: "B" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1944 Classifications: {'peptide': 242} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 227} Chain breaks: 2 Chain: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 385 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 42} Chain: "D" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "E" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2121 Classifications: {'peptide': 265} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 246} Chain: "F" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1896 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 222} Chain breaks: 3 Chain: "G" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1886 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1829 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 217} Chain breaks: 4 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 813 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "K" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 296 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "L" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "M" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 793 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "N" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} 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: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" 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 299 SG CYS a 37 125.286 142.773 61.608 1.00 95.44 S ATOM 320 SG CYS a 40 126.733 139.149 61.696 1.00 95.68 S ATOM 2413 SG CYS b 37 128.256 112.529 126.899 1.00120.05 S ATOM 2434 SG CYS b 40 130.337 109.306 126.569 1.00123.54 S ATOM 5147 SG CYS e 37 133.029 89.710 80.176 1.00102.13 S ATOM 5168 SG CYS e 40 134.087 93.455 80.673 1.00102.33 S ATOM 7261 SG CYS f 37 111.121 118.655 17.814 1.00142.84 S ATOM 7282 SG CYS f 40 112.978 121.937 17.354 1.00141.64 S ATOM 9208 SG CYS g 37 148.227 49.657 40.139 1.00163.94 S ATOM 9229 SG CYS g 40 145.863 51.940 37.762 1.00168.87 S ATOM 11069 SG CYS h 37 102.110 70.175 55.288 1.00145.15 S ATOM 11090 SG CYS h 40 105.701 70.006 56.762 1.00142.88 S ATOM 15968 SG CYS A 37 35.450 78.283 86.746 1.00171.04 S ATOM 15989 SG CYS A 40 37.938 75.306 86.852 1.00170.83 S ATOM 18082 SG CYS B 37 58.337 71.714 18.663 1.00223.27 S ATOM 18103 SG CYS B 40 60.406 68.388 18.643 1.00222.73 S ATOM 20803 SG CYS E 37 81.401 54.308 61.881 1.00148.42 S ATOM 20824 SG CYS E 40 78.069 54.189 62.930 1.00150.52 S ATOM 22924 SG CYS F 37 65.713 78.131 129.403 1.00244.27 S ATOM 22945 SG CYS F 40 61.882 77.353 129.916 1.00241.79 S ATOM 24816 SG CYS G 37 116.924 22.712 96.881 1.00208.80 S ATOM 24837 SG CYS G 40 115.546 25.412 99.277 1.00209.59 S ATOM 26670 SG CYS H 37 112.803 74.655 86.409 1.00178.82 S ATOM 26691 SG CYS H 40 110.378 72.151 84.664 1.00175.69 S Time building chain proxies: 6.39, per 1000 atoms: 0.20 Number of scatterers: 31319 At special positions: 0 Unit cell: (191.26, 168.99, 146.72, 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 12 29.99 S 108 16.00 P 294 15.00 O 6128 8.00 N 5707 7.00 C 19070 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: 1.93 Conformation dependent library (CDL) restraints added in 971.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 13 " pdb="ZN ZN A 500 " - pdb=" NE2 HIS A 9 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 37 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 13 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 9 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 13 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 9 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 37 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 40 " pdb=" ZN F 500 " pdb="ZN ZN F 500 " - pdb=" NE2 HIS F 9 " pdb="ZN ZN F 500 " - pdb=" ND1 HIS F 13 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 37 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 40 " pdb=" ZN G 500 " pdb="ZN ZN G 500 " - pdb=" NE2 HIS G 9 " pdb="ZN ZN G 500 " - pdb=" NE2 HIS G 13 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 37 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 40 " pdb=" ZN H 500 " pdb="ZN ZN H 500 " - pdb=" ND1 HIS H 13 " pdb="ZN ZN H 500 " - pdb=" NE2 HIS H 9 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 40 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 37 " pdb=" ZN a 500 " pdb="ZN ZN a 500 " - pdb=" NE2 HIS a 9 " pdb="ZN ZN a 500 " - pdb=" ND1 HIS a 13 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 40 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 37 " pdb=" ZN b 500 " pdb="ZN ZN b 500 " - pdb=" SG CYS b 37 " pdb="ZN ZN b 500 " - pdb=" ND1 HIS b 13 " pdb="ZN ZN b 500 " - pdb=" SG CYS b 40 " pdb="ZN ZN b 500 " - pdb=" NE2 HIS b 9 " pdb=" ZN e 500 " pdb="ZN ZN e 500 " - pdb=" SG CYS e 40 " pdb="ZN ZN e 500 " - pdb=" NE2 HIS e 13 " pdb="ZN ZN e 500 " - pdb=" NE2 HIS e 9 " pdb="ZN ZN e 500 " - pdb=" SG CYS e 37 " pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" ND1 HIS f 13 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 37 " pdb="ZN ZN f 500 " - pdb=" NE2 HIS f 9 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 40 " pdb=" ZN g 500 " pdb="ZN ZN g 500 " - pdb=" NE2 HIS g 9 " pdb="ZN ZN g 500 " - pdb=" ND1 HIS g 13 " pdb="ZN ZN g 500 " - pdb=" SG CYS g 37 " pdb="ZN ZN g 500 " - pdb=" SG CYS g 40 " pdb=" ZN h 500 " pdb="ZN ZN h 500 " - pdb=" ND1 HIS h 13 " pdb="ZN ZN h 500 " - pdb=" NE2 HIS h 9 " pdb="ZN ZN h 500 " - pdb=" SG CYS h 40 " pdb="ZN ZN h 500 " - pdb=" SG CYS h 37 " Number of angles added : 21 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5974 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 33 sheets defined 43.6% alpha, 17.6% beta 112 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'a' and resid 1 through 13 Processing helix chain 'a' and resid 15 through 24 Processing helix chain 'a' and resid 26 through 37 removed outlier: 3.520A pdb=" N CYS a 37 " --> pdb=" O ILE a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 75 removed outlier: 6.946A pdb=" N LYS a 74 " --> pdb=" O GLU a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 98 through 113 Processing helix chain 'a' and resid 124 through 128 Processing helix chain 'a' and resid 129 through 139 Processing helix chain 'a' and resid 150 through 153 Processing helix chain 'a' and resid 154 through 175 Processing helix chain 'a' and resid 179 through 194 Processing helix chain 'a' and resid 202 through 209 Processing helix chain 'a' and resid 257 through 261 Processing helix chain 'b' and resid 2 through 13 Processing helix chain 'b' and resid 15 through 23 removed outlier: 3.552A pdb=" N LEU b 19 " --> pdb=" O ASN b 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 37 Processing helix chain 'b' and resid 70 through 73 Processing helix chain 'b' and resid 98 through 114 Processing helix chain 'b' and resid 124 through 129 Processing helix chain 'b' and resid 129 through 139 removed outlier: 3.606A pdb=" N TRP b 139 " --> pdb=" O PHE b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 154 through 172 Processing helix chain 'b' and resid 179 through 194 Processing helix chain 'b' and resid 202 through 209 Processing helix chain 'd' and resid 259 through 261 No H-bonds generated for 'chain 'd' and resid 259 through 261' Processing helix chain 'e' and resid 2 through 13 Processing helix chain 'e' and resid 15 through 24 Processing helix chain 'e' and resid 26 through 37 removed outlier: 3.751A pdb=" N CYS e 37 " --> pdb=" O ILE e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 70 through 75 removed outlier: 6.774A pdb=" N LYS e 74 " --> pdb=" O GLU e 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 113 Processing helix chain 'e' and resid 124 through 129 Processing helix chain 'e' and resid 129 through 139 removed outlier: 3.680A pdb=" N GLN e 133 " --> pdb=" O SER e 129 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 153 Processing helix chain 'e' and resid 154 through 175 Processing helix chain 'e' and resid 179 through 194 Processing helix chain 'e' and resid 202 through 208 Processing helix chain 'e' and resid 257 through 259 No H-bonds generated for 'chain 'e' and resid 257 through 259' Processing helix chain 'f' and resid 2 through 13 Processing helix chain 'f' and resid 15 through 23 removed outlier: 3.598A pdb=" N LEU f 19 " --> pdb=" O ASN f 15 " (cutoff:3.500A) Processing helix chain 'f' and resid 26 through 36 Processing helix chain 'f' and resid 98 through 114 Processing helix chain 'f' and resid 124 through 129 Processing helix chain 'f' and resid 129 through 139 Processing helix chain 'f' and resid 156 through 172 Processing helix chain 'f' and resid 179 through 194 removed outlier: 3.514A pdb=" N LEU f 183 " --> pdb=" O THR f 179 " (cutoff:3.500A) Processing helix chain 'f' and resid 202 through 209 removed outlier: 3.565A pdb=" N ARG f 206 " --> pdb=" O THR f 202 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 13 Processing helix chain 'g' and resid 15 through 24 removed outlier: 3.862A pdb=" N LEU g 19 " --> pdb=" O ASN g 15 " (cutoff:3.500A) Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 70 through 75 removed outlier: 3.755A pdb=" N GLY g 73 " --> pdb=" O SER g 70 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS g 74 " --> pdb=" O GLU g 71 " (cutoff:3.500A) Processing helix chain 'g' and resid 98 through 113 Processing helix chain 'g' and resid 129 through 139 Processing helix chain 'g' and resid 156 through 172 Processing helix chain 'g' and resid 173 through 175 No H-bonds generated for 'chain 'g' and resid 173 through 175' Processing helix chain 'g' and resid 179 through 193 Processing helix chain 'g' and resid 202 through 207 Processing helix chain 'h' and resid 4 through 13 Processing helix chain 'h' and resid 15 through 23 Processing helix chain 'h' and resid 26 through 37 Processing helix chain 'h' and resid 72 through 75 Processing helix chain 'h' and resid 98 through 114 Processing helix chain 'h' and resid 129 through 139 removed outlier: 3.609A pdb=" N TRP h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 155 through 171 Processing helix chain 'h' and resid 179 through 194 removed outlier: 3.540A pdb=" N LEU h 183 " --> pdb=" O THR h 179 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL h 194 " --> pdb=" O VAL h 190 " (cutoff:3.500A) Processing helix chain 'h' and resid 202 through 208 Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 15 through 24 removed outlier: 3.524A pdb=" N LEU A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.823A pdb=" N CYS A 37 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 removed outlier: 3.619A pdb=" N GLY A 73 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 75 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 129 through 140 removed outlier: 3.572A pdb=" N GLN A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 154 through 175 Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 15 through 23 Processing helix chain 'B' and resid 26 through 37 Processing helix chain 'B' and resid 98 through 114 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 15 through 24 Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.505A pdb=" N CYS E 37 " --> pdb=" O ILE E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 75 removed outlier: 6.228A pdb=" N LYS E 74 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 129 through 139 Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 154 through 175 Processing helix chain 'E' and resid 179 through 194 Processing helix chain 'E' and resid 202 through 209 Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 15 through 24 removed outlier: 3.537A pdb=" N LEU F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.571A pdb=" N CYS F 37 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 114 Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 129 through 139 Processing helix chain 'F' and resid 155 through 172 Processing helix chain 'F' and resid 179 through 194 removed outlier: 3.604A pdb=" N LEU F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 209 Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'G' and resid 15 through 24 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 70 through 75 removed outlier: 3.807A pdb=" N GLY G 73 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS G 74 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 114 Processing helix chain 'G' and resid 129 through 139 Processing helix chain 'G' and resid 156 through 173 removed outlier: 4.728A pdb=" N LYS G 173 " --> pdb=" O ASN G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 194 removed outlier: 3.777A pdb=" N VAL G 194 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 208 Processing helix chain 'H' and resid 3 through 13 Processing helix chain 'H' and resid 15 through 24 Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 70 through 75 removed outlier: 6.874A pdb=" N LYS H 74 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 114 Processing helix chain 'H' and resid 129 through 139 Processing helix chain 'H' and resid 155 through 171 Processing helix chain 'H' and resid 179 through 194 removed outlier: 3.646A pdb=" N VAL H 194 " --> pdb=" O VAL H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 208 Processing sheet with id=AA1, first strand: chain 'a' and resid 91 through 93 removed outlier: 3.758A pdb=" N VAL a 78 " --> pdb=" O THR a 67 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TRP a 62 " --> pdb=" O LYS a 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 218 through 219 removed outlier: 4.369A pdb=" N VAL a 234 " --> pdb=" O PHE a 246 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N CYS a 244 " --> pdb=" O ILE a 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 222 through 223 Processing sheet with id=AA4, first strand: chain 'b' and resid 89 through 94 removed outlier: 3.649A pdb=" N TYR b 77 " --> pdb=" O ARG b 94 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP b 65 " --> pdb=" O VAL b 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 254 through 257 removed outlier: 3.942A pdb=" N THR b 237 " --> pdb=" O CYS b 244 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE b 246 " --> pdb=" O LEU b 235 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU b 235 " --> pdb=" O PHE b 246 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG b 262 " --> pdb=" O MET b 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 254 through 257 removed outlier: 3.677A pdb=" N THR c 237 " --> pdb=" O CYS c 244 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP c 233 " --> pdb=" O VAL c 219 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL c 219 " --> pdb=" O ASP c 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'd' and resid 219 through 222 removed outlier: 7.263A pdb=" N TRP d 221 " --> pdb=" O GLY d 231 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY d 231 " --> pdb=" O TRP d 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 235 through 237 removed outlier: 4.033A pdb=" N THR d 237 " --> pdb=" O CYS d 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 89 through 93 removed outlier: 3.738A pdb=" N VAL e 78 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP e 62 " --> pdb=" O LYS e 120 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE e 119 " --> pdb=" O VAL e 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'e' and resid 254 through 256 removed outlier: 6.667A pdb=" N CYS e 244 " --> pdb=" O ILE e 236 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL e 234 " --> pdb=" O PHE e 246 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER e 228 " --> pdb=" O ASP e 223 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL e 219 " --> pdb=" O PRO e 232 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 89 through 94 removed outlier: 3.595A pdb=" N TYR f 77 " --> pdb=" O ARG f 94 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TRP f 62 " --> pdb=" O LYS f 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 254 through 257 removed outlier: 6.699A pdb=" N TYR f 242 " --> pdb=" O ALA f 238 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA f 238 " --> pdb=" O TYR f 242 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS f 244 " --> pdb=" O ILE f 236 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL f 234 " --> pdb=" O PHE f 246 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG f 262 " --> pdb=" O MET f 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'g' and resid 89 through 94 removed outlier: 3.606A pdb=" N TYR g 77 " --> pdb=" O ARG g 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP g 65 " --> pdb=" O VAL g 80 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TRP g 62 " --> pdb=" O LYS g 120 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE g 119 " --> pdb=" O VAL g 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'g' and resid 254 through 257 removed outlier: 4.061A pdb=" N THR g 237 " --> pdb=" O CYS g 244 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE g 246 " --> pdb=" O LEU g 235 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU g 235 " --> pdb=" O PHE g 246 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'h' and resid 89 through 94 removed outlier: 3.648A pdb=" N TYR h 77 " --> pdb=" O ARG h 94 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TRP h 62 " --> pdb=" O LYS h 120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 254 through 257 removed outlier: 3.666A pdb=" N TYR h 242 " --> pdb=" O GLY h 239 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR h 237 " --> pdb=" O CYS h 244 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE h 246 " --> pdb=" O LEU h 235 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU h 235 " --> pdb=" O PHE h 246 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLY h 231 " --> pdb=" O TRP h 221 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TRP h 221 " --> pdb=" O GLY h 231 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 89 through 93 removed outlier: 3.535A pdb=" N HIS A 79 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TRP A 62 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.587A pdb=" N SER A 228 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS A 244 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 238 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.587A pdb=" N SER A 228 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 89 through 94 removed outlier: 3.581A pdb=" N TYR B 77 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 78 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TRP B 62 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 254 through 257 removed outlier: 3.546A pdb=" N THR B 237 " --> pdb=" O CYS B 244 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE B 246 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU B 235 " --> pdb=" O PHE B 246 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 245 through 246 removed outlier: 3.962A pdb=" N VAL C 234 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL C 219 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AC6, first strand: chain 'D' and resid 254 through 257 Processing sheet with id=AC7, first strand: chain 'E' and resid 89 through 93 removed outlier: 3.707A pdb=" N HIS E 79 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL E 78 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP E 62 " --> pdb=" O LYS E 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 254 through 256 removed outlier: 6.606A pdb=" N CYS E 244 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL E 234 " --> pdb=" O PHE E 246 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 219 " --> pdb=" O ASP E 233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 89 through 94 removed outlier: 3.704A pdb=" N TYR F 77 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP F 65 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TRP F 62 " --> pdb=" O LYS F 120 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE F 119 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 256 through 257 removed outlier: 3.888A pdb=" N THR F 237 " --> pdb=" O CYS F 244 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE F 246 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU F 235 " --> pdb=" O PHE F 246 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL F 219 " --> pdb=" O PRO F 232 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 89 through 94 removed outlier: 3.627A pdb=" N TYR G 77 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL G 80 " --> pdb=" O ASP G 65 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TRP G 62 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE G 119 " --> pdb=" O VAL G 144 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 254 through 257 removed outlier: 6.561A pdb=" N TYR G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA G 238 " --> pdb=" O TYR G 242 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS G 244 " --> pdb=" O ILE G 236 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL G 234 " --> pdb=" O PHE G 246 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLY G 231 " --> pdb=" O TRP G 221 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TRP G 221 " --> pdb=" O GLY G 231 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 67 through 68 removed outlier: 4.127A pdb=" N TYR H 77 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS H 79 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR H 92 " --> pdb=" O HIS H 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 67 through 68 removed outlier: 6.428A pdb=" N TRP H 62 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 254 through 257 removed outlier: 3.625A pdb=" N TYR H 242 " --> pdb=" O GLY H 239 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR H 237 " --> pdb=" O CYS H 244 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE H 246 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU H 235 " --> pdb=" O PHE H 246 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL H 219 " --> pdb=" O PRO H 232 " (cutoff:3.500A) 1159 hydrogen bonds defined for protein. 3294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 279 hydrogen bonds 538 hydrogen bond angles 0 basepair planarities 112 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 6.14 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9085 1.34 - 1.46: 9510 1.46 - 1.58: 13460 1.58 - 1.71: 580 1.71 - 1.83: 176 Bond restraints: 32811 Sorted by residual: bond pdb=" CG PRO d 232 " pdb=" CD PRO d 232 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.25e+00 bond pdb=" CB LYS E 74 " pdb=" CG LYS E 74 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CG GLU E 7 " pdb=" CD GLU E 7 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" CG LYS E 74 " pdb=" CD LYS E 74 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CG PRO D 232 " pdb=" CD PRO D 232 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.07e+00 ... (remaining 32806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 44930 1.73 - 3.46: 821 3.46 - 5.19: 64 5.19 - 6.92: 22 6.92 - 8.66: 8 Bond angle restraints: 45845 Sorted by residual: angle pdb=" N PRO f 210 " pdb=" CA PRO f 210 " pdb=" C PRO f 210 " ideal model delta sigma weight residual 114.68 110.86 3.82 1.04e+00 9.25e-01 1.35e+01 angle pdb=" CA ASP G 249 " pdb=" CB ASP G 249 " pdb=" CG ASP G 249 " ideal model delta sigma weight residual 112.60 108.93 3.67 1.00e+00 1.00e+00 1.35e+01 angle pdb=" N GLU f 32 " pdb=" CA GLU f 32 " pdb=" CB GLU f 32 " ideal model delta sigma weight residual 110.28 115.83 -5.55 1.55e+00 4.16e-01 1.28e+01 angle pdb=" N GLU E 7 " pdb=" CA GLU E 7 " pdb=" CB GLU E 7 " ideal model delta sigma weight residual 110.39 116.30 -5.91 1.66e+00 3.63e-01 1.27e+01 angle pdb=" C GLN E 6 " pdb=" N GLU E 7 " pdb=" CA GLU E 7 " ideal model delta sigma weight residual 120.72 115.24 5.48 1.67e+00 3.59e-01 1.08e+01 ... (remaining 45840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.34: 16508 28.34 - 56.68: 1751 56.68 - 85.02: 165 85.02 - 113.36: 7 113.36 - 141.70: 2 Dihedral angle restraints: 18433 sinusoidal: 9259 harmonic: 9174 Sorted by residual: dihedral pdb=" CA TYR H 112 " pdb=" C TYR H 112 " pdb=" N MET H 113 " pdb=" CA MET H 113 " ideal model delta harmonic sigma weight residual 180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA MET d 218 " pdb=" C MET d 218 " pdb=" N VAL d 219 " pdb=" CA VAL d 219 " ideal model delta harmonic sigma weight residual -180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA MET a 218 " pdb=" C MET a 218 " pdb=" N VAL a 219 " pdb=" CA VAL a 219 " ideal model delta harmonic sigma weight residual 180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 18430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4092 0.047 - 0.095: 735 0.095 - 0.142: 150 0.142 - 0.189: 6 0.189 - 0.236: 1 Chirality restraints: 4984 Sorted by residual: chirality pdb=" CB ILE a 211 " pdb=" CA ILE a 211 " pdb=" CG1 ILE a 211 " pdb=" CG2 ILE a 211 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB ILE G 115 " pdb=" CA ILE G 115 " pdb=" CG1 ILE G 115 " pdb=" CG2 ILE G 115 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CB VAL g 194 " pdb=" CA VAL g 194 " pdb=" CG1 VAL g 194 " pdb=" CG2 VAL g 194 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 4981 not shown) Planarity restraints: 4812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 13 " 0.021 2.00e-02 2.50e+03 2.73e-02 1.12e+01 pdb=" CG HIS E 13 " -0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS E 13 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 HIS E 13 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS E 13 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS E 13 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 115 " 0.047 5.00e-02 4.00e+02 7.07e-02 7.99e+00 pdb=" N PRO H 116 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO H 116 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 116 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 13 " 0.021 2.00e-02 2.50e+03 1.80e-02 4.84e+00 pdb=" CG HIS G 13 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS G 13 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS G 13 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS G 13 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS G 13 " 0.014 2.00e-02 2.50e+03 ... (remaining 4809 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1076 2.70 - 3.25: 30589 3.25 - 3.80: 55890 3.80 - 4.35: 68488 4.35 - 4.90: 105990 Nonbonded interactions: 262033 Sorted by model distance: nonbonded pdb=" OD1 ASN A 123 " pdb=" OG1 THR A 145 " model vdw 2.148 3.040 nonbonded pdb=" O ALA E 1 " pdb=" OG SER E 4 " model vdw 2.167 3.040 nonbonded pdb=" CG HIS E 13 " pdb="ZN ZN E 500 " model vdw 2.170 1.960 nonbonded pdb=" O ALA e 1 " pdb=" OG SER e 4 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR c 242 " pdb=" OP1 DG l 10 " model vdw 2.200 3.040 ... (remaining 262028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 155 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 208 or resid 218 through 500)) selection = (chain 'B' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 through 155 \ and (name N or name CA or name C or name O or name CB )) or resid 156 through 1 \ 61 or (resid 162 and (name N or name CA or name C or name O or name CB )) or res \ id 163 through 172 or (resid 173 and (name N or name CA or name C or name O or n \ ame CB )) or resid 177 through 208 or resid 218 through 264 or resid 500)) selection = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 155 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 208 or resid 218 through 264 or resid 500)) selection = (chain 'F' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 155 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 208 or resid 218 through 500)) selection = (chain 'G' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 through 155 \ and (name N or name CA or name C or name O or name CB )) or resid 156 through 1 \ 72 or (resid 173 and (name N or name CA or name C or name O or name CB )) or res \ id 177 through 208 or resid 218 through 500)) selection = (chain 'H' and (resid 2 through 144 or resid 155 through 161 or (resid 162 and ( \ name N or name CA or name C or name O or name CB )) or resid 163 through 208 or \ resid 218 through 264 or resid 500)) selection = (chain 'a' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 155 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 208 or resid 218 through 500)) selection = (chain 'b' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 155 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 208 or resid 218 through 500)) selection = (chain 'e' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 155 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 208 or resid 218 through 500)) selection = (chain 'f' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 155 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 208 or resid 218 through 264 or resid 500)) selection = (chain 'g' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 155 through 172 or (resid \ 173 and (name N or name CA or name C or name O or name CB )) or resid 177 throu \ gh 208 or resid 218 through 500)) selection = (chain 'h' and (resid 2 through 144 or resid 155 through 161 or (resid 162 and ( \ name N or name CA or name C or name O or name CB )) or resid 163 through 208 or \ resid 218 through 264 or resid 500)) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 217 through 264) selection = chain 'c' selection = (chain 'd' and resid 217 through 264) } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'i' selection = chain 'l' } ncs_group { reference = (chain 'J' and resid 1 through 38) selection = (chain 'M' and resid 1 through 38) selection = (chain 'j' and resid 1 through 38) selection = chain 'm' } ncs_group { reference = (chain 'K' and resid 5 through 16) selection = (chain 'N' and resid 5 through 16) selection = (chain 'k' and resid 5 through 16) selection = chain 'n' } 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.830 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.008 0.590 32859 Z= 0.273 Angle : 0.633 54.304 45866 Z= 0.312 Chirality : 0.038 0.236 4984 Planarity : 0.004 0.071 4812 Dihedral : 20.160 141.704 12459 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.17 (0.16), residues: 3069 helix: 1.16 (0.15), residues: 1195 sheet: 0.07 (0.22), residues: 586 loop : -0.82 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 138 TYR 0.012 0.001 TYR e 242 PHE 0.013 0.001 PHE H 88 TRP 0.021 0.001 TRP b 208 HIS 0.034 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00303 (32811) covalent geometry : angle 0.55241 (45845) hydrogen bonds : bond 0.21837 ( 1435) hydrogen bonds : angle 8.48241 ( 3832) metal coordination : bond 0.20363 ( 48) metal coordination : angle 14.47705 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 218 MET cc_start: 0.8184 (tpt) cc_final: 0.7885 (tpt) REVERT: f 113 MET cc_start: 0.8611 (mtm) cc_final: 0.8287 (mtp) REVERT: f 220 MET cc_start: 0.8848 (mmm) cc_final: 0.8094 (tpp) REVERT: g 32 GLU cc_start: 0.9155 (mp0) cc_final: 0.8793 (mp0) REVERT: A 39 ASN cc_start: 0.8221 (m-40) cc_final: 0.7824 (t0) REVERT: A 113 MET cc_start: 0.7939 (mtm) cc_final: 0.7452 (mtt) REVERT: B 7 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9265 (mt-10) REVERT: B 32 GLU cc_start: 0.9461 (tp30) cc_final: 0.9256 (tp30) REVERT: B 244 CYS cc_start: 0.8835 (t) cc_final: 0.8502 (t) REVERT: C 223 ASP cc_start: 0.7780 (t0) cc_final: 0.7471 (t0) REVERT: C 230 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8350 (mmmt) REVERT: F 7 GLU cc_start: 0.9333 (mp0) cc_final: 0.9106 (mp0) REVERT: F 15 ASN cc_start: 0.6600 (p0) cc_final: 0.6260 (p0) REVERT: F 64 MET cc_start: 0.7586 (mmm) cc_final: 0.7067 (mmt) REVERT: F 77 TYR cc_start: 0.8982 (m-80) cc_final: 0.8493 (m-80) REVERT: F 169 ASN cc_start: 0.9137 (m110) cc_final: 0.8651 (m110) REVERT: F 177 TYR cc_start: 0.7430 (m-80) cc_final: 0.7205 (m-80) REVERT: F 195 ASN cc_start: 0.7459 (m-40) cc_final: 0.7050 (m110) REVERT: F 205 GLU cc_start: 0.8348 (tt0) cc_final: 0.7995 (tt0) REVERT: F 208 TRP cc_start: 0.8137 (m100) cc_final: 0.7645 (m100) REVERT: G 7 GLU cc_start: 0.9117 (mp0) cc_final: 0.8483 (mp0) REVERT: G 134 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8279 (tm-30) REVERT: G 252 SER cc_start: 0.8996 (p) cc_final: 0.8679 (p) REVERT: H 123 ASN cc_start: 0.8147 (m-40) cc_final: 0.7862 (m-40) REVERT: H 242 TYR cc_start: 0.8832 (p90) cc_final: 0.8441 (p90) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1813 time to fit residues: 78.6195 Evaluate side-chains 209 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 0.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 20.0000 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 12 HIS a 193 HIS b 163 ASN ** b 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 ASN e 161 HIS ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS B 195 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN F 12 HIS F 193 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.066709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.047527 restraints weight = 145597.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.048831 restraints weight = 72774.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.049684 restraints weight = 48037.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.050227 restraints weight = 37395.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.050528 restraints weight = 32126.327| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 32859 Z= 0.287 Angle : 0.668 12.440 45866 Z= 0.365 Chirality : 0.043 0.185 4984 Planarity : 0.005 0.048 4812 Dihedral : 22.953 144.686 6532 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.57 % Allowed : 7.46 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: -0.04 (0.16), residues: 3069 helix: 0.96 (0.15), residues: 1227 sheet: 0.04 (0.22), residues: 618 loop : -1.02 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG h 20 TYR 0.019 0.002 TYR A 112 PHE 0.015 0.002 PHE H 88 TRP 0.018 0.002 TRP b 208 HIS 0.018 0.002 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00628 (32811) covalent geometry : angle 0.65954 (45845) hydrogen bonds : bond 0.05597 ( 1435) hydrogen bonds : angle 5.78748 ( 3832) metal coordination : bond 0.02182 ( 48) metal coordination : angle 5.07948 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 MET cc_start: 0.8378 (mmm) cc_final: 0.7991 (mmm) REVERT: d 218 MET cc_start: 0.8323 (tpt) cc_final: 0.7977 (tpt) REVERT: e 52 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8582 (m110) REVERT: f 77 TYR cc_start: 0.8176 (m-80) cc_final: 0.7869 (m-80) REVERT: f 113 MET cc_start: 0.8648 (mtm) cc_final: 0.8213 (mtp) REVERT: f 220 MET cc_start: 0.8591 (mmm) cc_final: 0.8185 (tpp) REVERT: g 32 GLU cc_start: 0.9198 (mp0) cc_final: 0.8756 (mp0) REVERT: g 220 MET cc_start: 0.8588 (mmm) cc_final: 0.8122 (mmm) REVERT: A 39 ASN cc_start: 0.8231 (m-40) cc_final: 0.7846 (m-40) REVERT: A 169 ASN cc_start: 0.9197 (t0) cc_final: 0.8909 (t0) REVERT: B 32 GLU cc_start: 0.9459 (tp30) cc_final: 0.9238 (tp30) REVERT: B 113 MET cc_start: 0.8877 (tpp) cc_final: 0.8586 (tpt) REVERT: B 196 MET cc_start: 0.8267 (tpp) cc_final: 0.7775 (tpp) REVERT: B 220 MET cc_start: 0.7151 (tpp) cc_final: 0.6731 (tpp) REVERT: C 223 ASP cc_start: 0.7563 (t0) cc_final: 0.7272 (t0) REVERT: E 28 GLU cc_start: 0.8857 (mp0) cc_final: 0.8646 (mp0) REVERT: F 7 GLU cc_start: 0.9318 (mp0) cc_final: 0.9075 (mp0) REVERT: F 64 MET cc_start: 0.7610 (mmm) cc_final: 0.7093 (mmt) REVERT: F 77 TYR cc_start: 0.9028 (m-80) cc_final: 0.8546 (m-80) REVERT: F 169 ASN cc_start: 0.9277 (m110) cc_final: 0.8797 (m110) REVERT: F 195 ASN cc_start: 0.7758 (m-40) cc_final: 0.7241 (m110) REVERT: F 205 GLU cc_start: 0.8411 (tt0) cc_final: 0.8092 (tt0) REVERT: F 220 MET cc_start: 0.8505 (tpp) cc_final: 0.7570 (tpp) REVERT: G 7 GLU cc_start: 0.9348 (mp0) cc_final: 0.8766 (mp0) REVERT: G 134 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8218 (tm-30) REVERT: H 15 ASN cc_start: 0.8586 (p0) cc_final: 0.8194 (p0) REVERT: H 158 GLU cc_start: 0.7860 (mp0) cc_final: 0.7600 (mp0) REVERT: H 242 TYR cc_start: 0.8752 (p90) cc_final: 0.8541 (p90) outliers start: 15 outliers final: 9 residues processed: 243 average time/residue: 0.1720 time to fit residues: 71.2673 Evaluate side-chains 222 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 52 ASN Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 7 GLU Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 242 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 223 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 268 optimal weight: 30.0000 chunk 278 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 GLN B 133 GLN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.068614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.049269 restraints weight = 142575.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050650 restraints weight = 69019.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051568 restraints weight = 44745.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.052128 restraints weight = 34340.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052511 restraints weight = 29214.167| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32859 Z= 0.138 Angle : 0.547 11.960 45866 Z= 0.301 Chirality : 0.038 0.134 4984 Planarity : 0.004 0.041 4812 Dihedral : 22.837 140.716 6532 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.64 % Allowed : 10.79 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.36 (0.16), residues: 3069 helix: 1.33 (0.15), residues: 1223 sheet: 0.17 (0.22), residues: 622 loop : -0.80 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 138 TYR 0.023 0.001 TYR a 112 PHE 0.012 0.001 PHE e 88 TRP 0.015 0.001 TRP b 208 HIS 0.013 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00301 (32811) covalent geometry : angle 0.54068 (45845) hydrogen bonds : bond 0.04530 ( 1435) hydrogen bonds : angle 5.18563 ( 3832) metal coordination : bond 0.01106 ( 48) metal coordination : angle 4.01816 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 249 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 MET cc_start: 0.8231 (mmm) cc_final: 0.7725 (mmm) REVERT: c 218 MET cc_start: 0.8592 (mmm) cc_final: 0.8261 (mmm) REVERT: d 218 MET cc_start: 0.8258 (tpt) cc_final: 0.7967 (tpp) REVERT: f 77 TYR cc_start: 0.8197 (m-80) cc_final: 0.7872 (m-80) REVERT: f 113 MET cc_start: 0.8469 (mtm) cc_final: 0.8252 (mtp) REVERT: f 220 MET cc_start: 0.8501 (mmm) cc_final: 0.8059 (tpp) REVERT: g 7 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8344 (tm-30) REVERT: g 218 MET cc_start: 0.8995 (mmp) cc_final: 0.8666 (mmp) REVERT: g 220 MET cc_start: 0.8670 (mmm) cc_final: 0.8440 (mmm) REVERT: A 39 ASN cc_start: 0.8183 (m-40) cc_final: 0.7841 (m-40) REVERT: A 62 TRP cc_start: 0.8174 (m-10) cc_final: 0.7952 (m-10) REVERT: A 134 GLU cc_start: 0.9025 (mp0) cc_final: 0.8734 (pm20) REVERT: A 205 GLU cc_start: 0.9113 (pp20) cc_final: 0.8748 (pp20) REVERT: B 32 GLU cc_start: 0.9497 (tp30) cc_final: 0.9286 (tp30) REVERT: B 64 MET cc_start: 0.8703 (ttp) cc_final: 0.8265 (ttm) REVERT: B 113 MET cc_start: 0.8942 (tpp) cc_final: 0.8655 (mmt) REVERT: B 196 MET cc_start: 0.8531 (tpp) cc_final: 0.8014 (tpp) REVERT: B 220 MET cc_start: 0.8031 (tpp) cc_final: 0.7796 (tpp) REVERT: C 218 MET cc_start: 0.7975 (ptt) cc_final: 0.7482 (mmp) REVERT: E 7 GLU cc_start: 0.8896 (pm20) cc_final: 0.8642 (pm20) REVERT: E 28 GLU cc_start: 0.8892 (mp0) cc_final: 0.8639 (mp0) REVERT: E 113 MET cc_start: 0.8137 (mtt) cc_final: 0.7755 (mpp) REVERT: F 7 GLU cc_start: 0.9229 (mp0) cc_final: 0.9019 (mp0) REVERT: F 15 ASN cc_start: 0.7024 (p0) cc_final: 0.6591 (p0) REVERT: F 64 MET cc_start: 0.7731 (mmm) cc_final: 0.7129 (mmt) REVERT: F 77 TYR cc_start: 0.8890 (m-80) cc_final: 0.8414 (m-80) REVERT: F 113 MET cc_start: 0.8958 (tpp) cc_final: 0.8576 (tpp) REVERT: F 169 ASN cc_start: 0.9233 (m110) cc_final: 0.8770 (m110) REVERT: F 177 TYR cc_start: 0.7799 (m-80) cc_final: 0.7580 (m-80) REVERT: F 195 ASN cc_start: 0.7583 (m-40) cc_final: 0.7167 (m110) REVERT: F 196 MET cc_start: 0.6410 (tmm) cc_final: 0.5781 (tmm) REVERT: F 205 GLU cc_start: 0.8359 (tt0) cc_final: 0.7999 (tt0) REVERT: F 220 MET cc_start: 0.8665 (tpp) cc_final: 0.7804 (tpp) REVERT: G 113 MET cc_start: 0.8231 (mtt) cc_final: 0.7864 (mtt) REVERT: G 134 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8203 (tm-30) REVERT: H 123 ASN cc_start: 0.8207 (m-40) cc_final: 0.7754 (m110) outliers start: 17 outliers final: 11 residues processed: 259 average time/residue: 0.1718 time to fit residues: 75.3985 Evaluate side-chains 229 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 218 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 51 VAL Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 34 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 4 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 201 optimal weight: 0.0050 chunk 161 optimal weight: 7.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 52 ASN ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.067734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.048615 restraints weight = 142226.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.049953 restraints weight = 70678.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.050813 restraints weight = 46368.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.051360 restraints weight = 35964.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.051720 restraints weight = 30735.824| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32859 Z= 0.188 Angle : 0.568 8.178 45866 Z= 0.311 Chirality : 0.039 0.133 4984 Planarity : 0.004 0.041 4812 Dihedral : 22.824 142.167 6532 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.48 % Allowed : 13.32 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.31 (0.16), residues: 3069 helix: 1.29 (0.15), residues: 1226 sheet: 0.07 (0.21), residues: 657 loop : -0.79 (0.19), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 138 TYR 0.018 0.001 TYR D 242 PHE 0.010 0.001 PHE g 189 TRP 0.018 0.001 TRP E 221 HIS 0.010 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00414 (32811) covalent geometry : angle 0.56356 (45845) hydrogen bonds : bond 0.04551 ( 1435) hydrogen bonds : angle 5.08282 ( 3832) metal coordination : bond 0.01101 ( 48) metal coordination : angle 3.41082 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 MET cc_start: 0.8196 (mmm) cc_final: 0.7682 (mmm) REVERT: d 218 MET cc_start: 0.8164 (tpt) cc_final: 0.7853 (tpt) REVERT: f 77 TYR cc_start: 0.8197 (m-80) cc_final: 0.7904 (m-80) REVERT: f 113 MET cc_start: 0.8501 (mtm) cc_final: 0.8265 (mtp) REVERT: f 220 MET cc_start: 0.8446 (mmm) cc_final: 0.8029 (tpp) REVERT: g 7 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8391 (tm-30) REVERT: g 32 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.9050 (mm-30) REVERT: g 218 MET cc_start: 0.9009 (mmp) cc_final: 0.8703 (mmp) REVERT: g 220 MET cc_start: 0.8557 (mmm) cc_final: 0.8224 (mmm) REVERT: A 39 ASN cc_start: 0.8199 (m-40) cc_final: 0.7875 (m-40) REVERT: A 62 TRP cc_start: 0.8266 (m-10) cc_final: 0.8033 (m-10) REVERT: A 134 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8757 (pp20) REVERT: A 205 GLU cc_start: 0.9122 (pp20) cc_final: 0.8713 (pp20) REVERT: A 220 MET cc_start: 0.8640 (tpp) cc_final: 0.8076 (tpp) REVERT: B 28 GLU cc_start: 0.9181 (mp0) cc_final: 0.8853 (pm20) REVERT: B 32 GLU cc_start: 0.9467 (tp30) cc_final: 0.9260 (tp30) REVERT: B 113 MET cc_start: 0.8997 (tpp) cc_final: 0.8766 (mmt) REVERT: B 196 MET cc_start: 0.8793 (tpp) cc_final: 0.8336 (tpp) REVERT: B 220 MET cc_start: 0.8117 (tpp) cc_final: 0.7750 (tpp) REVERT: C 218 MET cc_start: 0.8047 (ptt) cc_final: 0.7413 (mmp) REVERT: D 228 SER cc_start: 0.8990 (p) cc_final: 0.8235 (p) REVERT: D 230 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7698 (mmmt) REVERT: E 7 GLU cc_start: 0.8936 (pm20) cc_final: 0.8728 (pm20) REVERT: E 28 GLU cc_start: 0.8918 (mp0) cc_final: 0.8660 (mp0) REVERT: F 15 ASN cc_start: 0.6883 (p0) cc_final: 0.6424 (p0) REVERT: F 64 MET cc_start: 0.7649 (mmm) cc_final: 0.6788 (mmt) REVERT: F 77 TYR cc_start: 0.8871 (m-80) cc_final: 0.8387 (m-80) REVERT: F 169 ASN cc_start: 0.9276 (m110) cc_final: 0.8807 (m110) REVERT: F 177 TYR cc_start: 0.7718 (m-80) cc_final: 0.7477 (m-80) REVERT: F 195 ASN cc_start: 0.7732 (m-40) cc_final: 0.7258 (m110) REVERT: F 196 MET cc_start: 0.6577 (tmm) cc_final: 0.5834 (tmm) REVERT: F 205 GLU cc_start: 0.8364 (tt0) cc_final: 0.7989 (tt0) REVERT: F 220 MET cc_start: 0.8898 (tpp) cc_final: 0.8268 (tpp) REVERT: G 113 MET cc_start: 0.8221 (mtt) cc_final: 0.7887 (mtt) REVERT: G 134 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8249 (tm-30) REVERT: H 71 GLU cc_start: 0.8448 (pm20) cc_final: 0.8240 (pm20) REVERT: H 123 ASN cc_start: 0.8317 (m-40) cc_final: 0.7837 (m110) REVERT: H 134 GLU cc_start: 0.8672 (pt0) cc_final: 0.8437 (pp20) outliers start: 39 outliers final: 28 residues processed: 254 average time/residue: 0.1639 time to fit residues: 71.6383 Evaluate side-chains 247 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 64 MET Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 161 HIS Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain H residue 34 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 289 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 213 optimal weight: 0.0670 chunk 122 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.0970 chunk 147 optimal weight: 2.9990 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 143 HIS A 152 GLN B 104 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.069581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050568 restraints weight = 142218.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.051965 restraints weight = 69673.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052877 restraints weight = 45062.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.053455 restraints weight = 34561.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.053755 restraints weight = 29428.589| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32859 Z= 0.122 Angle : 0.527 8.335 45866 Z= 0.289 Chirality : 0.038 0.149 4984 Planarity : 0.003 0.043 4812 Dihedral : 22.772 139.066 6532 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.17 % Allowed : 14.57 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.61 (0.16), residues: 3069 helix: 1.52 (0.15), residues: 1225 sheet: 0.31 (0.22), residues: 606 loop : -0.63 (0.19), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 138 TYR 0.020 0.001 TYR D 242 PHE 0.009 0.001 PHE c 260 TRP 0.015 0.001 TRP b 208 HIS 0.008 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00265 (32811) covalent geometry : angle 0.52286 (45845) hydrogen bonds : bond 0.04067 ( 1435) hydrogen bonds : angle 4.83694 ( 3832) metal coordination : bond 0.01011 ( 48) metal coordination : angle 3.14692 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 MET cc_start: 0.8185 (mmm) cc_final: 0.7808 (mmm) REVERT: b 64 MET cc_start: 0.8942 (mtm) cc_final: 0.8615 (mtt) REVERT: e 130 ARG cc_start: 0.8392 (ptp90) cc_final: 0.7958 (ptp90) REVERT: e 134 GLU cc_start: 0.8714 (pm20) cc_final: 0.8489 (pm20) REVERT: f 77 TYR cc_start: 0.7958 (m-80) cc_final: 0.7670 (m-80) REVERT: f 220 MET cc_start: 0.8361 (mmm) cc_final: 0.8007 (tpp) REVERT: g 7 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8357 (tm-30) REVERT: g 218 MET cc_start: 0.9020 (mmp) cc_final: 0.8720 (mmp) REVERT: g 220 MET cc_start: 0.8641 (mmm) cc_final: 0.8354 (mmm) REVERT: A 39 ASN cc_start: 0.8124 (m-40) cc_final: 0.7756 (m-40) REVERT: A 68 HIS cc_start: 0.8240 (m90) cc_final: 0.7665 (m-70) REVERT: A 134 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8687 (pp20) REVERT: A 205 GLU cc_start: 0.9099 (pp20) cc_final: 0.8577 (pp20) REVERT: A 220 MET cc_start: 0.8762 (tpp) cc_final: 0.8127 (tpp) REVERT: B 28 GLU cc_start: 0.9161 (mp0) cc_final: 0.8824 (pm20) REVERT: B 32 GLU cc_start: 0.9463 (tp30) cc_final: 0.9248 (tp30) REVERT: B 64 MET cc_start: 0.8762 (ttm) cc_final: 0.8518 (ttm) REVERT: B 113 MET cc_start: 0.9011 (tpp) cc_final: 0.8767 (mmt) REVERT: B 196 MET cc_start: 0.8841 (tpp) cc_final: 0.8323 (tpp) REVERT: B 220 MET cc_start: 0.8290 (tpp) cc_final: 0.8019 (tpp) REVERT: B 244 CYS cc_start: 0.8650 (t) cc_final: 0.7823 (p) REVERT: C 235 LEU cc_start: 0.8527 (tt) cc_final: 0.7939 (mt) REVERT: D 228 SER cc_start: 0.8931 (p) cc_final: 0.8582 (p) REVERT: E 28 GLU cc_start: 0.8925 (mp0) cc_final: 0.8650 (mp0) REVERT: E 113 MET cc_start: 0.8137 (mtt) cc_final: 0.7886 (mpp) REVERT: E 123 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.7820 (m-40) REVERT: F 15 ASN cc_start: 0.6953 (p0) cc_final: 0.6466 (p0) REVERT: F 64 MET cc_start: 0.7736 (mmm) cc_final: 0.7139 (mmt) REVERT: F 77 TYR cc_start: 0.8761 (m-80) cc_final: 0.8261 (m-80) REVERT: F 113 MET cc_start: 0.8789 (tpp) cc_final: 0.8006 (mmm) REVERT: F 169 ASN cc_start: 0.9277 (m110) cc_final: 0.8828 (m110) REVERT: F 195 ASN cc_start: 0.7733 (m-40) cc_final: 0.7331 (m110) REVERT: F 196 MET cc_start: 0.6592 (tmm) cc_final: 0.5991 (tmm) REVERT: F 205 GLU cc_start: 0.8326 (tt0) cc_final: 0.7904 (tt0) REVERT: G 7 GLU cc_start: 0.9361 (OUTLIER) cc_final: 0.8865 (mp0) REVERT: G 113 MET cc_start: 0.8175 (mtt) cc_final: 0.7876 (mtt) REVERT: G 134 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8119 (tm-30) REVERT: H 71 GLU cc_start: 0.8397 (pm20) cc_final: 0.8187 (pm20) REVERT: H 123 ASN cc_start: 0.8132 (m-40) cc_final: 0.7680 (m110) outliers start: 31 outliers final: 19 residues processed: 258 average time/residue: 0.1731 time to fit residues: 76.0948 Evaluate side-chains 241 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain H residue 34 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 55 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 248 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.068397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.049233 restraints weight = 141395.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050577 restraints weight = 70040.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.051461 restraints weight = 45859.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.052017 restraints weight = 35445.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.052333 restraints weight = 30296.888| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 32859 Z= 0.169 Angle : 0.556 9.307 45866 Z= 0.303 Chirality : 0.038 0.158 4984 Planarity : 0.004 0.041 4812 Dihedral : 22.761 140.208 6532 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.85 % Allowed : 15.18 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.52 (0.16), residues: 3069 helix: 1.45 (0.15), residues: 1218 sheet: 0.26 (0.22), residues: 618 loop : -0.67 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 138 TYR 0.020 0.001 TYR D 242 PHE 0.010 0.001 PHE F 246 TRP 0.017 0.001 TRP A 62 HIS 0.007 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00372 (32811) covalent geometry : angle 0.55286 (45845) hydrogen bonds : bond 0.04235 ( 1435) hydrogen bonds : angle 4.86805 ( 3832) metal coordination : bond 0.00939 ( 48) metal coordination : angle 2.72900 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 205 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8294 (pp20) REVERT: a 218 MET cc_start: 0.8223 (mmm) cc_final: 0.7828 (mmm) REVERT: d 220 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7840 (mmp) REVERT: f 77 TYR cc_start: 0.8184 (m-80) cc_final: 0.7840 (m-80) REVERT: f 220 MET cc_start: 0.8339 (mmm) cc_final: 0.7946 (tpp) REVERT: g 7 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8369 (tm-30) REVERT: g 218 MET cc_start: 0.9012 (mmp) cc_final: 0.8711 (mmp) REVERT: g 220 MET cc_start: 0.8539 (mmm) cc_final: 0.8143 (mmm) REVERT: A 39 ASN cc_start: 0.8191 (m-40) cc_final: 0.7837 (m-40) REVERT: A 134 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8754 (pp20) REVERT: A 205 GLU cc_start: 0.9129 (pp20) cc_final: 0.8615 (pp20) REVERT: A 220 MET cc_start: 0.8751 (tpp) cc_final: 0.8150 (tpp) REVERT: B 28 GLU cc_start: 0.9203 (mp0) cc_final: 0.8827 (pm20) REVERT: B 32 GLU cc_start: 0.9492 (tp30) cc_final: 0.9272 (tp30) REVERT: B 113 MET cc_start: 0.9060 (tpp) cc_final: 0.8733 (mmm) REVERT: B 196 MET cc_start: 0.8763 (tpp) cc_final: 0.8307 (tpp) REVERT: B 244 CYS cc_start: 0.8689 (t) cc_final: 0.7815 (p) REVERT: C 218 MET cc_start: 0.8022 (ptt) cc_final: 0.7418 (mmp) REVERT: D 220 MET cc_start: 0.7860 (tpt) cc_final: 0.7461 (tpt) REVERT: E 7 GLU cc_start: 0.8999 (pm20) cc_final: 0.8742 (pm20) REVERT: E 28 GLU cc_start: 0.8942 (mp0) cc_final: 0.8586 (mp0) REVERT: E 113 MET cc_start: 0.8101 (mtt) cc_final: 0.7758 (mpp) REVERT: E 196 MET cc_start: 0.7682 (ptt) cc_final: 0.6908 (ttp) REVERT: F 15 ASN cc_start: 0.6979 (p0) cc_final: 0.6534 (p0) REVERT: F 64 MET cc_start: 0.7411 (mmm) cc_final: 0.6824 (mmt) REVERT: F 77 TYR cc_start: 0.8846 (m-80) cc_final: 0.8363 (m-80) REVERT: F 113 MET cc_start: 0.8799 (tpp) cc_final: 0.8106 (mmm) REVERT: F 169 ASN cc_start: 0.9278 (m110) cc_final: 0.8792 (m110) REVERT: F 195 ASN cc_start: 0.7773 (m-40) cc_final: 0.7313 (m110) REVERT: F 196 MET cc_start: 0.6577 (tmm) cc_final: 0.5974 (tmm) REVERT: F 205 GLU cc_start: 0.8329 (tt0) cc_final: 0.7917 (tt0) REVERT: G 7 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.8896 (mp0) REVERT: G 113 MET cc_start: 0.8228 (mtt) cc_final: 0.7920 (mtt) REVERT: G 134 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8195 (tm-30) REVERT: H 71 GLU cc_start: 0.8471 (pm20) cc_final: 0.8200 (pm20) REVERT: H 123 ASN cc_start: 0.8356 (m-40) cc_final: 0.7859 (m110) outliers start: 49 outliers final: 32 residues processed: 253 average time/residue: 0.1681 time to fit residues: 73.1050 Evaluate side-chains 252 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 64 MET Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 205 GLU Chi-restraints excluded: chain d residue 220 MET Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 161 HIS Chi-restraints excluded: chain e residue 211 ILE Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 196 MET Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 131 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 260 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 90 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 246 optimal weight: 20.0000 chunk 287 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.068893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.049756 restraints weight = 141510.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.051115 restraints weight = 69839.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.052019 restraints weight = 45612.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052575 restraints weight = 35066.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052863 restraints weight = 29968.229| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32859 Z= 0.144 Angle : 0.546 11.890 45866 Z= 0.297 Chirality : 0.038 0.223 4984 Planarity : 0.003 0.042 4812 Dihedral : 22.714 139.438 6532 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.70 % Allowed : 15.97 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.54 (0.16), residues: 3069 helix: 1.46 (0.15), residues: 1225 sheet: 0.32 (0.22), residues: 599 loop : -0.69 (0.19), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 138 TYR 0.021 0.001 TYR D 242 PHE 0.009 0.001 PHE F 246 TRP 0.023 0.001 TRP A 62 HIS 0.006 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00317 (32811) covalent geometry : angle 0.54392 (45845) hydrogen bonds : bond 0.04057 ( 1435) hydrogen bonds : angle 4.78753 ( 3832) metal coordination : bond 0.00685 ( 48) metal coordination : angle 2.30054 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 205 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8328 (pp20) REVERT: a 218 MET cc_start: 0.8290 (mmm) cc_final: 0.7934 (mmm) REVERT: b 64 MET cc_start: 0.9039 (mtm) cc_final: 0.8543 (mtp) REVERT: d 220 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7709 (mmp) REVERT: f 77 TYR cc_start: 0.8203 (m-80) cc_final: 0.7852 (m-80) REVERT: f 220 MET cc_start: 0.8294 (mmm) cc_final: 0.7917 (tpp) REVERT: g 7 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8374 (tm-30) REVERT: g 218 MET cc_start: 0.9013 (mmp) cc_final: 0.8711 (mmp) REVERT: g 220 MET cc_start: 0.8581 (mmm) cc_final: 0.8164 (mmm) REVERT: A 39 ASN cc_start: 0.8167 (m-40) cc_final: 0.7805 (m-40) REVERT: A 68 HIS cc_start: 0.8315 (m90) cc_final: 0.7689 (m-70) REVERT: A 80 VAL cc_start: 0.8794 (t) cc_final: 0.8481 (p) REVERT: A 134 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8766 (pp20) REVERT: A 205 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8611 (pp20) REVERT: A 218 MET cc_start: 0.8158 (tpt) cc_final: 0.7849 (mmm) REVERT: A 220 MET cc_start: 0.8759 (tpp) cc_final: 0.8153 (tpp) REVERT: B 28 GLU cc_start: 0.9196 (mp0) cc_final: 0.8815 (pm20) REVERT: B 32 GLU cc_start: 0.9492 (tp30) cc_final: 0.9281 (tp30) REVERT: B 64 MET cc_start: 0.8449 (ttp) cc_final: 0.8167 (ttm) REVERT: B 113 MET cc_start: 0.9035 (tpp) cc_final: 0.8723 (mmm) REVERT: B 196 MET cc_start: 0.8546 (tpp) cc_final: 0.8256 (tpp) REVERT: B 218 MET cc_start: 0.8286 (tpp) cc_final: 0.8034 (tpp) REVERT: B 220 MET cc_start: 0.6778 (tpp) cc_final: 0.6464 (tpp) REVERT: B 244 CYS cc_start: 0.8612 (t) cc_final: 0.7751 (p) REVERT: C 218 MET cc_start: 0.8008 (ptt) cc_final: 0.7585 (ptt) REVERT: D 220 MET cc_start: 0.7628 (tpt) cc_final: 0.6671 (mmm) REVERT: E 7 GLU cc_start: 0.8966 (pm20) cc_final: 0.8749 (pm20) REVERT: E 28 GLU cc_start: 0.8949 (mp0) cc_final: 0.8592 (mp0) REVERT: E 113 MET cc_start: 0.8072 (mtt) cc_final: 0.7781 (mpp) REVERT: F 15 ASN cc_start: 0.6972 (p0) cc_final: 0.6497 (p0) REVERT: F 77 TYR cc_start: 0.8840 (m-80) cc_final: 0.8331 (m-80) REVERT: F 113 MET cc_start: 0.8690 (tpp) cc_final: 0.7920 (mmm) REVERT: F 169 ASN cc_start: 0.9279 (m110) cc_final: 0.8794 (m110) REVERT: F 195 ASN cc_start: 0.7770 (m-40) cc_final: 0.7324 (m110) REVERT: F 196 MET cc_start: 0.6674 (tmm) cc_final: 0.6030 (tmm) REVERT: F 205 GLU cc_start: 0.8312 (tt0) cc_final: 0.8012 (tt0) REVERT: G 7 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8869 (mp0) REVERT: G 113 MET cc_start: 0.8150 (mtt) cc_final: 0.7898 (mtt) REVERT: G 134 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8144 (tm-30) REVERT: H 71 GLU cc_start: 0.8469 (pm20) cc_final: 0.8181 (pm20) REVERT: H 85 TYR cc_start: 0.8561 (t80) cc_final: 0.8359 (t80) REVERT: H 123 ASN cc_start: 0.8157 (m-40) cc_final: 0.7616 (m110) outliers start: 45 outliers final: 28 residues processed: 252 average time/residue: 0.1683 time to fit residues: 72.6568 Evaluate side-chains 252 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 205 GLU Chi-restraints excluded: chain d residue 220 MET Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 211 ILE Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 12 HIS Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 196 MET Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain H residue 34 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 269 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 284 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 52 ASN ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 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 = 0.3454 r_free = 0.3454 target = 0.066686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.047387 restraints weight = 143339.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.048685 restraints weight = 72028.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.049525 restraints weight = 47701.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.050068 restraints weight = 37272.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.050361 restraints weight = 32078.299| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 32859 Z= 0.271 Angle : 0.652 10.289 45866 Z= 0.351 Chirality : 0.041 0.178 4984 Planarity : 0.004 0.039 4812 Dihedral : 22.882 140.808 6532 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.82 % Allowed : 16.20 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.09 (0.16), residues: 3069 helix: 1.02 (0.15), residues: 1231 sheet: 0.22 (0.23), residues: 575 loop : -0.93 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 262 TYR 0.017 0.002 TYR D 242 PHE 0.016 0.002 PHE g 246 TRP 0.029 0.002 TRP A 62 HIS 0.009 0.001 HIS a 9 Details of bonding type rmsd covalent geometry : bond 0.00596 (32811) covalent geometry : angle 0.64646 (45845) hydrogen bonds : bond 0.04896 ( 1435) hydrogen bonds : angle 5.11316 ( 3832) metal coordination : bond 0.01819 ( 48) metal coordination : angle 4.04389 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 196 MET cc_start: 0.8179 (ttm) cc_final: 0.7810 (ptm) REVERT: a 218 MET cc_start: 0.8359 (mmm) cc_final: 0.7962 (mmm) REVERT: f 77 TYR cc_start: 0.8449 (m-80) cc_final: 0.7990 (m-80) REVERT: f 220 MET cc_start: 0.8363 (mmm) cc_final: 0.7997 (tpp) REVERT: g 7 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8443 (tm-30) REVERT: g 218 MET cc_start: 0.8936 (mmp) cc_final: 0.8655 (mmp) REVERT: g 220 MET cc_start: 0.8625 (mmm) cc_final: 0.8201 (mmm) REVERT: h 134 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: A 39 ASN cc_start: 0.8072 (m-40) cc_final: 0.7626 (m-40) REVERT: A 205 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8712 (pp20) REVERT: A 220 MET cc_start: 0.8700 (tpp) cc_final: 0.8371 (tpp) REVERT: B 28 GLU cc_start: 0.9219 (mp0) cc_final: 0.8843 (pm20) REVERT: B 32 GLU cc_start: 0.9481 (tp30) cc_final: 0.9262 (tp30) REVERT: B 220 MET cc_start: 0.7090 (tpp) cc_final: 0.6687 (tpp) REVERT: C 218 MET cc_start: 0.8066 (ptt) cc_final: 0.7536 (mmp) REVERT: E 7 GLU cc_start: 0.9003 (pm20) cc_final: 0.8797 (pm20) REVERT: E 28 GLU cc_start: 0.8944 (mp0) cc_final: 0.8581 (mp0) REVERT: E 74 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8198 (mmmt) REVERT: E 196 MET cc_start: 0.7808 (ptt) cc_final: 0.6881 (ttp) REVERT: F 15 ASN cc_start: 0.7017 (p0) cc_final: 0.6604 (p0) REVERT: F 64 MET cc_start: 0.7191 (mmt) cc_final: 0.6558 (tpp) REVERT: F 77 TYR cc_start: 0.8880 (m-80) cc_final: 0.8390 (m-80) REVERT: F 113 MET cc_start: 0.8553 (tpp) cc_final: 0.7859 (mmm) REVERT: F 169 ASN cc_start: 0.9273 (m110) cc_final: 0.8791 (m110) REVERT: F 195 ASN cc_start: 0.7882 (m-40) cc_final: 0.7448 (m110) REVERT: F 196 MET cc_start: 0.6913 (tmm) cc_final: 0.6160 (tmm) REVERT: F 205 GLU cc_start: 0.8397 (tt0) cc_final: 0.8111 (tt0) REVERT: G 7 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8920 (mp0) REVERT: G 113 MET cc_start: 0.8322 (mtt) cc_final: 0.7996 (mtt) REVERT: G 123 ASN cc_start: 0.7882 (t0) cc_final: 0.7670 (t0) REVERT: G 134 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8166 (tm-30) REVERT: H 71 GLU cc_start: 0.8592 (pm20) cc_final: 0.8253 (pm20) REVERT: H 123 ASN cc_start: 0.8649 (m-40) cc_final: 0.8419 (t0) REVERT: H 158 GLU cc_start: 0.8060 (pm20) cc_final: 0.7835 (pm20) outliers start: 48 outliers final: 36 residues processed: 247 average time/residue: 0.1684 time to fit residues: 71.1932 Evaluate side-chains 250 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 64 MET Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 211 ILE Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 12 HIS Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 196 MET Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 64 MET Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain H residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 62 optimal weight: 2.9990 chunk 330 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 39 ASN ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 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 = 0.3496 r_free = 0.3496 target = 0.068370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.049225 restraints weight = 141191.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050580 restraints weight = 69910.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.051459 restraints weight = 45721.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.052029 restraints weight = 35269.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052344 restraints weight = 30093.519| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32859 Z= 0.147 Angle : 0.573 12.424 45866 Z= 0.309 Chirality : 0.038 0.184 4984 Planarity : 0.004 0.043 4812 Dihedral : 22.848 139.894 6532 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.44 % Allowed : 16.96 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.38 (0.16), residues: 3069 helix: 1.28 (0.15), residues: 1230 sheet: 0.54 (0.24), residues: 525 loop : -0.83 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 138 TYR 0.021 0.001 TYR D 242 PHE 0.011 0.001 PHE F 246 TRP 0.019 0.001 TRP A 62 HIS 0.006 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00324 (32811) covalent geometry : angle 0.57091 (45845) hydrogen bonds : bond 0.04119 ( 1435) hydrogen bonds : angle 4.83390 ( 3832) metal coordination : bond 0.00752 ( 48) metal coordination : angle 2.42589 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 MET cc_start: 0.8257 (mmm) cc_final: 0.7902 (mmm) REVERT: b 64 MET cc_start: 0.8979 (mtm) cc_final: 0.8607 (mtt) REVERT: f 77 TYR cc_start: 0.8322 (m-80) cc_final: 0.7856 (m-80) REVERT: f 220 MET cc_start: 0.8345 (mmm) cc_final: 0.7989 (tpp) REVERT: g 7 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8415 (tm-30) REVERT: g 218 MET cc_start: 0.8958 (mmp) cc_final: 0.8637 (mmp) REVERT: g 220 MET cc_start: 0.8624 (mmm) cc_final: 0.8200 (mmm) REVERT: A 39 ASN cc_start: 0.8165 (m-40) cc_final: 0.7812 (m-40) REVERT: A 68 HIS cc_start: 0.8276 (m90) cc_final: 0.7706 (m-70) REVERT: A 205 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8682 (pp20) REVERT: A 220 MET cc_start: 0.8780 (tpp) cc_final: 0.8498 (tpp) REVERT: B 28 GLU cc_start: 0.9197 (mp0) cc_final: 0.8814 (pm20) REVERT: B 32 GLU cc_start: 0.9488 (tp30) cc_final: 0.9269 (tp30) REVERT: B 113 MET cc_start: 0.8803 (mmm) cc_final: 0.8564 (mmm) REVERT: B 127 TYR cc_start: 0.7405 (m-80) cc_final: 0.7179 (m-80) REVERT: B 220 MET cc_start: 0.7041 (tpp) cc_final: 0.6690 (tpp) REVERT: B 244 CYS cc_start: 0.8531 (t) cc_final: 0.7664 (p) REVERT: C 220 MET cc_start: 0.7005 (mmm) cc_final: 0.6013 (mtm) REVERT: C 235 LEU cc_start: 0.8566 (tt) cc_final: 0.7946 (mt) REVERT: D 218 MET cc_start: 0.8361 (mmm) cc_final: 0.7820 (mmm) REVERT: D 220 MET cc_start: 0.7735 (tpt) cc_final: 0.7399 (tpt) REVERT: E 7 GLU cc_start: 0.8910 (pm20) cc_final: 0.8704 (pm20) REVERT: E 28 GLU cc_start: 0.8938 (mp0) cc_final: 0.8616 (mp0) REVERT: E 74 LYS cc_start: 0.8547 (mmmt) cc_final: 0.8215 (mmmt) REVERT: E 113 MET cc_start: 0.8037 (mtt) cc_final: 0.7760 (mpp) REVERT: E 127 TYR cc_start: 0.8815 (m-80) cc_final: 0.8560 (m-80) REVERT: E 196 MET cc_start: 0.7700 (ptt) cc_final: 0.7252 (ttp) REVERT: F 15 ASN cc_start: 0.6934 (p0) cc_final: 0.6488 (p0) REVERT: F 77 TYR cc_start: 0.8853 (m-80) cc_final: 0.8359 (m-80) REVERT: F 113 MET cc_start: 0.8626 (tpp) cc_final: 0.7824 (mmm) REVERT: F 169 ASN cc_start: 0.9348 (m110) cc_final: 0.8875 (m110) REVERT: F 195 ASN cc_start: 0.7834 (m-40) cc_final: 0.7428 (m110) REVERT: F 196 MET cc_start: 0.6942 (tmm) cc_final: 0.6262 (tmm) REVERT: F 205 GLU cc_start: 0.8241 (tt0) cc_final: 0.7923 (tt0) REVERT: G 7 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.8903 (mp0) REVERT: G 113 MET cc_start: 0.8060 (mtt) cc_final: 0.7780 (mtt) REVERT: G 134 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8136 (tm-30) REVERT: H 15 ASN cc_start: 0.8769 (p0) cc_final: 0.8376 (p0) REVERT: H 71 GLU cc_start: 0.8517 (pm20) cc_final: 0.8216 (pm20) REVERT: H 123 ASN cc_start: 0.8407 (m-40) cc_final: 0.7919 (m110) REVERT: H 158 GLU cc_start: 0.8120 (pm20) cc_final: 0.7864 (pm20) REVERT: H 196 MET cc_start: 0.6985 (mtm) cc_final: 0.6783 (mtm) outliers start: 38 outliers final: 33 residues processed: 247 average time/residue: 0.1637 time to fit residues: 69.1730 Evaluate side-chains 251 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 12 HIS Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 196 MET Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 175 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 325 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 265 optimal weight: 0.9990 chunk 26 optimal weight: 40.0000 chunk 110 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 214 optimal weight: 30.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 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 = 0.3511 r_free = 0.3511 target = 0.069012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.049925 restraints weight = 141530.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.051279 restraints weight = 69807.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.052181 restraints weight = 45503.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.052749 restraints weight = 34969.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053051 restraints weight = 29812.111| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32859 Z= 0.135 Angle : 0.568 12.263 45866 Z= 0.304 Chirality : 0.038 0.190 4984 Planarity : 0.004 0.044 4812 Dihedral : 22.783 139.970 6532 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.59 % Allowed : 16.84 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.57 (0.16), residues: 3069 helix: 1.46 (0.15), residues: 1221 sheet: 0.46 (0.23), residues: 570 loop : -0.69 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 262 TYR 0.022 0.001 TYR D 242 PHE 0.011 0.001 PHE F 246 TRP 0.033 0.001 TRP A 62 HIS 0.006 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00299 (32811) covalent geometry : angle 0.56545 (45845) hydrogen bonds : bond 0.03988 ( 1435) hydrogen bonds : angle 4.72381 ( 3832) metal coordination : bond 0.00785 ( 48) metal coordination : angle 2.41067 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7643 (t) REVERT: a 196 MET cc_start: 0.8015 (ttm) cc_final: 0.7601 (ptm) REVERT: a 218 MET cc_start: 0.8281 (mmm) cc_final: 0.7959 (mmm) REVERT: b 64 MET cc_start: 0.8995 (mtm) cc_final: 0.8562 (mtt) REVERT: e 112 TYR cc_start: 0.8358 (t80) cc_final: 0.8121 (t80) REVERT: f 28 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7145 (tm-30) REVERT: f 77 TYR cc_start: 0.8298 (m-80) cc_final: 0.7871 (m-80) REVERT: f 220 MET cc_start: 0.8316 (mmm) cc_final: 0.7956 (tpp) REVERT: g 7 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8390 (tm-30) REVERT: g 218 MET cc_start: 0.9009 (mmp) cc_final: 0.8699 (mmp) REVERT: g 220 MET cc_start: 0.8654 (mmm) cc_final: 0.8310 (mmm) REVERT: h 134 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: A 39 ASN cc_start: 0.8187 (m-40) cc_final: 0.7816 (m-40) REVERT: A 68 HIS cc_start: 0.8273 (m90) cc_final: 0.7676 (m-70) REVERT: A 80 VAL cc_start: 0.8851 (t) cc_final: 0.8494 (p) REVERT: A 205 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8616 (pp20) REVERT: A 220 MET cc_start: 0.8736 (tpp) cc_final: 0.8202 (tpp) REVERT: B 28 GLU cc_start: 0.9192 (mp0) cc_final: 0.8798 (pm20) REVERT: B 32 GLU cc_start: 0.9478 (tp30) cc_final: 0.9262 (tp30) REVERT: B 64 MET cc_start: 0.8935 (ttm) cc_final: 0.8612 (tpp) REVERT: B 220 MET cc_start: 0.7196 (tpp) cc_final: 0.6834 (tpp) REVERT: B 244 CYS cc_start: 0.8525 (t) cc_final: 0.7672 (p) REVERT: C 218 MET cc_start: 0.7871 (ptt) cc_final: 0.7485 (mmp) REVERT: C 220 MET cc_start: 0.7143 (mmm) cc_final: 0.6204 (mtm) REVERT: C 235 LEU cc_start: 0.8374 (tt) cc_final: 0.7777 (mt) REVERT: D 218 MET cc_start: 0.8359 (mmm) cc_final: 0.7781 (mmm) REVERT: D 220 MET cc_start: 0.7935 (tpt) cc_final: 0.7458 (tpt) REVERT: E 28 GLU cc_start: 0.8913 (mp0) cc_final: 0.8547 (mp0) REVERT: E 74 LYS cc_start: 0.8519 (mmmt) cc_final: 0.8202 (mmmt) REVERT: E 113 MET cc_start: 0.8006 (mtt) cc_final: 0.7666 (mpp) REVERT: E 127 TYR cc_start: 0.8973 (m-80) cc_final: 0.8595 (m-80) REVERT: E 196 MET cc_start: 0.7697 (ptt) cc_final: 0.7206 (ttp) REVERT: F 15 ASN cc_start: 0.7012 (p0) cc_final: 0.6610 (p0) REVERT: F 64 MET cc_start: 0.7572 (mmt) cc_final: 0.7151 (tpt) REVERT: F 77 TYR cc_start: 0.8835 (m-80) cc_final: 0.8336 (m-80) REVERT: F 113 MET cc_start: 0.8648 (tpp) cc_final: 0.7858 (mmm) REVERT: F 169 ASN cc_start: 0.9336 (m110) cc_final: 0.8864 (m110) REVERT: F 195 ASN cc_start: 0.7833 (m-40) cc_final: 0.7423 (m110) REVERT: F 196 MET cc_start: 0.6923 (tmm) cc_final: 0.6261 (tmm) REVERT: F 205 GLU cc_start: 0.8247 (tt0) cc_final: 0.7929 (tt0) REVERT: G 7 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8933 (mp0) REVERT: G 134 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8120 (tm-30) REVERT: H 71 GLU cc_start: 0.8474 (pm20) cc_final: 0.8172 (pm20) REVERT: H 123 ASN cc_start: 0.8372 (m-40) cc_final: 0.7836 (m110) REVERT: H 158 GLU cc_start: 0.8111 (pm20) cc_final: 0.7849 (pm20) outliers start: 42 outliers final: 32 residues processed: 251 average time/residue: 0.1687 time to fit residues: 72.2696 Evaluate side-chains 256 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 12 HIS Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 196 MET Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 192 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 263 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 284 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.068104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.048782 restraints weight = 143420.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.050121 restraints weight = 71443.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.051013 restraints weight = 46929.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.051566 restraints weight = 36239.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.051855 restraints weight = 31083.173| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32859 Z= 0.185 Angle : 0.593 11.618 45866 Z= 0.318 Chirality : 0.039 0.176 4984 Planarity : 0.004 0.042 4812 Dihedral : 22.824 140.443 6532 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.48 % Allowed : 16.81 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.44 (0.16), residues: 3069 helix: 1.35 (0.15), residues: 1229 sheet: 0.47 (0.23), residues: 560 loop : -0.79 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 262 TYR 0.021 0.001 TYR B 112 PHE 0.021 0.001 PHE D 264 TRP 0.033 0.001 TRP A 62 HIS 0.007 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00410 (32811) covalent geometry : angle 0.59034 (45845) hydrogen bonds : bond 0.04178 ( 1435) hydrogen bonds : angle 4.81609 ( 3832) metal coordination : bond 0.01024 ( 48) metal coordination : angle 2.63226 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5259.93 seconds wall clock time: 91 minutes 47.53 seconds (5507.53 seconds total)