Starting phenix.real_space_refine on Mon Sep 14 13:58:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ut1_26744/09_2026/7ut1_26744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut1_26744/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ut1_26744/09_2026/7ut1_26744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut1_26744/09_2026/7ut1_26744.map" model { file = "/net/cci-nas-00/data/ceres_data/7ut1_26744/09_2026/7ut1_26744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut1_26744/09_2026/7ut1_26744.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ut1_26744/09_2026/7ut1_26744.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ut1_26744/09_2026/7ut1_26744.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 7.58, per 1000 atoms: 0.24 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.22 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: 6.26 Time building geometry restraints manager: 3.58 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=" C3' DG N 10 " pdb=" C2' DG N 10 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DA m 12 " pdb=" C2' DA m 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DG k 10 " pdb=" C2' DG k 10 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DG J 26 " pdb=" C2' DG J 26 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC j 9 " pdb=" C2' DC j 9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 ... (remaining 32806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 44537 1.73 - 3.46: 1214 3.46 - 5.19: 64 5.19 - 6.92: 22 6.92 - 8.66: 8 Bond angle restraints: 45845 Sorted by residual: angle pdb=" N3 DT i 11 " pdb=" C4 DT i 11 " pdb=" O4 DT i 11 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT j 31 " pdb=" C4 DT j 31 " pdb=" O4 DT j 31 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT l 3 " pdb=" C4 DT l 3 " pdb=" O4 DT l 3 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT J 22 " pdb=" C4 DT J 22 " pdb=" O4 DT J 22 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT L 11 " pdb=" C4 DT L 11 " pdb=" O4 DT L 11 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+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: 3776 0.047 - 0.095: 981 0.095 - 0.142: 220 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 35.200 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.070 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.009 0.590 32859 Z= 0.406 Angle : 0.696 54.304 45866 Z= 0.454 Chirality : 0.044 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/Z covalent geometry : bond 0.00406 / 0.33 (32811) covalent geometry : angle 0.62369 / 0.45 (45845) hydrogen bonds : bond 0.21837 / 15.06 ( 1435) hydrogen bonds : angle 8.48241 / 6.03 ( 3832) metal coordination : bond 0.20363 / 13.23 ( 48) metal coordination : angle 14.47705 / 9.62 ( 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 : 1.135 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: 0.7823 (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: 0.7475 (t0) REVERT: C 230 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8351 (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: 0.6259 (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: 0.7644 (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: 0.1788 time to fit residues: 78.3702 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 : 0.966 ------------------------------------------------------------------------------- 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: 30.0000 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... ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 193 HIS b 163 ASN ** b 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** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 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 = 0.3462 r_free = 0.3462 target = 0.066999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.047694 restraints weight = 145610.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.049005 restraints weight = 73002.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.049882 restraints weight = 48319.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.050401 restraints weight = 37578.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.050777 restraints weight = 32335.432| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 32859 Z= 0.272 Angle : 0.692 11.993 45866 Z= 0.382 Chirality : 0.046 0.238 4984 Planarity : 0.005 0.054 4812 Dihedral : 23.057 145.602 6532 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.64 % Allowed : 6.43 % Favored : 92.92 % 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: -0.02 (0.15), residues: 3069 helix: 0.97 (0.15), residues: 1237 sheet: 0.03 (0.22), residues: 616 loop : -1.01 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 262 TYR 0.022 0.002 TYR A 112 PHE 0.020 0.002 PHE D 246 TRP 0.017 0.002 TRP b 208 HIS 0.017 0.002 HIS G 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.27 (32811) covalent geometry : angle 0.68311 / 0.38 (45845) hydrogen bonds : bond 0.06612 / 4.48 ( 1435) hydrogen bonds : angle 6.04523 / 4.38 ( 3832) metal coordination : bond 0.02385 / 1.61 ( 48) metal coordination : angle 5.31474 / 3.32 ( 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 245 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 77 TYR cc_start: 0.7834 (m-80) cc_final: 0.7594 (m-80) REVERT: f 113 MET cc_start: 0.8681 (mtm) cc_final: 0.8200 (mtp) REVERT: f 220 MET cc_start: 0.8648 (mmm) cc_final: 0.8148 (tpp) REVERT: g 32 GLU cc_start: 0.9179 (mp0) cc_final: 0.8759 (mp0) REVERT: A 28 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8807 (pt0) REVERT: A 39 ASN cc_start: 0.8274 (m-40) cc_final: 0.7903 (t0) REVERT: B 7 GLU cc_start: 0.9503 (mt-10) cc_final: 0.9293 (mt-10) REVERT: B 32 GLU cc_start: 0.9419 (tp30) cc_final: 0.9184 (tp30) REVERT: B 113 MET cc_start: 0.8952 (tpp) cc_final: 0.8625 (tpt) REVERT: B 196 MET cc_start: 0.8143 (tpp) cc_final: 0.7496 (tpp) REVERT: B 220 MET cc_start: 0.7276 (tpp) cc_final: 0.6923 (tpp) REVERT: C 223 ASP cc_start: 0.7607 (t0) cc_final: 0.7299 (t0) REVERT: E 28 GLU cc_start: 0.8771 (mp0) cc_final: 0.8488 (mp0) REVERT: F 7 GLU cc_start: 0.9321 (mp0) cc_final: 0.9069 (mp0) REVERT: F 15 ASN cc_start: 0.7023 (p0) cc_final: 0.6773 (p0) REVERT: F 64 MET cc_start: 0.7667 (mmm) cc_final: 0.7275 (tpt) REVERT: F 77 TYR cc_start: 0.9026 (m-80) cc_final: 0.8598 (m-80) REVERT: F 169 ASN cc_start: 0.9270 (m110) cc_final: 0.8779 (m110) REVERT: F 177 TYR cc_start: 0.7812 (m-80) cc_final: 0.7597 (m-80) REVERT: F 195 ASN cc_start: 0.7784 (m-40) cc_final: 0.7235 (m110) REVERT: F 205 GLU cc_start: 0.8415 (tt0) cc_final: 0.8077 (tt0) REVERT: F 220 MET cc_start: 0.8405 (tpp) cc_final: 0.7503 (tpp) REVERT: G 7 GLU cc_start: 0.9310 (mp0) cc_final: 0.8722 (mp0) REVERT: G 113 MET cc_start: 0.8161 (mtt) cc_final: 0.7887 (mtt) REVERT: G 134 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8250 (tm-30) REVERT: H 242 TYR cc_start: 0.8760 (p90) cc_final: 0.8523 (p90) outliers start: 17 outliers final: 14 residues processed: 235 average time/residue: 0.1760 time to fit residues: 70.4938 Evaluate side-chains 225 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 28 GLU Chi-restraints excluded: chain e residue 64 MET 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 h residue 171 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 242 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 151 optimal weight: 0.4980 chunk 208 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 11 optimal weight: 0.0170 chunk 268 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 overall best weight: 1.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 12 HIS a 193 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 207 HIS B 195 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.049296 restraints weight = 143121.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.050649 restraints weight = 71303.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.051531 restraints weight = 46795.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.052095 restraints weight = 36218.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.052387 restraints weight = 30988.100| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32859 Z= 0.143 Angle : 0.585 12.069 45866 Z= 0.329 Chirality : 0.042 0.199 4984 Planarity : 0.004 0.041 4812 Dihedral : 23.117 143.201 6532 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.79 % Allowed : 9.80 % Favored : 89.40 % 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: 0.27 (0.16), residues: 3069 helix: 1.20 (0.15), residues: 1224 sheet: 0.18 (0.22), residues: 613 loop : -0.80 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 259 TYR 0.027 0.001 TYR A 112 PHE 0.021 0.001 PHE D 246 TRP 0.014 0.001 TRP b 208 HIS 0.014 0.001 HIS G 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (32811) covalent geometry : angle 0.57602 / 0.33 (45845) hydrogen bonds : bond 0.05449 / 3.72 ( 1435) hydrogen bonds : angle 5.44359 / 3.95 ( 3832) metal coordination : bond 0.01151 / 0.68 ( 48) metal coordination : angle 4.73297 / 3.19 ( 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 263 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.988 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: c 218 MET cc_start: 0.8446 (mmm) cc_final: 0.8096 (mmm) REVERT: f 28 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7115 (tm-30) REVERT: f 113 MET cc_start: 0.8439 (mtm) cc_final: 0.8114 (mtp) REVERT: f 220 MET cc_start: 0.8542 (mmm) cc_final: 0.8166 (tpp) REVERT: g 32 GLU cc_start: 0.9074 (mp0) cc_final: 0.8708 (mp0) REVERT: g 220 MET cc_start: 0.8677 (mmm) cc_final: 0.8321 (mmm) REVERT: A 28 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8880 (pt0) REVERT: A 39 ASN cc_start: 0.8273 (m-40) cc_final: 0.7946 (t0) REVERT: A 127 TYR cc_start: 0.8290 (m-80) cc_final: 0.8040 (m-80) REVERT: A 134 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8652 (mp0) REVERT: B 7 GLU cc_start: 0.9507 (mt-10) cc_final: 0.9301 (mt-10) REVERT: B 32 GLU cc_start: 0.9416 (tp30) cc_final: 0.9189 (tp30) REVERT: B 113 MET cc_start: 0.8955 (tpp) cc_final: 0.8704 (mmt) REVERT: B 196 MET cc_start: 0.8251 (tpp) cc_final: 0.7783 (tpp) REVERT: C 218 MET cc_start: 0.7935 (ptt) cc_final: 0.7224 (mmp) REVERT: D 218 MET cc_start: 0.8724 (mmm) cc_final: 0.8275 (mmm) REVERT: E 7 GLU cc_start: 0.8870 (pm20) cc_final: 0.8598 (pm20) REVERT: E 220 MET cc_start: 0.7578 (tpp) cc_final: 0.7313 (tpt) REVERT: F 15 ASN cc_start: 0.6888 (p0) cc_final: 0.6616 (p0) REVERT: F 64 MET cc_start: 0.7819 (mmm) cc_final: 0.7321 (mmt) REVERT: F 77 TYR cc_start: 0.8871 (m-80) cc_final: 0.8381 (m-80) REVERT: F 113 MET cc_start: 0.8877 (tpp) cc_final: 0.8515 (tpp) REVERT: F 169 ASN cc_start: 0.9235 (m110) cc_final: 0.8739 (m110) REVERT: F 195 ASN cc_start: 0.7775 (m-40) cc_final: 0.7297 (m110) REVERT: F 196 MET cc_start: 0.6567 (tmm) cc_final: 0.5599 (tmm) REVERT: F 205 GLU cc_start: 0.8340 (tt0) cc_final: 0.7957 (tt0) REVERT: F 208 TRP cc_start: 0.8058 (m100) cc_final: 0.7558 (m100) REVERT: F 220 MET cc_start: 0.8674 (tpp) cc_final: 0.8462 (tpp) REVERT: G 7 GLU cc_start: 0.9364 (mp0) cc_final: 0.8873 (mp0) REVERT: G 134 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8211 (tm-30) REVERT: H 242 TYR cc_start: 0.8770 (p90) cc_final: 0.8481 (p90) outliers start: 21 outliers final: 11 residues processed: 252 average time/residue: 0.1744 time to fit residues: 74.6397 Evaluate side-chains 226 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 218 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 197 ASP 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: 40.0000 chunk 81 optimal weight: 5.9990 chunk 258 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 215 optimal weight: 0.0970 chunk 192 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 overall best weight: 3.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 52 ASN ** 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 B 182 HIS ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.067584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.048333 restraints weight = 142067.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.049663 restraints weight = 70922.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050522 restraints weight = 46694.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.051075 restraints weight = 36274.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.051364 restraints weight = 31089.071| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32859 Z= 0.194 Angle : 0.606 9.571 45866 Z= 0.337 Chirality : 0.042 0.197 4984 Planarity : 0.004 0.040 4812 Dihedral : 23.192 143.785 6532 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.21 % Allowed : 11.85 % Favored : 86.94 % 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: 0.25 (0.16), residues: 3069 helix: 1.20 (0.15), residues: 1231 sheet: 0.37 (0.23), residues: 552 loop : -0.92 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 262 TYR 0.022 0.001 TYR A 112 PHE 0.015 0.001 PHE D 264 TRP 0.020 0.001 TRP b 208 HIS 0.012 0.001 HIS G 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (32811) covalent geometry : angle 0.60146 / 0.34 (45845) hydrogen bonds : bond 0.05208 / 3.55 ( 1435) hydrogen bonds : angle 5.35706 / 3.88 ( 3832) metal coordination : bond 0.01231 / 0.81 ( 48) metal coordination : angle 3.64434 / 2.27 ( 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 253 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 0.954 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: f 28 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7306 (tm-30) REVERT: f 113 MET cc_start: 0.8600 (mtm) cc_final: 0.8160 (mtp) REVERT: f 220 MET cc_start: 0.8537 (mmm) cc_final: 0.8092 (tpp) REVERT: g 32 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.9023 (mm-30) REVERT: g 220 MET cc_start: 0.8483 (mmm) cc_final: 0.8243 (mmm) REVERT: A 28 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8869 (pt0) REVERT: A 39 ASN cc_start: 0.8143 (m-40) cc_final: 0.7729 (m-40) REVERT: A 68 HIS cc_start: 0.8240 (m90) cc_final: 0.7685 (m-70) REVERT: A 134 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8698 (mp0) REVERT: B 7 GLU cc_start: 0.9545 (mt-10) cc_final: 0.9336 (mt-10) REVERT: B 32 GLU cc_start: 0.9452 (tp30) cc_final: 0.9226 (tp30) REVERT: B 113 MET cc_start: 0.9009 (tpp) cc_final: 0.8738 (mmt) REVERT: B 196 MET cc_start: 0.8376 (tpp) cc_final: 0.7914 (tpp) REVERT: B 220 MET cc_start: 0.7312 (tpp) cc_final: 0.7078 (tpp) REVERT: C 218 MET cc_start: 0.8023 (ptt) cc_final: 0.7296 (mmp) REVERT: F 15 ASN cc_start: 0.6858 (p0) cc_final: 0.6605 (p0) REVERT: F 64 MET cc_start: 0.7727 (mmm) cc_final: 0.7299 (tpt) REVERT: F 77 TYR cc_start: 0.8969 (m-80) cc_final: 0.8469 (m-80) REVERT: F 113 MET cc_start: 0.8878 (tpp) cc_final: 0.8478 (tpp) REVERT: F 169 ASN cc_start: 0.9248 (m110) cc_final: 0.8771 (m110) REVERT: F 195 ASN cc_start: 0.7804 (m-40) cc_final: 0.7320 (m110) REVERT: F 196 MET cc_start: 0.6686 (tmm) cc_final: 0.5675 (tmm) REVERT: F 205 GLU cc_start: 0.8352 (tt0) cc_final: 0.7967 (tt0) REVERT: F 208 TRP cc_start: 0.8016 (m100) cc_final: 0.7640 (m100) REVERT: F 220 MET cc_start: 0.8762 (tpp) cc_final: 0.8503 (tpp) REVERT: G 7 GLU cc_start: 0.9392 (mp0) cc_final: 0.8913 (mp0) REVERT: G 113 MET cc_start: 0.8281 (mtt) cc_final: 0.8014 (mtt) REVERT: G 134 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8218 (tm-30) REVERT: H 134 GLU cc_start: 0.8756 (pt0) cc_final: 0.8550 (pt0) REVERT: H 158 GLU cc_start: 0.7717 (mp0) cc_final: 0.7490 (mp0) REVERT: H 242 TYR cc_start: 0.8709 (p90) cc_final: 0.8417 (p90) outliers start: 32 outliers final: 21 residues processed: 236 average time/residue: 0.1693 time to fit residues: 67.9525 Evaluate side-chains 232 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain d residue 218 MET Chi-restraints excluded: chain e residue 26 THR 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 196 MET Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL 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 D residue 235 LEU 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 F residue 26 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 233 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 289 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 213 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 119 optimal weight: 0.0060 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.0270 chunk 147 optimal weight: 10.0000 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 52 ASN ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 GLN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN B 133 GLN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.049835 restraints weight = 141952.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.051246 restraints weight = 68704.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.052171 restraints weight = 44363.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052722 restraints weight = 33972.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053128 restraints weight = 28940.835| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32859 Z= 0.123 Angle : 0.569 10.210 45866 Z= 0.318 Chirality : 0.041 0.244 4984 Planarity : 0.004 0.045 4812 Dihedral : 23.148 141.428 6532 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.32 % Allowed : 12.83 % Favored : 85.84 % 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: 0.45 (0.16), residues: 3069 helix: 1.37 (0.15), residues: 1224 sheet: 0.38 (0.23), residues: 578 loop : -0.76 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 262 TYR 0.024 0.001 TYR a 112 PHE 0.011 0.001 PHE D 264 TRP 0.031 0.001 TRP C 229 HIS 0.010 0.001 HIS G 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (32811) covalent geometry : angle 0.56262 / 0.32 (45845) hydrogen bonds : bond 0.04758 / 3.26 ( 1435) hydrogen bonds : angle 5.12241 / 3.72 ( 3832) metal coordination : bond 0.01161 / 0.73 ( 48) metal coordination : angle 3.90775 / 2.69 ( 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: 35 poor density : 238 time to evaluate : 1.140 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: e 134 GLU cc_start: 0.8757 (pm20) cc_final: 0.8546 (pm20) REVERT: f 32 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7769 (pm20) REVERT: f 113 MET cc_start: 0.8416 (mtm) cc_final: 0.8187 (mtp) REVERT: f 220 MET cc_start: 0.8444 (mmm) cc_final: 0.7970 (tpp) REVERT: g 32 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.9029 (mm-30) REVERT: g 220 MET cc_start: 0.8414 (mmm) cc_final: 0.8117 (mmm) REVERT: A 28 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8821 (pt0) REVERT: A 39 ASN cc_start: 0.8193 (m-40) cc_final: 0.7840 (m-40) REVERT: A 68 HIS cc_start: 0.8221 (m90) cc_final: 0.7684 (m-70) REVERT: A 134 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8699 (mp0) REVERT: A 205 GLU cc_start: 0.9036 (pp20) cc_final: 0.8591 (pp20) REVERT: A 218 MET cc_start: 0.8087 (tpt) cc_final: 0.7871 (mmm) REVERT: A 220 MET cc_start: 0.8674 (tpp) cc_final: 0.7890 (tpp) REVERT: B 7 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9320 (mt-10) REVERT: B 32 GLU cc_start: 0.9467 (tp30) cc_final: 0.9247 (tp30) REVERT: B 113 MET cc_start: 0.9011 (tpp) cc_final: 0.8650 (mmt) REVERT: B 196 MET cc_start: 0.8556 (tpp) cc_final: 0.8068 (tpp) REVERT: B 244 CYS cc_start: 0.8620 (t) cc_final: 0.7867 (p) REVERT: C 218 MET cc_start: 0.8027 (ptt) cc_final: 0.7461 (mmp) REVERT: E 7 GLU cc_start: 0.9016 (pm20) cc_final: 0.8743 (pm20) REVERT: E 113 MET cc_start: 0.8210 (mtt) cc_final: 0.7592 (mpp) REVERT: E 149 TYR cc_start: 0.8884 (m-10) cc_final: 0.8674 (m-10) REVERT: F 15 ASN cc_start: 0.6422 (p0) cc_final: 0.6215 (p0) REVERT: F 64 MET cc_start: 0.7661 (mmm) cc_final: 0.7178 (mmt) REVERT: F 77 TYR cc_start: 0.8947 (m-80) cc_final: 0.8503 (m-80) REVERT: F 169 ASN cc_start: 0.9228 (m110) cc_final: 0.8724 (m110) REVERT: F 195 ASN cc_start: 0.7741 (m-40) cc_final: 0.7260 (m110) REVERT: F 196 MET cc_start: 0.6470 (tmm) cc_final: 0.5590 (tmm) REVERT: F 205 GLU cc_start: 0.8369 (tt0) cc_final: 0.7993 (tt0) REVERT: G 113 MET cc_start: 0.8154 (mtt) cc_final: 0.7829 (mtt) REVERT: G 134 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8198 (tm-30) REVERT: H 134 GLU cc_start: 0.8788 (pt0) cc_final: 0.8574 (pt0) outliers start: 35 outliers final: 19 residues processed: 257 average time/residue: 0.1810 time to fit residues: 79.5875 Evaluate side-chains 236 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain d residue 218 MET Chi-restraints excluded: chain e residue 26 THR 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 249 ASP 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 235 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 188 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 chunk 162 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** 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 = 0.3498 r_free = 0.3498 target = 0.068383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.049330 restraints weight = 142221.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.050673 restraints weight = 70162.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.051560 restraints weight = 45816.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.052127 restraints weight = 35370.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.052423 restraints weight = 30216.491| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32859 Z= 0.160 Angle : 0.576 8.948 45866 Z= 0.321 Chirality : 0.041 0.179 4984 Planarity : 0.004 0.042 4812 Dihedral : 23.186 141.463 6532 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.55 % Allowed : 13.97 % Favored : 84.48 % 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: 0.47 (0.16), residues: 3069 helix: 1.41 (0.15), residues: 1227 sheet: 0.42 (0.23), residues: 590 loop : -0.82 (0.19), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 262 TYR 0.019 0.001 TYR A 112 PHE 0.009 0.001 PHE g 189 TRP 0.017 0.001 TRP A 62 HIS 0.009 0.001 HIS G 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (32811) covalent geometry : angle 0.57227 / 0.32 (45845) hydrogen bonds : bond 0.04724 / 3.23 ( 1435) hydrogen bonds : angle 5.08596 / 3.69 ( 3832) metal coordination : bond 0.00897 / 0.57 ( 48) metal coordination : angle 2.97171 / 1.88 ( 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 263 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 1.188 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: d 220 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7675 (mmp) REVERT: f 113 MET cc_start: 0.8435 (mtm) cc_final: 0.8103 (mtp) REVERT: f 220 MET cc_start: 0.8460 (mmm) cc_final: 0.8072 (tpp) REVERT: g 220 MET cc_start: 0.8479 (mmm) cc_final: 0.8208 (mmm) REVERT: A 28 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8839 (pt0) REVERT: A 39 ASN cc_start: 0.8185 (m-40) cc_final: 0.7859 (m-40) REVERT: A 68 HIS cc_start: 0.8248 (m90) cc_final: 0.7752 (m-70) REVERT: A 134 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8657 (mp0) REVERT: A 220 MET cc_start: 0.8835 (tpp) cc_final: 0.8000 (tpp) REVERT: B 7 GLU cc_start: 0.9517 (mt-10) cc_final: 0.9309 (mt-10) REVERT: B 32 GLU cc_start: 0.9441 (tp30) cc_final: 0.9233 (tp30) REVERT: B 113 MET cc_start: 0.8995 (tpp) cc_final: 0.8685 (mmt) REVERT: B 196 MET cc_start: 0.8666 (tpp) cc_final: 0.8172 (tpp) REVERT: B 220 MET cc_start: 0.7252 (tpp) cc_final: 0.7015 (tpp) REVERT: E 7 GLU cc_start: 0.8937 (pm20) cc_final: 0.8691 (pm20) REVERT: F 15 ASN cc_start: 0.6578 (p0) cc_final: 0.6345 (p0) REVERT: F 64 MET cc_start: 0.7688 (mmm) cc_final: 0.6940 (mmt) REVERT: F 77 TYR cc_start: 0.8815 (m-80) cc_final: 0.8378 (m-80) REVERT: F 113 MET cc_start: 0.8763 (tpp) cc_final: 0.7915 (mmm) REVERT: F 169 ASN cc_start: 0.9302 (m110) cc_final: 0.8817 (m110) REVERT: F 195 ASN cc_start: 0.7868 (m-40) cc_final: 0.7382 (m110) REVERT: F 196 MET cc_start: 0.6632 (tmm) cc_final: 0.5750 (tmm) REVERT: F 205 GLU cc_start: 0.8374 (tt0) cc_final: 0.7977 (tt0) REVERT: F 220 MET cc_start: 0.8578 (tpp) cc_final: 0.7678 (tpp) REVERT: G 113 MET cc_start: 0.8213 (mtt) cc_final: 0.7888 (mtt) REVERT: G 134 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8193 (tm-30) outliers start: 41 outliers final: 28 residues processed: 247 average time/residue: 0.1815 time to fit residues: 76.9729 Evaluate side-chains 245 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain d residue 218 MET Chi-restraints excluded: chain d residue 220 MET Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 218 MET 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 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 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 235 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 260 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 50.0000 chunk 246 optimal weight: 6.9990 chunk 287 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 193 HIS e 161 HIS ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 198 ASN E 12 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.067789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.048653 restraints weight = 142289.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.049991 restraints weight = 70692.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050846 restraints weight = 46374.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.051407 restraints weight = 35970.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051695 restraints weight = 30763.328| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32859 Z= 0.194 Angle : 0.610 10.856 45866 Z= 0.336 Chirality : 0.041 0.175 4984 Planarity : 0.004 0.041 4812 Dihedral : 23.238 142.010 6532 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.82 % Allowed : 15.14 % Favored : 83.04 % 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: 0.35 (0.16), residues: 3069 helix: 1.32 (0.15), residues: 1231 sheet: 0.30 (0.23), residues: 583 loop : -0.86 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 27 TYR 0.015 0.001 TYR H 242 PHE 0.014 0.001 PHE D 264 TRP 0.021 0.001 TRP A 62 HIS 0.008 0.001 HIS G 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (32811) covalent geometry : angle 0.60692 / 0.34 (45845) hydrogen bonds : bond 0.04805 / 3.27 ( 1435) hydrogen bonds : angle 5.11291 / 3.71 ( 3832) metal coordination : bond 0.01240 / 0.84 ( 48) metal coordination : angle 3.01665 / 1.78 ( 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: 48 poor density : 222 time to evaluate : 0.941 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: d 220 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7763 (mmp) REVERT: e 134 GLU cc_start: 0.8811 (pm20) cc_final: 0.8518 (pm20) REVERT: f 113 MET cc_start: 0.8554 (mtm) cc_final: 0.8160 (mtp) REVERT: f 220 MET cc_start: 0.8447 (mmm) cc_final: 0.8018 (tpp) REVERT: g 220 MET cc_start: 0.8452 (mmm) cc_final: 0.8146 (mmm) REVERT: A 28 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8831 (pt0) REVERT: A 39 ASN cc_start: 0.8120 (m-40) cc_final: 0.7697 (m-40) REVERT: A 68 HIS cc_start: 0.8445 (m90) cc_final: 0.7863 (m-70) REVERT: A 205 GLU cc_start: 0.9127 (pp20) cc_final: 0.8647 (pp20) REVERT: A 220 MET cc_start: 0.8831 (tpp) cc_final: 0.8036 (tpp) REVERT: B 7 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9327 (mt-10) REVERT: B 32 GLU cc_start: 0.9456 (tp30) cc_final: 0.9239 (tp30) REVERT: B 113 MET cc_start: 0.9093 (tpp) cc_final: 0.8766 (mmm) REVERT: B 196 MET cc_start: 0.8801 (tpp) cc_final: 0.8308 (tpp) REVERT: B 220 MET cc_start: 0.7270 (tpp) cc_final: 0.6994 (tpp) REVERT: E 7 GLU cc_start: 0.8997 (pm20) cc_final: 0.8758 (pm20) REVERT: E 28 GLU cc_start: 0.8823 (mp0) cc_final: 0.8585 (mp0) REVERT: F 15 ASN cc_start: 0.6534 (p0) cc_final: 0.6320 (p0) REVERT: F 64 MET cc_start: 0.7501 (mmm) cc_final: 0.6729 (mmt) REVERT: F 77 TYR cc_start: 0.8870 (m-80) cc_final: 0.8415 (m-80) REVERT: F 113 MET cc_start: 0.8694 (tpp) cc_final: 0.8423 (mmp) REVERT: F 169 ASN cc_start: 0.9297 (m110) cc_final: 0.8812 (m110) REVERT: F 195 ASN cc_start: 0.7842 (m-40) cc_final: 0.7454 (m110) REVERT: F 196 MET cc_start: 0.6479 (tmm) cc_final: 0.5586 (tmm) REVERT: F 205 GLU cc_start: 0.8384 (tt0) cc_final: 0.8111 (tt0) REVERT: F 220 MET cc_start: 0.8675 (tpp) cc_final: 0.7780 (tpp) REVERT: G 7 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.8963 (mp0) REVERT: G 113 MET cc_start: 0.8169 (mtt) cc_final: 0.7820 (mtt) REVERT: G 134 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8209 (tm-30) outliers start: 48 outliers final: 35 residues processed: 251 average time/residue: 0.1641 time to fit residues: 71.3985 Evaluate side-chains 256 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain d residue 218 MET Chi-restraints excluded: chain d residue 220 MET Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 66 VAL 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 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 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 235 LEU 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 69 VAL 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 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: 4.9990 chunk 212 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 284 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 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** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.066830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.047710 restraints weight = 143202.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.048972 restraints weight = 73990.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.049784 restraints weight = 49687.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.050293 restraints weight = 39014.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050620 restraints weight = 33687.268| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2230 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= 0.261 Angle : 0.664 10.852 45866 Z= 0.362 Chirality : 0.043 0.192 4984 Planarity : 0.004 0.041 4812 Dihedral : 23.322 141.500 6532 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.27 % Allowed : 15.37 % Favored : 82.36 % 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: 0.05 (0.16), residues: 3069 helix: 1.10 (0.15), residues: 1232 sheet: 0.08 (0.22), residues: 593 loop : -1.03 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 27 TYR 0.015 0.002 TYR h 112 PHE 0.014 0.002 PHE g 246 TRP 0.014 0.002 TRP A 62 HIS 0.014 0.001 HIS e 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.26 (32811) covalent geometry : angle 0.65849 / 0.36 (45845) hydrogen bonds : bond 0.05145 / 3.48 ( 1435) hydrogen bonds : angle 5.25453 / 3.82 ( 3832) metal coordination : bond 0.01950 / 1.35 ( 48) metal coordination : angle 3.98163 / 2.38 ( 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 278 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 218 time to evaluate : 1.141 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: c 220 MET cc_start: 0.8387 (mmm) cc_final: 0.8037 (mmm) REVERT: d 220 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7912 (mmp) REVERT: f 113 MET cc_start: 0.8522 (mtm) cc_final: 0.8196 (mtp) REVERT: g 220 MET cc_start: 0.8528 (mmm) cc_final: 0.8238 (mmm) REVERT: A 28 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8837 (pt0) REVERT: A 39 ASN cc_start: 0.8056 (m-40) cc_final: 0.7637 (m-40) REVERT: A 169 ASN cc_start: 0.9203 (t0) cc_final: 0.8922 (t0) REVERT: A 205 GLU cc_start: 0.9203 (pp20) cc_final: 0.8748 (pp20) REVERT: B 7 GLU cc_start: 0.9503 (mt-10) cc_final: 0.9276 (mt-10) REVERT: B 113 MET cc_start: 0.8976 (tpp) cc_final: 0.8700 (mmm) REVERT: B 196 MET cc_start: 0.8693 (tpp) cc_final: 0.8295 (tpp) REVERT: E 7 GLU cc_start: 0.8988 (pm20) cc_final: 0.8764 (pm20) REVERT: E 28 GLU cc_start: 0.8872 (mp0) cc_final: 0.8637 (mp0) REVERT: F 15 ASN cc_start: 0.6876 (p0) cc_final: 0.6651 (p0) REVERT: F 64 MET cc_start: 0.7452 (mmm) cc_final: 0.6610 (mmt) REVERT: F 77 TYR cc_start: 0.8874 (m-80) cc_final: 0.8388 (m-80) REVERT: F 113 MET cc_start: 0.8528 (tpp) cc_final: 0.7958 (mmm) REVERT: F 127 TYR cc_start: 0.7522 (m-10) cc_final: 0.7303 (m-80) REVERT: F 169 ASN cc_start: 0.9291 (m110) cc_final: 0.8815 (m110) REVERT: F 195 ASN cc_start: 0.7933 (m-40) cc_final: 0.7482 (m110) REVERT: F 196 MET cc_start: 0.6690 (tmm) cc_final: 0.5757 (tmm) REVERT: F 205 GLU cc_start: 0.8401 (tt0) cc_final: 0.8120 (tt0) REVERT: F 220 MET cc_start: 0.8695 (tpp) cc_final: 0.7810 (tpp) REVERT: G 113 MET cc_start: 0.8258 (mtt) cc_final: 0.7924 (mtt) REVERT: G 134 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8200 (tm-30) REVERT: H 158 GLU cc_start: 0.8041 (pm20) cc_final: 0.7801 (pm20) outliers start: 60 outliers final: 44 residues processed: 254 average time/residue: 0.1767 time to fit residues: 77.6385 Evaluate side-chains 258 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 95 THR Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain d residue 218 MET Chi-restraints excluded: chain d residue 220 MET Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 66 VAL 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 f residue 64 MET 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 134 GLU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 235 LEU 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 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 69 VAL 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 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: 0.1980 chunk 330 optimal weight: 40.0000 chunk 145 optimal weight: 3.9990 chunk 156 optimal weight: 40.0000 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 159 optimal weight: 30.0000 chunk 101 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 161 HIS ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** 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 = 0.3495 r_free = 0.3495 target = 0.068276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.049256 restraints weight = 141260.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.050546 restraints weight = 71967.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.051391 restraints weight = 47908.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.051927 restraints weight = 37481.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.052234 restraints weight = 32248.865| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32859 Z= 0.141 Angle : 0.597 11.342 45866 Z= 0.329 Chirality : 0.041 0.192 4984 Planarity : 0.004 0.043 4812 Dihedral : 23.271 139.587 6532 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.63 % Allowed : 16.24 % Favored : 82.13 % 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: 0.33 (0.16), residues: 3069 helix: 1.30 (0.15), residues: 1232 sheet: 0.32 (0.23), residues: 563 loop : -0.87 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 31 TYR 0.018 0.001 TYR e 177 PHE 0.013 0.001 PHE e 88 TRP 0.020 0.001 TRP A 62 HIS 0.008 0.001 HIS G 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (32811) covalent geometry : angle 0.59393 / 0.33 (45845) hydrogen bonds : bond 0.04547 / 3.10 ( 1435) hydrogen bonds : angle 5.05805 / 3.67 ( 3832) metal coordination : bond 0.00909 / 0.56 ( 48) metal coordination : angle 3.06881 / 2.09 ( 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 269 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 1.108 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 218 MET cc_start: 0.8390 (mmm) cc_final: 0.8189 (tpt) REVERT: c 220 MET cc_start: 0.8383 (mmm) cc_final: 0.8067 (mmm) REVERT: f 113 MET cc_start: 0.8385 (mtm) cc_final: 0.8069 (mtp) REVERT: g 220 MET cc_start: 0.8467 (mmm) cc_final: 0.8192 (mmm) REVERT: A 28 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8802 (pt0) REVERT: A 39 ASN cc_start: 0.8061 (m-40) cc_final: 0.7623 (m-40) REVERT: A 68 HIS cc_start: 0.8251 (m90) cc_final: 0.7611 (m90) REVERT: A 134 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8699 (mp0) REVERT: A 205 GLU cc_start: 0.9159 (pp20) cc_final: 0.8628 (pp20) REVERT: B 7 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9262 (mt-10) REVERT: B 28 GLU cc_start: 0.9121 (pm20) cc_final: 0.8712 (pm20) REVERT: B 32 GLU cc_start: 0.9334 (tp30) cc_final: 0.9082 (tp30) REVERT: B 64 MET cc_start: 0.8558 (ttm) cc_final: 0.8301 (ttm) REVERT: B 196 MET cc_start: 0.8690 (tpp) cc_final: 0.8273 (tpp) REVERT: B 220 MET cc_start: 0.7001 (tpp) cc_final: 0.6746 (tpp) REVERT: B 244 CYS cc_start: 0.8529 (t) cc_final: 0.7720 (p) REVERT: D 220 MET cc_start: 0.7984 (tpt) cc_final: 0.7356 (tpt) REVERT: E 7 GLU cc_start: 0.8978 (pm20) cc_final: 0.8752 (pm20) REVERT: E 28 GLU cc_start: 0.8846 (mp0) cc_final: 0.8593 (mp0) REVERT: E 113 MET cc_start: 0.8154 (mtt) cc_final: 0.7652 (mpp) REVERT: F 15 ASN cc_start: 0.6556 (p0) cc_final: 0.6338 (p0) REVERT: F 64 MET cc_start: 0.7491 (mmm) cc_final: 0.6720 (mmt) REVERT: F 77 TYR cc_start: 0.8855 (m-80) cc_final: 0.8363 (m-80) REVERT: F 113 MET cc_start: 0.8561 (tpp) cc_final: 0.7981 (mmm) REVERT: F 169 ASN cc_start: 0.9269 (m110) cc_final: 0.8799 (m110) REVERT: F 195 ASN cc_start: 0.7887 (m-40) cc_final: 0.7451 (m110) REVERT: F 196 MET cc_start: 0.6838 (tmm) cc_final: 0.5921 (tmm) REVERT: F 205 GLU cc_start: 0.8371 (tt0) cc_final: 0.8082 (tt0) REVERT: F 220 MET cc_start: 0.8703 (tpp) cc_final: 0.7821 (tpp) REVERT: G 7 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.8915 (mp0) REVERT: G 113 MET cc_start: 0.8173 (mtt) cc_final: 0.7798 (mtt) REVERT: G 134 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8176 (tm-30) REVERT: H 158 GLU cc_start: 0.8079 (pm20) cc_final: 0.7811 (pm20) outliers start: 43 outliers final: 36 residues processed: 250 average time/residue: 0.1739 time to fit residues: 74.9593 Evaluate side-chains 255 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain d residue 218 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 f residue 64 MET 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 134 GLU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 51 VAL 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 69 VAL Chi-restraints excluded: chain F residue 177 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 175 optimal weight: 10.0000 chunk 259 optimal weight: 0.3980 chunk 117 optimal weight: 0.8980 chunk 325 optimal weight: 50.0000 chunk 83 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 265 optimal weight: 7.9990 chunk 26 optimal weight: 40.0000 chunk 110 optimal weight: 0.4980 chunk 243 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** 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 = 0.3501 r_free = 0.3501 target = 0.068521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.049367 restraints weight = 141631.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.050725 restraints weight = 70253.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.051602 restraints weight = 45966.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.052166 restraints weight = 35605.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052509 restraints weight = 30409.315| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32859 Z= 0.137 Angle : 0.593 10.733 45866 Z= 0.326 Chirality : 0.040 0.178 4984 Planarity : 0.004 0.044 4812 Dihedral : 23.256 139.444 6532 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.51 % Allowed : 16.50 % 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: 0.42 (0.16), residues: 3069 helix: 1.38 (0.15), residues: 1227 sheet: 0.38 (0.23), residues: 563 loop : -0.82 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG e 159 TYR 0.017 0.001 TYR e 177 PHE 0.009 0.001 PHE e 88 TRP 0.033 0.001 TRP A 62 HIS 0.042 0.001 HIS e 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (32811) covalent geometry : angle 0.58965 / 0.33 (45845) hydrogen bonds : bond 0.04483 / 3.07 ( 1435) hydrogen bonds : angle 4.98252 / 3.63 ( 3832) metal coordination : bond 0.00783 / 0.48 ( 48) metal coordination : angle 2.78542 / 1.87 ( 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 264 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 1.097 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 218 MET cc_start: 0.8158 (mmm) cc_final: 0.7952 (tpt) REVERT: b 64 MET cc_start: 0.8923 (mtm) cc_final: 0.8643 (mtt) REVERT: c 220 MET cc_start: 0.8381 (mmm) cc_final: 0.8059 (mmm) REVERT: f 113 MET cc_start: 0.8378 (mtm) cc_final: 0.8091 (mtp) REVERT: g 220 MET cc_start: 0.8460 (mmm) cc_final: 0.8192 (mmm) REVERT: A 28 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8793 (pt0) REVERT: A 39 ASN cc_start: 0.8056 (m-40) cc_final: 0.7606 (m-40) REVERT: A 68 HIS cc_start: 0.8276 (m90) cc_final: 0.7682 (m90) REVERT: A 134 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8688 (mp0) REVERT: A 205 GLU cc_start: 0.9174 (pp20) cc_final: 0.8657 (pp20) REVERT: B 7 GLU cc_start: 0.9500 (mt-10) cc_final: 0.9255 (mt-10) REVERT: B 64 MET cc_start: 0.8528 (ttm) cc_final: 0.8265 (ttm) REVERT: B 113 MET cc_start: 0.8679 (mmm) cc_final: 0.8255 (mmm) REVERT: B 196 MET cc_start: 0.8625 (tpp) cc_final: 0.8202 (tpp) REVERT: B 220 MET cc_start: 0.7121 (tpp) cc_final: 0.6833 (tpp) REVERT: B 244 CYS cc_start: 0.8608 (t) cc_final: 0.7756 (p) REVERT: D 220 MET cc_start: 0.7979 (tpt) cc_final: 0.7343 (tpt) REVERT: E 7 GLU cc_start: 0.8997 (pm20) cc_final: 0.8781 (pm20) REVERT: E 28 GLU cc_start: 0.8870 (mp0) cc_final: 0.8620 (mp0) REVERT: E 113 MET cc_start: 0.8142 (mtt) cc_final: 0.7655 (mpp) REVERT: F 15 ASN cc_start: 0.6563 (p0) cc_final: 0.6342 (p0) REVERT: F 64 MET cc_start: 0.7474 (mmm) cc_final: 0.6708 (mmt) REVERT: F 77 TYR cc_start: 0.8847 (m-80) cc_final: 0.8353 (m-80) REVERT: F 113 MET cc_start: 0.8645 (tpp) cc_final: 0.8049 (mmm) REVERT: F 169 ASN cc_start: 0.9261 (m110) cc_final: 0.8793 (m110) REVERT: F 195 ASN cc_start: 0.7882 (m-40) cc_final: 0.7450 (m110) REVERT: F 196 MET cc_start: 0.6871 (tmm) cc_final: 0.5957 (tmm) REVERT: F 205 GLU cc_start: 0.8352 (tt0) cc_final: 0.8063 (tt0) REVERT: F 220 MET cc_start: 0.8731 (tpp) cc_final: 0.7917 (tpp) REVERT: G 7 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.8948 (mp0) REVERT: G 113 MET cc_start: 0.8132 (mtt) cc_final: 0.7761 (mtt) REVERT: G 134 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8175 (tm-30) REVERT: H 218 MET cc_start: 0.8989 (mmm) cc_final: 0.8643 (mmm) outliers start: 40 outliers final: 34 residues processed: 249 average time/residue: 0.1720 time to fit residues: 73.6510 Evaluate side-chains 257 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain d residue 218 MET Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 66 VAL 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 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 C residue 245 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 51 VAL 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 26 THR Chi-restraints excluded: chain F residue 69 VAL 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 220 MET 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: 0.7980 chunk 55 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 284 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 252 optimal weight: 30.0000 chunk 9 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 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** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.068517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.049364 restraints weight = 142191.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.050727 restraints weight = 70300.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.051610 restraints weight = 45905.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.052126 restraints weight = 35435.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052523 restraints weight = 30384.724| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2368 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= 0.144 Angle : 0.592 10.717 45866 Z= 0.325 Chirality : 0.040 0.185 4984 Planarity : 0.004 0.044 4812 Dihedral : 23.252 139.485 6532 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.59 % Allowed : 16.50 % Favored : 81.91 % 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: 0.43 (0.16), residues: 3069 helix: 1.40 (0.15), residues: 1232 sheet: 0.32 (0.23), residues: 578 loop : -0.81 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 259 TYR 0.015 0.001 TYR e 177 PHE 0.012 0.001 PHE e 88 TRP 0.030 0.001 TRP A 62 HIS 0.007 0.001 HIS G 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (32811) covalent geometry : angle 0.58875 / 0.32 (45845) hydrogen bonds : bond 0.04420 / 3.02 ( 1435) hydrogen bonds : angle 4.94154 / 3.60 ( 3832) metal coordination : bond 0.00918 / 0.63 ( 48) metal coordination : angle 2.78390 / 1.93 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5528.63 seconds wall clock time: 96 minutes 33.61 seconds (5793.61 seconds total)