Starting phenix.real_space_refine on Wed May 28 17:11:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ut1_26744/05_2025/7ut1_26744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut1_26744/05_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_26744/05_2025/7ut1_26744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut1_26744/05_2025/7ut1_26744.map" model { file = "/net/cci-nas-00/data/ceres_data/7ut1_26744/05_2025/7ut1_26744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut1_26744/05_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 20.31, per 1000 atoms: 0.65 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: 7.95 Conformation dependent library (CDL) restraints added in 3.2 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: 12.48 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: 12.28 Time building geometry restraints manager: 9.33 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.530 Check model and map are aligned: 0.000 Set scattering table: 0.070 Process input model: 84.950 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.880 ------------------------------------------------------------------------------- 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 : 3.035 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: 0.3934 time to fit residues: 169.8157 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 : 3.186 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.046709 restraints weight = 145645.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.047994 restraints weight = 73649.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.048824 restraints weight = 48992.286| |-----------------------------------------------------------------------------| 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 : 2.995 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: 0.8322 (tpt) cc_final: 0.8044 (tpt) REVERT: e 52 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8618 (m110) REVERT: f 77 TYR cc_start: 0.8271 (m-80) cc_final: 0.8002 (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: 0.8203 (tpp) REVERT: g 32 GLU cc_start: 0.9219 (mp0) cc_final: 0.8714 (mp0) REVERT: g 220 MET cc_start: 0.8571 (mmm) cc_final: 0.8124 (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: 0.8949 (t0) REVERT: B 32 GLU cc_start: 0.9481 (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: 0.7116 (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: 0.8860 (mp0) cc_final: 0.8659 (mp0) REVERT: F 7 GLU cc_start: 0.9293 (mp0) cc_final: 0.9012 (mp0) REVERT: F 64 MET cc_start: 0.7566 (mmm) cc_final: 0.6904 (tpt) REVERT: F 77 TYR cc_start: 0.9093 (m-80) cc_final: 0.8638 (m-80) REVERT: F 169 ASN cc_start: 0.9294 (m110) cc_final: 0.8821 (m110) REVERT: F 195 ASN cc_start: 0.7752 (m-40) cc_final: 0.7243 (m110) REVERT: F 205 GLU cc_start: 0.8439 (tt0) cc_final: 0.8128 (tt0) REVERT: F 220 MET cc_start: 0.8440 (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: 0.8171 (p0) REVERT: H 158 GLU cc_start: 0.7878 (mp0) cc_final: 0.7617 (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: 0.3782 time to fit residues: 149.0968 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 : 2.998 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.9980 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.068622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.049289 restraints weight = 142754.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.050713 restraints weight = 68057.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.051644 restraints weight = 43608.576| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32859 Z= 0.133 Angle : 0.547 12.217 45866 Z= 0.300 Chirality : 0.039 0.135 4984 Planarity : 0.004 0.041 4812 Dihedral : 22.871 139.913 6532 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.79 % Allowed : 11.17 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.29 (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 0.016 0.001 PHE D 246 TYR 0.022 0.001 TYR a 112 ARG 0.004 0.000 ARG e 54 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 1435) hydrogen bonds : angle 5.17473 ( 3832) metal coordination : bond 0.01202 ( 48) metal coordination : angle 4.11997 ( 21) covalent geometry : bond 0.00289 (32811) covalent geometry : angle 0.54018 (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 272 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 2.984 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: 0.8188 (mmm) cc_final: 0.7628 (mmm) REVERT: c 218 MET cc_start: 0.8708 (mmm) cc_final: 0.8416 (mmm) REVERT: d 218 MET cc_start: 0.8295 (tpt) cc_final: 0.7940 (tpp) REVERT: f 77 TYR cc_start: 0.8386 (m-80) cc_final: 0.8001 (m-80) REVERT: f 220 MET cc_start: 0.8507 (mmm) cc_final: 0.7990 (tpp) REVERT: g 7 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8358 (tm-30) REVERT: g 218 MET cc_start: 0.9006 (mmp) cc_final: 0.8644 (mmp) REVERT: g 220 MET cc_start: 0.8562 (mmm) cc_final: 0.8280 (mmm) REVERT: A 39 ASN cc_start: 0.8196 (m-40) cc_final: 0.7851 (m-40) REVERT: A 134 GLU cc_start: 0.9068 (mp0) cc_final: 0.8775 (pm20) REVERT: A 205 GLU cc_start: 0.9121 (pp20) cc_final: 0.8732 (pp20) REVERT: B 32 GLU cc_start: 0.9522 (tp30) cc_final: 0.9311 (tp30) REVERT: B 64 MET cc_start: 0.8726 (ttp) cc_final: 0.8337 (ttm) REVERT: B 113 MET cc_start: 0.8964 (tpp) cc_final: 0.8671 (mmt) REVERT: B 127 TYR cc_start: 0.7619 (m-10) cc_final: 0.7415 (m-80) REVERT: B 196 MET cc_start: 0.8455 (tpp) cc_final: 0.7923 (tpp) REVERT: B 220 MET cc_start: 0.7941 (tpp) cc_final: 0.7677 (tpp) REVERT: D 236 ILE cc_start: 0.9169 (mm) cc_final: 0.8933 (mt) REVERT: E 7 GLU cc_start: 0.8933 (pm20) cc_final: 0.8721 (pm20) REVERT: E 28 GLU cc_start: 0.8893 (mp0) cc_final: 0.8613 (mp0) REVERT: E 113 MET cc_start: 0.8150 (mtt) cc_final: 0.7752 (mpp) REVERT: F 7 GLU cc_start: 0.9237 (mp0) cc_final: 0.9005 (mp0) REVERT: F 15 ASN cc_start: 0.6984 (p0) cc_final: 0.6558 (p0) REVERT: F 64 MET cc_start: 0.7691 (mmm) cc_final: 0.6994 (mmt) REVERT: F 77 TYR cc_start: 0.8947 (m-80) cc_final: 0.8477 (m-80) REVERT: F 113 MET cc_start: 0.8965 (tpp) cc_final: 0.8676 (tpp) REVERT: F 127 TYR cc_start: 0.7825 (m-10) cc_final: 0.7594 (m-80) REVERT: F 169 ASN cc_start: 0.9245 (m110) cc_final: 0.8792 (m110) REVERT: F 195 ASN cc_start: 0.7509 (m-40) cc_final: 0.7102 (m110) REVERT: F 196 MET cc_start: 0.6372 (tmm) cc_final: 0.5748 (tmm) REVERT: F 205 GLU cc_start: 0.8358 (tt0) cc_final: 0.8005 (tt0) REVERT: F 220 MET cc_start: 0.8713 (tpp) cc_final: 0.7830 (tpp) REVERT: G 7 GLU cc_start: 0.9384 (mp0) cc_final: 0.8882 (mp0) REVERT: G 113 MET cc_start: 0.8183 (mtt) cc_final: 0.7862 (mtt) REVERT: G 134 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8225 (tm-30) REVERT: H 71 GLU cc_start: 0.8514 (pm20) cc_final: 0.8311 (pm20) REVERT: H 242 TYR cc_start: 0.8786 (p90) cc_final: 0.8557 (p90) outliers start: 21 outliers final: 13 residues processed: 263 average time/residue: 0.3750 time to fit residues: 164.6576 Evaluate side-chains 235 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 2.927 ------------------------------------------------------------------------------- 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: 0.7980 chunk 255 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 175 optimal weight: 0.2980 chunk 140 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 303 optimal weight: 9.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- 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** ** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.066966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.047787 restraints weight = 143460.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.049098 restraints weight = 71457.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.049953 restraints weight = 47060.576| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 32859 Z= 0.238 Angle : 0.605 8.002 45866 Z= 0.329 Chirality : 0.040 0.170 4984 Planarity : 0.004 0.041 4812 Dihedral : 22.875 142.611 6532 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.48 % Allowed : 14.19 % Favored : 84.33 % 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: 0.12 (0.16), residues: 3069 helix: 1.15 (0.15), residues: 1230 sheet: 0.04 (0.22), residues: 626 loop : -0.95 (0.19), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 221 HIS 0.011 0.001 HIS G 9 PHE 0.013 0.001 PHE D 264 TYR 0.023 0.002 TYR a 112 ARG 0.003 0.000 ARG e 259 Details of bonding type rmsd hydrogen bonds : bond 0.04816 ( 1435) hydrogen bonds : angle 5.21220 ( 3832) metal coordination : bond 0.01499 ( 48) metal coordination : angle 3.77306 ( 21) covalent geometry : bond 0.00522 (32811) covalent geometry : angle 0.59939 (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: 39 poor density : 226 time to evaluate : 2.964 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: 0.8216 (mmm) cc_final: 0.7687 (mmm) REVERT: d 218 MET cc_start: 0.8235 (tpt) cc_final: 0.7942 (tpt) REVERT: f 32 GLU cc_start: 0.8641 (pm20) cc_final: 0.8332 (pm20) REVERT: f 77 TYR cc_start: 0.8235 (m-80) cc_final: 0.7917 (m-80) REVERT: f 220 MET cc_start: 0.8525 (mmm) cc_final: 0.8098 (tpp) REVERT: g 7 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8440 (tm-30) REVERT: g 32 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.9061 (mm-30) REVERT: g 218 MET cc_start: 0.8979 (mmp) cc_final: 0.8675 (mmp) REVERT: g 220 MET cc_start: 0.8542 (mmm) cc_final: 0.8222 (mmm) REVERT: h 134 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8507 (pm20) REVERT: A 39 ASN cc_start: 0.8145 (m-40) cc_final: 0.7737 (m-40) REVERT: A 134 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8805 (pp20) REVERT: A 169 ASN cc_start: 0.9209 (t0) cc_final: 0.8889 (t0) REVERT: A 205 GLU cc_start: 0.9167 (pp20) cc_final: 0.8776 (pp20) REVERT: A 220 MET cc_start: 0.8662 (tpp) cc_final: 0.8124 (tpp) REVERT: B 28 GLU cc_start: 0.9226 (mp0) cc_final: 0.8854 (pm20) REVERT: B 32 GLU cc_start: 0.9481 (tp30) cc_final: 0.9261 (tp30) REVERT: B 64 MET cc_start: 0.8715 (ttp) cc_final: 0.8139 (ttm) REVERT: B 113 MET cc_start: 0.8964 (tpp) cc_final: 0.8700 (mmt) REVERT: B 196 MET cc_start: 0.8751 (tpp) cc_final: 0.8325 (tpp) REVERT: B 220 MET cc_start: 0.8098 (tpp) cc_final: 0.7762 (tpp) REVERT: D 228 SER cc_start: 0.9000 (p) cc_final: 0.8434 (p) REVERT: D 230 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7685 (mmmt) REVERT: E 28 GLU cc_start: 0.8924 (mp0) cc_final: 0.8675 (mp0) REVERT: F 15 ASN cc_start: 0.6880 (p0) cc_final: 0.6436 (p0) REVERT: F 64 MET cc_start: 0.7538 (mmm) cc_final: 0.6601 (mmt) REVERT: F 77 TYR cc_start: 0.8920 (m-80) cc_final: 0.8467 (m-80) REVERT: F 169 ASN cc_start: 0.9307 (m110) cc_final: 0.8865 (m110) REVERT: F 195 ASN cc_start: 0.7712 (m-40) cc_final: 0.7289 (m110) REVERT: F 196 MET cc_start: 0.6569 (tmm) cc_final: 0.5851 (tmm) REVERT: F 205 GLU cc_start: 0.8348 (tt0) cc_final: 0.7981 (tt0) REVERT: F 220 MET cc_start: 0.8873 (tpp) cc_final: 0.8236 (tpp) REVERT: G 7 GLU cc_start: 0.9444 (mp0) cc_final: 0.8984 (mp0) REVERT: G 113 MET cc_start: 0.8232 (mtt) cc_final: 0.7919 (mtt) REVERT: G 134 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8274 (tm-30) REVERT: H 71 GLU cc_start: 0.8583 (pm20) cc_final: 0.8313 (pm20) REVERT: H 242 TYR cc_start: 0.8850 (p90) cc_final: 0.8519 (p90) outliers start: 39 outliers final: 19 residues processed: 250 average time/residue: 0.3651 time to fit residues: 153.8917 Evaluate side-chains 237 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 64 MET 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 7 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 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 H residue 34 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.0655 > 50: distance: 30 - 135: 30.250 distance: 33 - 132: 29.528 distance: 41 - 113: 30.576 distance: 44 - 110: 27.377 distance: 61 - 66: 33.916 distance: 66 - 67: 39.726 distance: 67 - 68: 12.549 distance: 67 - 70: 40.256 distance: 68 - 69: 11.402 distance: 72 - 73: 38.155 distance: 72 - 74: 31.999 distance: 75 - 76: 10.506 distance: 76 - 77: 25.265 distance: 76 - 79: 14.866 distance: 77 - 78: 7.313 distance: 77 - 83: 3.893 distance: 79 - 80: 22.806 distance: 80 - 81: 12.970 distance: 80 - 82: 17.187 distance: 83 - 84: 5.520 distance: 84 - 87: 38.918 distance: 85 - 86: 39.360 distance: 85 - 88: 14.602 distance: 88 - 89: 13.771 distance: 89 - 90: 13.777 distance: 89 - 92: 40.106 distance: 90 - 91: 46.789 distance: 90 - 97: 13.888 distance: 92 - 93: 32.013 distance: 93 - 94: 21.855 distance: 94 - 95: 37.520 distance: 94 - 96: 17.338 distance: 97 - 98: 11.157 distance: 98 - 99: 31.717 distance: 98 - 101: 30.978 distance: 99 - 100: 22.607 distance: 99 - 103: 15.889 distance: 101 - 102: 44.183 distance: 103 - 104: 6.778 distance: 103 - 109: 4.913 distance: 104 - 105: 17.340 distance: 104 - 107: 29.882 distance: 105 - 106: 31.870 distance: 105 - 110: 14.676 distance: 107 - 108: 33.424 distance: 108 - 109: 31.608 distance: 110 - 111: 36.313 distance: 111 - 112: 39.539 distance: 112 - 113: 10.587 distance: 112 - 118: 55.471 distance: 114 - 115: 57.100 distance: 114 - 116: 15.494 distance: 115 - 117: 40.979 distance: 118 - 119: 18.664 distance: 119 - 120: 26.493 distance: 119 - 122: 6.452 distance: 120 - 121: 10.985 distance: 120 - 132: 28.311 distance: 122 - 123: 28.066 distance: 123 - 124: 23.727 distance: 123 - 125: 14.989 distance: 125 - 127: 12.866 distance: 125 - 128: 24.286 distance: 126 - 127: 8.922 distance: 127 - 129: 14.862 distance: 128 - 130: 34.909 distance: 129 - 131: 31.072 distance: 130 - 131: 8.117 distance: 132 - 133: 25.005 distance: 133 - 134: 30.075 distance: 133 - 136: 32.523 distance: 134 - 135: 14.673 distance: 134 - 139: 16.781 distance: 136 - 137: 23.750 distance: 136 - 138: 23.682 distance: 139 - 140: 13.207 distance: 139 - 145: 36.746 distance: 140 - 141: 24.310 distance: 140 - 143: 19.626 distance: 141 - 142: 31.007 distance: 141 - 146: 30.805 distance: 143 - 144: 28.044 distance: 144 - 145: 44.726