Starting phenix.real_space_refine on Thu Jun 26 21:04:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ut1_26744/06_2025/7ut1_26744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut1_26744/06_2025/7ut1_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_26744/06_2025/7ut1_26744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut1_26744/06_2025/7ut1_26744.map" model { file = "/net/cci-nas-00/data/ceres_data/7ut1_26744/06_2025/7ut1_26744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut1_26744/06_2025/7ut1_26744.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 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: 18.87, per 1000 atoms: 0.60 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: 7.72 Conformation dependent library (CDL) restraints added in 2.9 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: 13.02 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: 13.34 Time building geometry restraints manager: 9.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9085 1.34 - 1.46: 9510 1.46 - 1.58: 13460 1.58 - 1.71: 580 1.71 - 1.83: 176 Bond restraints: 32811 Sorted by residual: bond pdb=" CG PRO d 232 " pdb=" CD PRO d 232 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.25e+00 bond pdb=" CB LYS E 74 " pdb=" CG LYS E 74 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CG GLU E 7 " pdb=" CD GLU E 7 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" CG LYS E 74 " pdb=" CD LYS E 74 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CG PRO D 232 " pdb=" CD PRO D 232 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.07e+00 ... (remaining 32806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 44930 1.73 - 3.46: 821 3.46 - 5.19: 64 5.19 - 6.92: 22 6.92 - 8.66: 8 Bond angle restraints: 45845 Sorted by residual: angle pdb=" N PRO f 210 " pdb=" CA PRO f 210 " pdb=" C PRO f 210 " ideal model delta sigma weight residual 114.68 110.86 3.82 1.04e+00 9.25e-01 1.35e+01 angle pdb=" CA ASP G 249 " pdb=" CB ASP G 249 " pdb=" CG ASP G 249 " ideal model delta sigma weight residual 112.60 108.93 3.67 1.00e+00 1.00e+00 1.35e+01 angle pdb=" N GLU f 32 " pdb=" CA GLU f 32 " pdb=" CB GLU f 32 " ideal model delta sigma weight residual 110.28 115.83 -5.55 1.55e+00 4.16e-01 1.28e+01 angle pdb=" N GLU E 7 " pdb=" CA GLU E 7 " pdb=" CB GLU E 7 " ideal model delta sigma weight residual 110.39 116.30 -5.91 1.66e+00 3.63e-01 1.27e+01 angle pdb=" C GLN E 6 " pdb=" N GLU E 7 " pdb=" CA GLU E 7 " ideal model delta sigma weight residual 120.72 115.24 5.48 1.67e+00 3.59e-01 1.08e+01 ... (remaining 45840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.34: 16508 28.34 - 56.68: 1751 56.68 - 85.02: 165 85.02 - 113.36: 7 113.36 - 141.70: 2 Dihedral angle restraints: 18433 sinusoidal: 9259 harmonic: 9174 Sorted by residual: dihedral pdb=" CA TYR H 112 " pdb=" C TYR H 112 " pdb=" N MET H 113 " pdb=" CA MET H 113 " ideal model delta harmonic sigma weight residual 180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA MET d 218 " pdb=" C MET d 218 " pdb=" N VAL d 219 " pdb=" CA VAL d 219 " ideal model delta harmonic sigma weight residual -180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA MET a 218 " pdb=" C MET a 218 " pdb=" N VAL a 219 " pdb=" CA VAL a 219 " ideal model delta harmonic sigma weight residual 180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 18430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4092 0.047 - 0.095: 735 0.095 - 0.142: 150 0.142 - 0.189: 6 0.189 - 0.236: 1 Chirality restraints: 4984 Sorted by residual: chirality pdb=" CB ILE a 211 " pdb=" CA ILE a 211 " pdb=" CG1 ILE a 211 " pdb=" CG2 ILE a 211 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB ILE G 115 " pdb=" CA ILE G 115 " pdb=" CG1 ILE G 115 " pdb=" CG2 ILE G 115 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CB VAL g 194 " pdb=" CA VAL g 194 " pdb=" CG1 VAL g 194 " pdb=" CG2 VAL g 194 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 4981 not shown) Planarity restraints: 4812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 13 " 0.021 2.00e-02 2.50e+03 2.73e-02 1.12e+01 pdb=" CG HIS E 13 " -0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS E 13 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 HIS E 13 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS E 13 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS E 13 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 115 " 0.047 5.00e-02 4.00e+02 7.07e-02 7.99e+00 pdb=" N PRO H 116 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO H 116 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 116 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 13 " 0.021 2.00e-02 2.50e+03 1.80e-02 4.84e+00 pdb=" CG HIS G 13 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS G 13 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS G 13 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS G 13 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS G 13 " 0.014 2.00e-02 2.50e+03 ... (remaining 4809 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1076 2.70 - 3.25: 30589 3.25 - 3.80: 55890 3.80 - 4.35: 68488 4.35 - 4.90: 105990 Nonbonded interactions: 262033 Sorted by model distance: nonbonded pdb=" OD1 ASN A 123 " pdb=" OG1 THR A 145 " model vdw 2.148 3.040 nonbonded pdb=" O ALA E 1 " pdb=" OG SER E 4 " model vdw 2.167 3.040 nonbonded pdb=" CG HIS E 13 " pdb="ZN ZN E 500 " model vdw 2.170 1.960 nonbonded pdb=" O ALA e 1 " pdb=" OG SER e 4 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR c 242 " pdb=" OP1 DG l 10 " model vdw 2.200 3.040 ... (remaining 262028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 155 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 208 or resid 218 through 264 or resid 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 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 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 264 or resid 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 264 or resid 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 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 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 264 or resid 500)) selection = (chain 'h' and (resid 2 through 144 or resid 155 through 161 or (resid 162 and ( \ name N or name CA or name C or name O or name CB )) or resid 163 through 208 or \ resid 218 through 264 or resid 500)) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 217 through 264) selection = chain 'c' selection = (chain 'd' and resid 217 through 264) } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'i' selection = chain 'l' } ncs_group { reference = (chain 'J' and resid 1 through 38) selection = (chain 'M' and resid 1 through 38) selection = (chain 'j' and resid 1 through 38) selection = chain 'm' } ncs_group { reference = (chain 'K' and resid 5 through 16) selection = (chain 'N' and resid 5 through 16) selection = (chain 'k' and resid 5 through 16) selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 84.580 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.590 32859 Z= 0.273 Angle : 0.633 54.304 45866 Z= 0.312 Chirality : 0.038 0.236 4984 Planarity : 0.004 0.071 4812 Dihedral : 20.160 141.704 12459 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.001 TRP b 208 HIS 0.034 0.001 HIS E 13 PHE 0.013 0.001 PHE H 88 TYR 0.012 0.001 TYR e 242 ARG 0.004 0.000 ARG g 138 Details of bonding type rmsd hydrogen bonds : bond 0.21837 ( 1435) hydrogen bonds : angle 8.48241 ( 3832) metal coordination : bond 0.20363 ( 48) metal coordination : angle 14.47705 ( 21) covalent geometry : bond 0.00303 (32811) covalent geometry : angle 0.55241 (45845) *********************** 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 : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 218 MET cc_start: 0.8184 (tpt) cc_final: 0.7885 (tpt) REVERT: f 113 MET cc_start: 0.8611 (mtm) cc_final: 0.8287 (mtp) REVERT: f 220 MET cc_start: 0.8848 (mmm) cc_final: 0.8094 (tpp) REVERT: g 32 GLU cc_start: 0.9155 (mp0) cc_final: 0.8793 (mp0) REVERT: A 39 ASN cc_start: 0.8221 (m-40) cc_final: 0.7824 (t0) REVERT: A 113 MET cc_start: 0.7940 (mtm) cc_final: 0.7452 (mtt) REVERT: B 7 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9265 (mt-10) REVERT: B 32 GLU cc_start: 0.9461 (tp30) cc_final: 0.9256 (tp30) REVERT: B 244 CYS cc_start: 0.8835 (t) cc_final: 0.8502 (t) REVERT: C 223 ASP cc_start: 0.7780 (t0) cc_final: 0.7471 (t0) REVERT: C 230 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8350 (mmmt) REVERT: F 7 GLU cc_start: 0.9333 (mp0) cc_final: 0.9106 (mp0) REVERT: F 15 ASN cc_start: 0.6600 (p0) cc_final: 0.6260 (p0) REVERT: F 64 MET cc_start: 0.7586 (mmm) cc_final: 0.7067 (mmt) REVERT: F 77 TYR cc_start: 0.8982 (m-80) cc_final: 0.8493 (m-80) REVERT: F 169 ASN cc_start: 0.9137 (m110) cc_final: 0.8651 (m110) REVERT: F 177 TYR cc_start: 0.7430 (m-80) cc_final: 0.7205 (m-80) REVERT: F 195 ASN cc_start: 0.7459 (m-40) cc_final: 0.7050 (m110) REVERT: F 205 GLU cc_start: 0.8349 (tt0) cc_final: 0.7995 (tt0) REVERT: F 208 TRP cc_start: 0.8137 (m100) cc_final: 0.7645 (m100) REVERT: G 7 GLU cc_start: 0.9117 (mp0) cc_final: 0.8483 (mp0) REVERT: G 134 GLU cc_start: 0.8548 (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: 0.3952 time to fit residues: 171.5444 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 : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 302 optimal weight: 4.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 12 HIS a 193 HIS b 163 ASN ** b 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 ASN e 161 HIS ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN F 12 HIS F 193 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.065955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.046709 restraints weight = 145645.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.047993 restraints weight = 73649.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.048831 restraints weight = 48943.082| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 32859 Z= 0.353 Angle : 0.724 11.712 45866 Z= 0.393 Chirality : 0.045 0.196 4984 Planarity : 0.005 0.049 4812 Dihedral : 23.001 145.385 6532 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.61 % Allowed : 7.95 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3069 helix: 0.73 (0.15), residues: 1229 sheet: -0.03 (0.23), residues: 578 loop : -1.11 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 208 HIS 0.018 0.002 HIS G 9 PHE 0.018 0.002 PHE F 90 TYR 0.021 0.002 TYR h 112 ARG 0.006 0.001 ARG g 27 Details of bonding type rmsd hydrogen bonds : bond 0.06106 ( 1435) hydrogen bonds : angle 5.96613 ( 3832) metal coordination : bond 0.02274 ( 48) metal coordination : angle 5.66926 ( 21) covalent geometry : bond 0.00772 (32811) covalent geometry : angle 0.71369 (45845) *********************** 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: 16 poor density : 229 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 MET cc_start: 0.8392 (mmm) cc_final: 0.7998 (mmm) REVERT: d 218 MET cc_start: 0.8321 (tpt) cc_final: 0.8043 (tpt) REVERT: e 52 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8618 (m110) REVERT: f 77 TYR cc_start: 0.8271 (m-80) cc_final: 0.8001 (m-80) REVERT: f 113 MET cc_start: 0.8649 (mtm) cc_final: 0.8319 (mtp) REVERT: f 220 MET cc_start: 0.8634 (mmm) cc_final: 0.8202 (tpp) REVERT: g 32 GLU cc_start: 0.9218 (mp0) cc_final: 0.8713 (mp0) REVERT: g 220 MET cc_start: 0.8572 (mmm) cc_final: 0.8125 (mmm) REVERT: A 39 ASN cc_start: 0.8271 (m-40) cc_final: 0.7921 (m-40) REVERT: A 169 ASN cc_start: 0.9237 (t0) cc_final: 0.8948 (t0) REVERT: B 32 GLU cc_start: 0.9480 (tp30) cc_final: 0.9260 (tp30) REVERT: B 113 MET cc_start: 0.8963 (tpp) cc_final: 0.8686 (tpt) REVERT: B 196 MET cc_start: 0.8021 (tpp) cc_final: 0.7553 (tpp) REVERT: B 220 MET cc_start: 0.7117 (tpp) cc_final: 0.6727 (tpp) REVERT: C 223 ASP cc_start: 0.7561 (t0) cc_final: 0.7264 (t0) REVERT: E 28 GLU cc_start: 0.8861 (mp0) cc_final: 0.8660 (mp0) REVERT: F 7 GLU cc_start: 0.9294 (mp0) cc_final: 0.9012 (mp0) REVERT: F 64 MET cc_start: 0.7565 (mmm) cc_final: 0.6904 (tpt) REVERT: F 77 TYR cc_start: 0.9093 (m-80) cc_final: 0.8637 (m-80) REVERT: F 169 ASN cc_start: 0.9294 (m110) cc_final: 0.8821 (m110) REVERT: F 195 ASN cc_start: 0.7750 (m-40) cc_final: 0.7242 (m110) REVERT: F 205 GLU cc_start: 0.8440 (tt0) cc_final: 0.8128 (tt0) REVERT: F 220 MET cc_start: 0.8441 (tpp) cc_final: 0.7457 (tpp) REVERT: G 7 GLU cc_start: 0.9359 (mp0) cc_final: 0.8781 (mp0) REVERT: G 134 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8238 (tm-30) REVERT: H 15 ASN cc_start: 0.8595 (p0) cc_final: 0.8170 (p0) REVERT: H 158 GLU cc_start: 0.7877 (mp0) cc_final: 0.7616 (mp0) REVERT: H 242 TYR cc_start: 0.8852 (p90) cc_final: 0.8600 (p90) outliers start: 16 outliers final: 11 residues processed: 235 average time/residue: 0.3861 time to fit residues: 153.6392 Evaluate side-chains 221 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain e residue 52 ASN Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain g residue 7 GLU Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 22 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 123 optimal weight: 0.0020 chunk 94 optimal weight: 7.9990 chunk 279 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 216 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 HIS ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN B 133 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.049187 restraints weight = 142420.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.050609 restraints weight = 67974.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051542 restraints weight = 43599.046| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32859 Z= 0.134 Angle : 0.548 12.202 45866 Z= 0.301 Chirality : 0.039 0.132 4984 Planarity : 0.004 0.041 4812 Dihedral : 22.874 140.041 6532 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.79 % Allowed : 11.20 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 3069 helix: 1.28 (0.15), residues: 1223 sheet: 0.17 (0.22), residues: 612 loop : -0.86 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 208 HIS 0.012 0.001 HIS G 9 PHE 0.027 0.001 PHE D 246 TYR 0.021 0.001 TYR a 112 ARG 0.003 0.000 ARG e 54 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 1435) hydrogen bonds : angle 5.18954 ( 3832) metal coordination : bond 0.01208 ( 48) metal coordination : angle 4.12418 ( 21) covalent geometry : bond 0.00291 (32811) covalent geometry : angle 0.54120 (45845) *********************** 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 270 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 3.191 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: 0.8196 (mmm) cc_final: 0.7634 (mmm) REVERT: c 218 MET cc_start: 0.8720 (mmm) cc_final: 0.8434 (mmm) REVERT: d 218 MET cc_start: 0.8300 (tpt) cc_final: 0.7948 (tpp) REVERT: f 77 TYR cc_start: 0.8390 (m-80) cc_final: 0.8007 (m-80) REVERT: f 220 MET cc_start: 0.8510 (mmm) cc_final: 0.7993 (tpp) REVERT: g 7 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8370 (tm-30) REVERT: g 218 MET cc_start: 0.9007 (mmp) cc_final: 0.8650 (mmp) REVERT: g 220 MET cc_start: 0.8563 (mmm) cc_final: 0.8286 (mmm) REVERT: A 39 ASN cc_start: 0.8201 (m-40) cc_final: 0.7856 (m-40) REVERT: A 134 GLU cc_start: 0.9012 (mp0) cc_final: 0.8716 (pm20) REVERT: A 205 GLU cc_start: 0.9121 (pp20) cc_final: 0.8732 (pp20) REVERT: B 32 GLU cc_start: 0.9524 (tp30) cc_final: 0.9314 (tp30) REVERT: B 64 MET cc_start: 0.8725 (ttp) cc_final: 0.8331 (ttm) REVERT: B 113 MET cc_start: 0.8961 (tpp) cc_final: 0.8672 (mmt) REVERT: B 127 TYR cc_start: 0.7607 (m-10) cc_final: 0.7391 (m-80) REVERT: B 196 MET cc_start: 0.8448 (tpp) cc_final: 0.7961 (tpp) REVERT: B 220 MET cc_start: 0.7935 (tpp) cc_final: 0.7674 (tpp) REVERT: D 236 ILE cc_start: 0.9169 (mm) cc_final: 0.8934 (mt) REVERT: E 7 GLU cc_start: 0.8935 (pm20) cc_final: 0.8722 (pm20) REVERT: E 28 GLU cc_start: 0.8887 (mp0) cc_final: 0.8639 (mp0) REVERT: E 113 MET cc_start: 0.8148 (mtt) cc_final: 0.7749 (mpp) REVERT: F 7 GLU cc_start: 0.9243 (mp0) cc_final: 0.9009 (mp0) REVERT: F 15 ASN cc_start: 0.6966 (p0) cc_final: 0.6546 (p0) REVERT: F 64 MET cc_start: 0.7691 (mmm) cc_final: 0.7014 (mmt) REVERT: F 77 TYR cc_start: 0.8954 (m-80) cc_final: 0.8503 (m-80) REVERT: F 113 MET cc_start: 0.8954 (tpp) cc_final: 0.8661 (tpp) REVERT: F 127 TYR cc_start: 0.7813 (m-10) cc_final: 0.7590 (m-80) REVERT: F 169 ASN cc_start: 0.9250 (m110) cc_final: 0.8799 (m110) REVERT: F 195 ASN cc_start: 0.7492 (m-40) cc_final: 0.7087 (m110) REVERT: F 196 MET cc_start: 0.6350 (tmm) cc_final: 0.5740 (tmm) REVERT: F 205 GLU cc_start: 0.8358 (tt0) cc_final: 0.8009 (tt0) REVERT: F 220 MET cc_start: 0.8713 (tpp) cc_final: 0.7831 (tpp) REVERT: G 7 GLU cc_start: 0.9385 (mp0) cc_final: 0.8886 (mp0) REVERT: G 113 MET cc_start: 0.8084 (mtt) cc_final: 0.7782 (mtt) REVERT: G 134 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8226 (tm-30) REVERT: H 242 TYR cc_start: 0.8788 (p90) cc_final: 0.8556 (p90) outliers start: 21 outliers final: 13 residues processed: 261 average time/residue: 0.3910 time to fit residues: 171.6961 Evaluate side-chains 234 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 221 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 51 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 34 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 322 optimal weight: 20.0000 chunk 235 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 247 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 303 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 ASN ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS E 207 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.066402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.047208 restraints weight = 143838.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.048505 restraints weight = 72099.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.049350 restraints weight = 47644.724| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 32859 Z= 0.282 Angle : 0.641 8.688 45866 Z= 0.348 Chirality : 0.042 0.153 4984 Planarity : 0.004 0.040 4812 Dihedral : 22.923 142.429 6532 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.70 % Allowed : 14.19 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 3069 helix: 1.01 (0.15), residues: 1230 sheet: -0.03 (0.22), residues: 626 loop : -1.03 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 208 HIS 0.011 0.001 HIS G 9 PHE 0.014 0.002 PHE F 90 TYR 0.023 0.002 TYR a 112 ARG 0.004 0.000 ARG g 27 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 1435) hydrogen bonds : angle 5.33571 ( 3832) metal coordination : bond 0.01812 ( 48) metal coordination : angle 4.27622 ( 21) covalent geometry : bond 0.00619 (32811) covalent geometry : angle 0.63422 (45845) *********************** 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 265 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 MET cc_start: 0.8225 (mmm) cc_final: 0.7666 (mmm) REVERT: d 218 MET cc_start: 0.8182 (tpt) cc_final: 0.7931 (tpt) REVERT: f 32 GLU cc_start: 0.8667 (pm20) cc_final: 0.8371 (pm20) REVERT: f 77 TYR cc_start: 0.8391 (m-80) cc_final: 0.7920 (m-80) REVERT: f 220 MET cc_start: 0.8537 (mmm) cc_final: 0.8135 (tpp) REVERT: g 7 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8421 (tm-30) REVERT: g 32 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.9033 (mm-30) REVERT: g 218 MET cc_start: 0.8982 (mmp) cc_final: 0.8673 (mmp) REVERT: g 220 MET cc_start: 0.8575 (mmm) cc_final: 0.8333 (mmm) REVERT: h 134 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8520 (pm20) REVERT: A 39 ASN cc_start: 0.8163 (m-40) cc_final: 0.7770 (m-40) REVERT: A 134 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8816 (pp20) REVERT: A 169 ASN cc_start: 0.9220 (t0) cc_final: 0.8902 (t0) REVERT: A 205 GLU cc_start: 0.9205 (pp20) cc_final: 0.8797 (pp20) REVERT: B 28 GLU cc_start: 0.9236 (mp0) cc_final: 0.8901 (pm20) REVERT: B 32 GLU cc_start: 0.9485 (tp30) cc_final: 0.9277 (tp30) REVERT: B 64 MET cc_start: 0.8731 (ttp) cc_final: 0.8210 (ttm) REVERT: B 113 MET cc_start: 0.8944 (tpp) cc_final: 0.8719 (mmt) REVERT: B 196 MET cc_start: 0.8737 (tpp) cc_final: 0.8337 (tpp) REVERT: B 220 MET cc_start: 0.8037 (tpp) cc_final: 0.7713 (tpp) REVERT: D 228 SER cc_start: 0.9021 (p) cc_final: 0.8452 (p) REVERT: D 230 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7747 (mmmt) REVERT: E 28 GLU cc_start: 0.8924 (mp0) cc_final: 0.8680 (mp0) REVERT: F 15 ASN cc_start: 0.6870 (p0) cc_final: 0.6452 (p0) REVERT: F 64 MET cc_start: 0.7528 (mmm) cc_final: 0.6597 (mmt) REVERT: F 77 TYR cc_start: 0.8948 (m-80) cc_final: 0.8450 (m-80) REVERT: F 127 TYR cc_start: 0.7947 (m-10) cc_final: 0.7746 (m-80) REVERT: F 169 ASN cc_start: 0.9220 (m110) cc_final: 0.8763 (m110) REVERT: F 195 ASN cc_start: 0.7719 (m-40) cc_final: 0.7296 (m110) REVERT: F 196 MET cc_start: 0.6616 (tmm) cc_final: 0.5826 (tmm) REVERT: F 205 GLU cc_start: 0.8366 (tt0) cc_final: 0.8123 (tt0) REVERT: F 220 MET cc_start: 0.8910 (tpp) cc_final: 0.8295 (tpp) REVERT: G 7 GLU cc_start: 0.9397 (mp0) cc_final: 0.8847 (mp0) REVERT: G 113 MET cc_start: 0.8225 (mtt) cc_final: 0.7866 (mtt) REVERT: G 134 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8274 (tm-30) REVERT: H 242 TYR cc_start: 0.8868 (p90) cc_final: 0.8585 (p90) outliers start: 45 outliers final: 25 residues processed: 249 average time/residue: 0.3930 time to fit residues: 166.4688 Evaluate side-chains 241 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 64 MET Chi-restraints excluded: chain b residue 191 LEU Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 32 GLU Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 115 ILE Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain g residue 7 GLU Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain H residue 34 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 9 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 252 optimal weight: 30.0000 chunk 302 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 250 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 193 HIS ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 143 HIS ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.068188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.049179 restraints weight = 141793.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050472 restraints weight = 72018.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.051313 restraints weight = 47916.290| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32859 Z= 0.150 Angle : 0.549 8.561 45866 Z= 0.301 Chirality : 0.038 0.129 4984 Planarity : 0.004 0.044 4812 Dihedral : 22.894 139.596 6532 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.55 % Allowed : 15.56 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 3069 helix: 1.29 (0.15), residues: 1225 sheet: 0.35 (0.23), residues: 557 loop : -0.90 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 208 HIS 0.009 0.001 HIS G 9 PHE 0.010 0.001 PHE F 246 TYR 0.020 0.001 TYR D 242 ARG 0.003 0.000 ARG e 259 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 1435) hydrogen bonds : angle 5.00533 ( 3832) metal coordination : bond 0.00861 ( 48) metal coordination : angle 3.13757 ( 21) covalent geometry : bond 0.00329 (32811) covalent geometry : angle 0.54468 (45845) *********************** 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 277 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 MET cc_start: 0.8190 (mmm) cc_final: 0.7774 (mmm) REVERT: d 218 MET cc_start: 0.8128 (tpt) cc_final: 0.7884 (tpt) REVERT: f 77 TYR cc_start: 0.8178 (m-80) cc_final: 0.7868 (m-80) REVERT: f 220 MET cc_start: 0.8476 (mmm) cc_final: 0.8104 (tpp) REVERT: g 7 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8406 (tm-30) REVERT: g 218 MET cc_start: 0.8947 (mmp) cc_final: 0.8652 (mmp) REVERT: g 220 MET cc_start: 0.8585 (mmm) cc_final: 0.8271 (mmm) REVERT: h 134 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: A 39 ASN cc_start: 0.8169 (m-40) cc_final: 0.7832 (m-40) REVERT: A 134 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8746 (pp20) REVERT: A 205 GLU cc_start: 0.9148 (pp20) cc_final: 0.8607 (pp20) REVERT: B 28 GLU cc_start: 0.9191 (mp0) cc_final: 0.8823 (pm20) REVERT: B 32 GLU cc_start: 0.9466 (tp30) cc_final: 0.9251 (tp30) REVERT: B 64 MET cc_start: 0.8501 (ttp) cc_final: 0.8016 (ttm) REVERT: B 113 MET cc_start: 0.9014 (tpp) cc_final: 0.8540 (mmm) REVERT: B 196 MET cc_start: 0.8844 (tpp) cc_final: 0.8286 (tpp) REVERT: B 220 MET cc_start: 0.8234 (tpp) cc_final: 0.7973 (tpp) REVERT: B 244 CYS cc_start: 0.8579 (t) cc_final: 0.7734 (p) REVERT: C 218 MET cc_start: 0.8080 (ptt) cc_final: 0.7565 (mmp) REVERT: C 235 LEU cc_start: 0.8605 (tt) cc_final: 0.8001 (mt) REVERT: D 228 SER cc_start: 0.8999 (p) cc_final: 0.8249 (p) REVERT: D 230 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7747 (mmmt) REVERT: E 7 GLU cc_start: 0.8993 (pm20) cc_final: 0.8759 (pm20) REVERT: E 28 GLU cc_start: 0.8924 (mp0) cc_final: 0.8650 (mp0) REVERT: E 74 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8204 (mmmt) REVERT: E 112 TYR cc_start: 0.8570 (t80) cc_final: 0.8168 (t80) REVERT: E 113 MET cc_start: 0.8190 (mtt) cc_final: 0.7790 (mpp) REVERT: F 15 ASN cc_start: 0.6940 (p0) cc_final: 0.6457 (p0) REVERT: F 64 MET cc_start: 0.7669 (mmm) cc_final: 0.6774 (mmt) REVERT: F 77 TYR cc_start: 0.8889 (m-80) cc_final: 0.8377 (m-80) REVERT: F 113 MET cc_start: 0.8812 (tpp) cc_final: 0.7939 (mmm) REVERT: F 169 ASN cc_start: 0.9274 (m110) cc_final: 0.8812 (m110) REVERT: F 195 ASN cc_start: 0.7769 (m-40) cc_final: 0.7326 (m110) REVERT: F 196 MET cc_start: 0.6644 (tmm) cc_final: 0.5934 (tmm) REVERT: F 205 GLU cc_start: 0.8372 (tt0) cc_final: 0.8097 (tt0) REVERT: F 220 MET cc_start: 0.8909 (tpp) cc_final: 0.8230 (tpp) REVERT: G 7 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.8959 (mp0) REVERT: G 113 MET cc_start: 0.8150 (mtt) cc_final: 0.7888 (mtt) REVERT: G 134 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8200 (tm-30) REVERT: H 242 TYR cc_start: 0.8850 (p90) cc_final: 0.8586 (p90) outliers start: 41 outliers final: 25 residues processed: 260 average time/residue: 0.3821 time to fit residues: 167.6011 Evaluate side-chains 246 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain e residue 26 THR 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 113 MET Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 249 ASP 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 221 TRP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 300 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 310 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 288 optimal weight: 4.9990 chunk 266 optimal weight: 0.6980 chunk 284 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 HIS ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 198 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 HIS C 248 GLN ** E 39 ASN ** 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 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.066760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.047431 restraints weight = 142988.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.048721 restraints weight = 71759.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.049574 restraints weight = 47583.086| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 32859 Z= 0.253 Angle : 0.620 9.203 45866 Z= 0.336 Chirality : 0.041 0.145 4984 Planarity : 0.004 0.042 4812 Dihedral : 22.926 140.561 6532 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.16 % Allowed : 16.05 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 3069 helix: 1.06 (0.15), residues: 1232 sheet: 0.08 (0.23), residues: 587 loop : -0.97 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 62 HIS 0.009 0.001 HIS G 9 PHE 0.014 0.001 PHE F 246 TYR 0.018 0.002 TYR a 112 ARG 0.004 0.000 ARG g 27 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 1435) hydrogen bonds : angle 5.15526 ( 3832) metal coordination : bond 0.01616 ( 48) metal coordination : angle 3.88311 ( 21) covalent geometry : bond 0.00555 (32811) covalent geometry : angle 0.61420 (45845) *********************** 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 275 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 205 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: a 218 MET cc_start: 0.8296 (mmm) cc_final: 0.7788 (mmm) REVERT: f 77 TYR cc_start: 0.8415 (m-80) cc_final: 0.7955 (m-80) REVERT: f 220 MET cc_start: 0.8455 (mmm) cc_final: 0.8074 (tpp) REVERT: g 7 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8436 (tm-30) REVERT: g 218 MET cc_start: 0.8987 (mmp) cc_final: 0.8679 (mmp) REVERT: g 220 MET cc_start: 0.8540 (mmm) cc_final: 0.8195 (mmm) REVERT: h 134 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: A 39 ASN cc_start: 0.8147 (m-40) cc_final: 0.7733 (m-40) REVERT: A 134 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8808 (pp20) REVERT: A 169 ASN cc_start: 0.9239 (t0) cc_final: 0.8924 (t0) REVERT: A 205 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8725 (pp20) REVERT: B 28 GLU cc_start: 0.9242 (mp0) cc_final: 0.8868 (pm20) REVERT: B 32 GLU cc_start: 0.9493 (tp30) cc_final: 0.9275 (tp30) REVERT: B 64 MET cc_start: 0.8509 (ttp) cc_final: 0.7856 (ttm) REVERT: B 113 MET cc_start: 0.8977 (tpp) cc_final: 0.8723 (mmm) REVERT: B 127 TYR cc_start: 0.7401 (m-80) cc_final: 0.7126 (m-80) REVERT: B 196 MET cc_start: 0.8687 (tpp) cc_final: 0.8341 (tpp) REVERT: B 244 CYS cc_start: 0.8685 (t) cc_final: 0.7782 (p) REVERT: C 218 MET cc_start: 0.8140 (ptt) cc_final: 0.7615 (mmp) REVERT: C 262 ARG cc_start: 0.8656 (mpt90) cc_final: 0.8454 (mmt180) REVERT: D 228 SER cc_start: 0.8871 (p) cc_final: 0.8076 (p) REVERT: D 230 LYS cc_start: 0.7811 (mmmt) cc_final: 0.7566 (mmmt) REVERT: E 7 GLU cc_start: 0.8961 (pm20) cc_final: 0.8735 (pm20) REVERT: E 28 GLU cc_start: 0.8916 (mp0) cc_final: 0.8650 (mp0) REVERT: E 74 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8207 (mmmt) REVERT: F 15 ASN cc_start: 0.6926 (p0) cc_final: 0.6467 (p0) REVERT: F 64 MET cc_start: 0.7360 (mmm) cc_final: 0.7077 (mmt) REVERT: F 77 TYR cc_start: 0.8976 (m-80) cc_final: 0.8499 (m-80) REVERT: F 113 MET cc_start: 0.8622 (tpp) cc_final: 0.7946 (mmm) REVERT: F 169 ASN cc_start: 0.9276 (m110) cc_final: 0.8803 (m110) REVERT: F 195 ASN cc_start: 0.7814 (m-40) cc_final: 0.7342 (m110) REVERT: F 196 MET cc_start: 0.6596 (tmm) cc_final: 0.5885 (tmm) REVERT: F 205 GLU cc_start: 0.8390 (tt0) cc_final: 0.8110 (tt0) REVERT: G 7 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.8985 (mp0) REVERT: G 113 MET cc_start: 0.8176 (mtt) cc_final: 0.7848 (mtt) REVERT: G 134 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8182 (tm-30) REVERT: H 242 TYR cc_start: 0.8882 (p90) cc_final: 0.8601 (p90) outliers start: 57 outliers final: 39 residues processed: 259 average time/residue: 0.3772 time to fit residues: 165.2089 Evaluate side-chains 255 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 64 MET Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 205 GLU Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain e residue 26 THR 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 g residue 12 HIS Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 82 VAL 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 A residue 205 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 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 171 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 131 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 162 optimal weight: 8.9990 chunk 280 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 192 optimal weight: 0.0670 chunk 131 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 259 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 304 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 GLN A 152 GLN ** B 167 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.069320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.050258 restraints weight = 141924.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.051641 restraints weight = 69561.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052535 restraints weight = 45139.291| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32859 Z= 0.122 Angle : 0.556 13.495 45866 Z= 0.300 Chirality : 0.038 0.142 4984 Planarity : 0.004 0.047 4812 Dihedral : 22.830 139.259 6532 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.74 % Allowed : 16.92 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 3069 helix: 1.40 (0.15), residues: 1222 sheet: 0.37 (0.23), residues: 556 loop : -0.76 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 62 HIS 0.017 0.001 HIS g 12 PHE 0.010 0.001 PHE c 260 TYR 0.025 0.001 TYR D 242 ARG 0.003 0.000 ARG C 262 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 1435) hydrogen bonds : angle 4.84330 ( 3832) metal coordination : bond 0.01107 ( 48) metal coordination : angle 3.26948 ( 21) covalent geometry : bond 0.00266 (32811) covalent geometry : angle 0.55154 (45845) *********************** 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 280 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 MET cc_start: 0.8247 (mmm) cc_final: 0.7879 (mmm) REVERT: b 64 MET cc_start: 0.8872 (mtm) cc_final: 0.8526 (mtt) REVERT: f 77 TYR cc_start: 0.8135 (m-80) cc_final: 0.7845 (m-80) REVERT: f 220 MET cc_start: 0.8384 (mmm) cc_final: 0.8045 (tpp) REVERT: g 7 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8422 (tm-30) REVERT: g 218 MET cc_start: 0.8962 (mmp) cc_final: 0.8647 (mmp) REVERT: g 220 MET cc_start: 0.8660 (mmm) cc_final: 0.8393 (mmm) REVERT: A 39 ASN cc_start: 0.8141 (m-40) cc_final: 0.7774 (m-40) REVERT: A 68 HIS cc_start: 0.8243 (m90) cc_final: 0.7726 (m-70) REVERT: A 134 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8736 (pp20) REVERT: A 205 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8633 (pp20) REVERT: B 28 GLU cc_start: 0.9193 (mp0) cc_final: 0.8812 (pm20) REVERT: B 32 GLU cc_start: 0.9483 (tp30) cc_final: 0.9272 (tp30) REVERT: B 64 MET cc_start: 0.8503 (ttp) cc_final: 0.7555 (ttm) REVERT: B 113 MET cc_start: 0.9020 (tpp) cc_final: 0.8775 (mmm) REVERT: B 196 MET cc_start: 0.8674 (tpp) cc_final: 0.8422 (tpp) REVERT: B 220 MET cc_start: 0.6670 (tpp) cc_final: 0.6394 (tpp) REVERT: B 244 CYS cc_start: 0.8585 (t) cc_final: 0.7726 (p) REVERT: C 218 MET cc_start: 0.8133 (ptt) cc_final: 0.7645 (mmp) REVERT: C 235 LEU cc_start: 0.8680 (tt) cc_final: 0.7983 (mt) REVERT: D 218 MET cc_start: 0.8403 (mmm) cc_final: 0.7839 (mmm) REVERT: D 220 MET cc_start: 0.7978 (tpt) cc_final: 0.7405 (tpt) REVERT: D 228 SER cc_start: 0.8855 (p) cc_final: 0.8383 (p) REVERT: E 28 GLU cc_start: 0.8909 (mp0) cc_final: 0.8616 (mp0) REVERT: E 74 LYS cc_start: 0.8487 (mmmt) cc_final: 0.8150 (mmmt) REVERT: E 123 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.7834 (m-40) REVERT: F 15 ASN cc_start: 0.6946 (p0) cc_final: 0.6567 (p0) REVERT: F 77 TYR cc_start: 0.8831 (m-80) cc_final: 0.8327 (m-80) REVERT: F 113 MET cc_start: 0.8746 (tpp) cc_final: 0.8145 (mmm) REVERT: F 169 ASN cc_start: 0.9362 (m110) cc_final: 0.8927 (m110) REVERT: F 195 ASN cc_start: 0.7786 (m-40) cc_final: 0.7348 (m110) REVERT: F 196 MET cc_start: 0.6826 (tmm) cc_final: 0.6199 (tmm) REVERT: F 205 GLU cc_start: 0.8270 (tt0) cc_final: 0.7946 (tt0) REVERT: G 7 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.8963 (mp0) REVERT: G 113 MET cc_start: 0.8011 (mtt) cc_final: 0.7714 (mtt) REVERT: G 134 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8131 (tm-30) REVERT: G 196 MET cc_start: 0.7786 (ptp) cc_final: 0.7442 (ptp) REVERT: H 15 ASN cc_start: 0.8764 (p0) cc_final: 0.8352 (p0) REVERT: H 218 MET cc_start: 0.9017 (mmm) cc_final: 0.8752 (mmm) REVERT: H 242 TYR cc_start: 0.8864 (p90) cc_final: 0.8617 (p90) outliers start: 46 outliers final: 30 residues processed: 263 average time/residue: 0.3900 time to fit residues: 174.2813 Evaluate side-chains 255 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 2.999 ------------------------------------------------------------------------------- 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 234 VAL Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain f residue 113 MET Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 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 171 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 212 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 281 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 272 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 HIS ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN ** F 195 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.067810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.048938 restraints weight = 144236.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.050203 restraints weight = 74747.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051034 restraints weight = 50201.584| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 32859 Z= 0.223 Angle : 0.614 10.512 45866 Z= 0.330 Chirality : 0.040 0.218 4984 Planarity : 0.004 0.042 4812 Dihedral : 22.862 140.652 6532 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.08 % Allowed : 17.37 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 3069 helix: 1.25 (0.15), residues: 1229 sheet: 0.21 (0.23), residues: 587 loop : -0.87 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 62 HIS 0.008 0.001 HIS G 9 PHE 0.016 0.001 PHE E 88 TYR 0.020 0.002 TYR F 127 ARG 0.004 0.000 ARG g 27 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 1435) hydrogen bonds : angle 4.97860 ( 3832) metal coordination : bond 0.01401 ( 48) metal coordination : angle 3.24672 ( 21) covalent geometry : bond 0.00493 (32811) covalent geometry : angle 0.60982 (45845) *********************** 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 275 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 208 TRP cc_start: 0.8874 (OUTLIER) cc_final: 0.7655 (m-10) REVERT: a 218 MET cc_start: 0.8285 (mmm) cc_final: 0.8049 (mmm) REVERT: f 77 TYR cc_start: 0.8040 (m-80) cc_final: 0.7658 (m-80) REVERT: f 220 MET cc_start: 0.8390 (mmm) cc_final: 0.8136 (tpp) REVERT: g 7 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8413 (tm-30) REVERT: g 218 MET cc_start: 0.8867 (mmp) cc_final: 0.8649 (mmp) REVERT: g 220 MET cc_start: 0.8722 (mmm) cc_final: 0.8432 (mmm) REVERT: h 134 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8230 (pm20) REVERT: A 39 ASN cc_start: 0.8088 (m-40) cc_final: 0.7661 (m-40) REVERT: A 205 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8643 (pp20) REVERT: A 220 MET cc_start: 0.8938 (tpp) cc_final: 0.8529 (tpp) REVERT: B 28 GLU cc_start: 0.9164 (mp0) cc_final: 0.8787 (pm20) REVERT: B 32 GLU cc_start: 0.9435 (tp30) cc_final: 0.9221 (tp30) REVERT: B 64 MET cc_start: 0.8433 (ttp) cc_final: 0.7847 (ttm) REVERT: B 127 TYR cc_start: 0.7091 (m-80) cc_final: 0.6744 (m-80) REVERT: B 220 MET cc_start: 0.6818 (tpp) cc_final: 0.6554 (tpp) REVERT: B 244 CYS cc_start: 0.8484 (t) cc_final: 0.7805 (p) REVERT: C 218 MET cc_start: 0.8196 (ptt) cc_final: 0.7679 (mmp) REVERT: D 220 MET cc_start: 0.7896 (tpt) cc_final: 0.7509 (tpt) REVERT: E 28 GLU cc_start: 0.8884 (mp0) cc_final: 0.8600 (mp0) REVERT: E 74 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8114 (mmmt) REVERT: E 152 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7973 (mm-40) REVERT: F 15 ASN cc_start: 0.7075 (p0) cc_final: 0.6628 (p0) REVERT: F 77 TYR cc_start: 0.8804 (m-80) cc_final: 0.8298 (m-80) REVERT: F 113 MET cc_start: 0.8557 (tpp) cc_final: 0.7851 (mmm) REVERT: F 127 TYR cc_start: 0.7849 (t80) cc_final: 0.7633 (t80) REVERT: F 169 ASN cc_start: 0.9318 (m110) cc_final: 0.8790 (m110) REVERT: F 195 ASN cc_start: 0.7950 (m-40) cc_final: 0.7487 (m110) REVERT: F 196 MET cc_start: 0.7035 (tmm) cc_final: 0.6324 (tmm) REVERT: F 205 GLU cc_start: 0.8350 (tt0) cc_final: 0.8032 (tt0) REVERT: G 7 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8942 (mp0) REVERT: G 113 MET cc_start: 0.8268 (mtt) cc_final: 0.7843 (mtt) REVERT: G 134 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8113 (tm-30) REVERT: G 196 MET cc_start: 0.7999 (ptp) cc_final: 0.7755 (ptp) REVERT: H 242 TYR cc_start: 0.8851 (p90) cc_final: 0.8493 (p90) outliers start: 55 outliers final: 39 residues processed: 260 average time/residue: 0.3728 time to fit residues: 165.0493 Evaluate side-chains 257 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 234 VAL Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 32 GLU 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 g residue 12 HIS Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 82 VAL 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 h residue 244 CYS Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain 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 152 GLN Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 131 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 181 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 chunk 287 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 213 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 HIS ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** 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 = 0.3518 r_free = 0.3518 target = 0.069268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.050633 restraints weight = 142779.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.051936 restraints weight = 73321.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052790 restraints weight = 48840.685| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32859 Z= 0.139 Angle : 0.579 11.643 45866 Z= 0.310 Chirality : 0.038 0.212 4984 Planarity : 0.004 0.045 4812 Dihedral : 22.794 139.920 6532 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.36 % Allowed : 18.43 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 3069 helix: 1.37 (0.15), residues: 1224 sheet: 0.41 (0.24), residues: 544 loop : -0.79 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 62 HIS 0.009 0.001 HIS g 12 PHE 0.013 0.001 PHE E 88 TYR 0.024 0.001 TYR D 242 ARG 0.004 0.000 ARG C 262 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 1435) hydrogen bonds : angle 4.81005 ( 3832) metal coordination : bond 0.00829 ( 48) metal coordination : angle 2.59694 ( 21) covalent geometry : bond 0.00308 (32811) covalent geometry : angle 0.57629 (45845) *********************** 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 265 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 2.920 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: b 64 MET cc_start: 0.8755 (mtm) cc_final: 0.8505 (mtt) REVERT: f 77 TYR cc_start: 0.7961 (m-80) cc_final: 0.7599 (m-80) REVERT: f 220 MET cc_start: 0.8341 (mmm) cc_final: 0.8121 (tpp) REVERT: g 7 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8437 (tm-30) REVERT: g 218 MET cc_start: 0.8877 (mmp) cc_final: 0.8642 (mmp) REVERT: g 220 MET cc_start: 0.8707 (mmm) cc_final: 0.8487 (mmm) REVERT: h 64 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7970 (tmm) REVERT: h 169 ASN cc_start: 0.9096 (t0) cc_final: 0.8893 (t0) REVERT: A 39 ASN cc_start: 0.8110 (m-40) cc_final: 0.7766 (m-40) REVERT: A 68 HIS cc_start: 0.8255 (m90) cc_final: 0.7792 (m-70) REVERT: A 80 VAL cc_start: 0.8946 (t) cc_final: 0.8579 (p) REVERT: A 205 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8603 (pp20) REVERT: A 220 MET cc_start: 0.9014 (tpp) cc_final: 0.8636 (tpp) REVERT: B 28 GLU cc_start: 0.9141 (mp0) cc_final: 0.8764 (pm20) REVERT: B 32 GLU cc_start: 0.9447 (tp30) cc_final: 0.9241 (tp30) REVERT: B 64 MET cc_start: 0.8466 (ttp) cc_final: 0.7956 (ttm) REVERT: B 113 MET cc_start: 0.8802 (mmm) cc_final: 0.8431 (mmm) REVERT: B 244 CYS cc_start: 0.8621 (t) cc_final: 0.7760 (p) REVERT: C 218 MET cc_start: 0.8110 (ptt) cc_final: 0.7669 (mmp) REVERT: D 218 MET cc_start: 0.8175 (mmm) cc_final: 0.7628 (mmm) REVERT: D 220 MET cc_start: 0.7811 (tpt) cc_final: 0.7199 (tpt) REVERT: E 28 GLU cc_start: 0.8878 (mp0) cc_final: 0.8514 (mp0) REVERT: E 74 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8143 (mmmt) REVERT: E 196 MET cc_start: 0.7548 (ptt) cc_final: 0.6911 (ttp) REVERT: F 15 ASN cc_start: 0.7057 (p0) cc_final: 0.6660 (p0) REVERT: F 77 TYR cc_start: 0.8778 (m-80) cc_final: 0.8286 (m-80) REVERT: F 113 MET cc_start: 0.8759 (tpp) cc_final: 0.8052 (mmm) REVERT: F 169 ASN cc_start: 0.9265 (m110) cc_final: 0.8736 (m110) REVERT: F 183 LEU cc_start: 0.9068 (mt) cc_final: 0.8475 (mp) REVERT: F 195 ASN cc_start: 0.7899 (m-40) cc_final: 0.7507 (m110) REVERT: F 196 MET cc_start: 0.7072 (tmm) cc_final: 0.6404 (tmm) REVERT: F 205 GLU cc_start: 0.8249 (tt0) cc_final: 0.7908 (tt0) REVERT: G 7 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8963 (mp0) REVERT: G 113 MET cc_start: 0.8050 (mtt) cc_final: 0.7689 (mtt) REVERT: G 134 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8086 (tm-30) REVERT: H 15 ASN cc_start: 0.8687 (p0) cc_final: 0.8253 (p0) REVERT: H 242 TYR cc_start: 0.8849 (p90) cc_final: 0.8525 (p90) outliers start: 36 outliers final: 30 residues processed: 252 average time/residue: 0.3829 time to fit residues: 163.3246 Evaluate side-chains 256 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 2.903 ------------------------------------------------------------------------------- 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 234 VAL Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain g residue 12 HIS Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 82 VAL 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 h residue 236 ILE Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain 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 194 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 131 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 133 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 313 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 14 GLN ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 HIS ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.067252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.048456 restraints weight = 143731.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.049703 restraints weight = 74627.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.050524 restraints weight = 50168.037| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 32859 Z= 0.269 Angle : 0.666 12.128 45866 Z= 0.355 Chirality : 0.041 0.179 4984 Planarity : 0.004 0.041 4812 Dihedral : 22.903 141.255 6532 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.55 % Allowed : 18.32 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 3069 helix: 1.08 (0.15), residues: 1232 sheet: 0.08 (0.22), residues: 612 loop : -0.93 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 62 HIS 0.015 0.001 HIS g 12 PHE 0.017 0.002 PHE g 246 TYR 0.019 0.002 TYR D 242 ARG 0.006 0.000 ARG C 262 Details of bonding type rmsd hydrogen bonds : bond 0.04754 ( 1435) hydrogen bonds : angle 5.06639 ( 3832) metal coordination : bond 0.01928 ( 48) metal coordination : angle 3.73988 ( 21) covalent geometry : bond 0.00592 (32811) covalent geometry : angle 0.66128 (45845) ********************** 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 260 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 196 MET cc_start: 0.8082 (ttm) cc_final: 0.7687 (ptm) REVERT: a 218 MET cc_start: 0.8591 (mmm) cc_final: 0.8184 (tpp) REVERT: f 77 TYR cc_start: 0.8239 (m-80) cc_final: 0.7850 (m-80) REVERT: g 7 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8304 (tm-30) REVERT: g 218 MET cc_start: 0.8850 (mmp) cc_final: 0.8630 (mmp) REVERT: g 220 MET cc_start: 0.8723 (mmm) cc_final: 0.8413 (mmm) REVERT: A 39 ASN cc_start: 0.8115 (m-40) cc_final: 0.7704 (m-40) REVERT: A 205 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8675 (pp20) REVERT: A 220 MET cc_start: 0.8839 (tpp) cc_final: 0.8495 (tpp) REVERT: B 28 GLU cc_start: 0.9173 (mp0) cc_final: 0.8797 (pm20) REVERT: B 32 GLU cc_start: 0.9440 (tp30) cc_final: 0.9227 (tp30) REVERT: C 218 MET cc_start: 0.8186 (ptt) cc_final: 0.7732 (mmp) REVERT: D 220 MET cc_start: 0.7957 (tpt) cc_final: 0.7647 (tpt) REVERT: E 28 GLU cc_start: 0.8891 (mp0) cc_final: 0.8602 (mp0) REVERT: E 74 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8149 (mmmt) REVERT: E 196 MET cc_start: 0.7789 (ptt) cc_final: 0.7065 (ttp) REVERT: F 15 ASN cc_start: 0.7113 (p0) cc_final: 0.6684 (p0) REVERT: F 64 MET cc_start: 0.6447 (mmm) cc_final: 0.5773 (tpp) REVERT: F 77 TYR cc_start: 0.8841 (m-80) cc_final: 0.8363 (m-80) REVERT: F 113 MET cc_start: 0.8534 (tpp) cc_final: 0.7818 (mmm) REVERT: F 169 ASN cc_start: 0.9320 (m110) cc_final: 0.8839 (m110) REVERT: F 183 LEU cc_start: 0.9163 (mt) cc_final: 0.8555 (mp) REVERT: F 195 ASN cc_start: 0.7979 (m-40) cc_final: 0.7546 (m110) REVERT: F 196 MET cc_start: 0.7079 (tmm) cc_final: 0.6370 (tmm) REVERT: G 7 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8973 (mp0) REVERT: G 113 MET cc_start: 0.8314 (mtt) cc_final: 0.7974 (mtt) REVERT: G 134 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8118 (tm-30) REVERT: H 242 TYR cc_start: 0.8896 (p90) cc_final: 0.8510 (p90) outliers start: 41 outliers final: 35 residues processed: 249 average time/residue: 0.3850 time to fit residues: 161.9046 Evaluate side-chains 251 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain b residue 234 VAL Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 190 VAL Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain f residue 64 MET Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 82 VAL 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 h residue 236 ILE Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 60 VAL 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 102 VAL Chi-restraints excluded: chain H residue 131 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 242 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 299 optimal weight: 0.9980 chunk 216 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 319 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 HIS ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.068256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.049425 restraints weight = 144000.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.050707 restraints weight = 74354.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.051553 restraints weight = 49840.770| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32859 Z= 0.180 Angle : 0.613 11.009 45866 Z= 0.327 Chirality : 0.039 0.178 4984 Planarity : 0.004 0.044 4812 Dihedral : 22.893 140.640 6532 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.85 % Allowed : 18.09 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 3069 helix: 1.20 (0.15), residues: 1230 sheet: 0.12 (0.23), residues: 604 loop : -0.89 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 62 HIS 0.007 0.001 HIS G 9 PHE 0.014 0.001 PHE F 246 TYR 0.021 0.001 TYR D 242 ARG 0.018 0.000 ARG C 262 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 1435) hydrogen bonds : angle 4.92891 ( 3832) metal coordination : bond 0.00936 ( 48) metal coordination : angle 2.71748 ( 21) covalent geometry : bond 0.00397 (32811) covalent geometry : angle 0.61057 (45845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10035.00 seconds wall clock time: 176 minutes 39.80 seconds (10599.80 seconds total)