Starting phenix.real_space_refine on Fri Dec 15 11:58:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut1_26744/12_2023/7ut1_26744.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut1_26744/12_2023/7ut1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut1_26744/12_2023/7ut1_26744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut1_26744/12_2023/7ut1_26744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut1_26744/12_2023/7ut1_26744.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut1_26744/12_2023/7ut1_26744.pdb" } 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 Residue "a TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 134": "OE1" <-> "OE2" Residue "e GLU 3": "OE1" <-> "OE2" Residue "e TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 97": "OE1" <-> "OE2" Residue "e TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 97": "OE1" <-> "OE2" Residue "f TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 122": "OD1" <-> "OD2" Residue "h TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 158": "OE1" <-> "OE2" Residue "h ASP 249": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "E TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 251": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 16.67, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 13.13 Conformation dependent library (CDL) restraints added in 4.4 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: 13.65 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: 12.90 Time building geometry restraints manager: 14.10 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: 99.60 - 106.49: 2983 106.49 - 113.37: 17610 113.37 - 120.25: 11767 120.25 - 127.14: 12415 127.14 - 134.02: 1070 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 2.440 nonbonded pdb=" O ALA E 1 " pdb=" OG SER E 4 " model vdw 2.167 2.440 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 2.440 nonbonded pdb=" OH TYR c 242 " pdb=" OP1 DG l 10 " model vdw 2.200 2.440 ... (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 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: 1.520 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: 0.020 Extract box with map and model: 5.180 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 95.730 Find NCS groups from input model: 2.680 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.040 ------------------------------------------------------------------------------- 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 : 0.003 0.035 32811 Z= 0.189 Angle : 0.552 8.656 45845 Z= 0.306 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.4251 time to fit residues: 183.2261 Evaluate side-chains 200 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 3.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9428 ------------------------------------------------------------------------------- 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: 8.9990 chunk 140 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 194 optimal weight: 0.9990 chunk 302 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 32811 Z= 0.391 Angle : 0.655 9.166 45845 Z= 0.362 Chirality : 0.043 0.182 4984 Planarity : 0.005 0.049 4812 Dihedral : 22.906 143.672 6532 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.64 % Allowed : 7.99 % Favored : 91.37 % 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: -0.09 (0.15), residues: 3069 helix: 0.92 (0.15), residues: 1224 sheet: 0.12 (0.22), residues: 576 loop : -1.08 (0.18), residues: 1269 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 0.014 0.002 PHE F 90 TYR 0.016 0.002 TYR A 112 ARG 0.006 0.001 ARG h 20 *********************** 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 238 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 221 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 229 average time/residue: 0.3865 time to fit residues: 148.8785 Evaluate side-chains 216 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 205 time to evaluate : 3.186 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2870 time to fit residues: 9.8180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 251 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 302 optimal weight: 5.9990 chunk 327 optimal weight: 10.0000 chunk 269 optimal weight: 20.0000 chunk 300 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 13 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 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 143 HIS ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 HIS ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 32811 Z= 0.396 Angle : 0.647 9.385 45845 Z= 0.357 Chirality : 0.042 0.168 4984 Planarity : 0.004 0.040 4812 Dihedral : 22.936 142.355 6532 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.48 % Allowed : 13.85 % Favored : 84.67 % 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: -0.33 (0.15), residues: 3069 helix: 0.72 (0.15), residues: 1231 sheet: -0.07 (0.22), residues: 605 loop : -1.21 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 208 HIS 0.013 0.001 HIS G 9 PHE 0.014 0.002 PHE F 90 TYR 0.016 0.002 TYR B 177 ARG 0.006 0.000 ARG A 130 *********************** 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 255 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 216 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 239 average time/residue: 0.3869 time to fit residues: 156.2281 Evaluate side-chains 224 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 201 time to evaluate : 3.176 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2792 time to fit residues: 16.1261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 299 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 203 optimal weight: 0.4980 chunk 304 optimal weight: 8.9990 chunk 321 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 ASN e 161 HIS ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 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** F 104 GLN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32811 Z= 0.261 Angle : 0.577 8.219 45845 Z= 0.318 Chirality : 0.039 0.142 4984 Planarity : 0.004 0.041 4812 Dihedral : 22.909 140.254 6532 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.02 % Allowed : 15.78 % Favored : 83.19 % 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: -0.04 (0.16), residues: 3069 helix: 1.00 (0.15), residues: 1226 sheet: 0.04 (0.22), residues: 607 loop : -1.07 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 208 HIS 0.010 0.001 HIS G 9 PHE 0.012 0.001 PHE F 246 TYR 0.018 0.001 TYR D 242 ARG 0.006 0.000 ARG H 138 *********************** 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 256 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 245 average time/residue: 0.3854 time to fit residues: 159.3890 Evaluate side-chains 214 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 203 time to evaluate : 3.077 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3810 time to fit residues: 11.1613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 274 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 199 GLN ** b 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 195 ASN ** 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 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 ASN ** A 161 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 32811 Z= 0.401 Angle : 0.654 9.050 45845 Z= 0.358 Chirality : 0.042 0.155 4984 Planarity : 0.004 0.041 4812 Dihedral : 22.969 140.263 6532 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.23 % Allowed : 17.30 % Favored : 80.47 % 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 (0.15), residues: 3069 helix: 0.75 (0.15), residues: 1230 sheet: -0.06 (0.22), residues: 592 loop : -1.20 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 62 HIS 0.010 0.001 HIS F 105 PHE 0.016 0.002 PHE F 246 TYR 0.017 0.002 TYR D 242 ARG 0.006 0.000 ARG g 27 *********************** 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 267 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 208 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 36 residues processed: 256 average time/residue: 0.3800 time to fit residues: 164.4063 Evaluate side-chains 232 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 196 time to evaluate : 3.190 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2940 time to fit residues: 23.1514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 188 optimal weight: 50.0000 chunk 79 optimal weight: 6.9990 chunk 322 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 169 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 39 ASN ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 207 HIS ** h 9 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 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 32811 Z= 0.399 Angle : 0.657 8.846 45845 Z= 0.358 Chirality : 0.042 0.161 4984 Planarity : 0.004 0.042 4812 Dihedral : 23.026 140.285 6532 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.93 % Allowed : 18.13 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.38 (0.15), residues: 3069 helix: 0.67 (0.15), residues: 1225 sheet: -0.08 (0.22), residues: 596 loop : -1.21 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP a 208 HIS 0.008 0.001 HIS a 9 PHE 0.017 0.002 PHE F 246 TYR 0.018 0.002 TYR D 242 ARG 0.005 0.000 ARG a 262 *********************** 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 262 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 211 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 29 residues processed: 251 average time/residue: 0.3851 time to fit residues: 164.1083 Evaluate side-chains 229 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 200 time to evaluate : 2.960 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2736 time to fit residues: 18.5892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 310 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 271 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 320 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 195 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 HIS ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32811 Z= 0.240 Angle : 0.588 10.408 45845 Z= 0.320 Chirality : 0.039 0.156 4984 Planarity : 0.004 0.047 4812 Dihedral : 22.927 140.354 6532 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.72 % Allowed : 19.83 % Favored : 79.45 % 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: -0.04 (0.16), residues: 3069 helix: 0.99 (0.15), residues: 1224 sheet: 0.16 (0.23), residues: 567 loop : -1.07 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP e 221 HIS 0.007 0.001 HIS g 182 PHE 0.013 0.001 PHE F 246 TYR 0.023 0.001 TYR D 242 ARG 0.004 0.000 ARG D 259 *********************** 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 240 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 221 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 234 average time/residue: 0.4003 time to fit residues: 156.9942 Evaluate side-chains 216 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 204 time to evaluate : 3.011 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3021 time to fit residues: 10.6117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 252 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN G 172 GLN ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32811 Z= 0.251 Angle : 0.600 10.137 45845 Z= 0.324 Chirality : 0.039 0.150 4984 Planarity : 0.004 0.046 4812 Dihedral : 22.857 140.956 6532 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.42 % Allowed : 20.44 % Favored : 79.14 % 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: -0.00 (0.16), residues: 3069 helix: 1.01 (0.15), residues: 1221 sheet: 0.05 (0.22), residues: 619 loop : -1.01 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP e 221 HIS 0.007 0.001 HIS A 68 PHE 0.014 0.001 PHE F 246 TYR 0.024 0.001 TYR D 242 ARG 0.006 0.000 ARG H 138 *********************** 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 226 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 215 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 221 average time/residue: 0.3823 time to fit residues: 142.2190 Evaluate side-chains 207 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 201 time to evaluate : 3.054 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2749 time to fit residues: 6.8707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 10.0000 chunk 307 optimal weight: 0.3980 chunk 280 optimal weight: 9.9990 chunk 299 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 298 optimal weight: 30.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 HIS ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32811 Z= 0.300 Angle : 0.627 11.813 45845 Z= 0.337 Chirality : 0.040 0.211 4984 Planarity : 0.004 0.045 4812 Dihedral : 22.872 141.541 6532 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.34 % Allowed : 20.97 % Favored : 78.69 % 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: -0.08 (0.16), residues: 3069 helix: 0.93 (0.15), residues: 1227 sheet: 0.05 (0.22), residues: 620 loop : -1.07 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 221 HIS 0.007 0.001 HIS e 13 PHE 0.015 0.001 PHE F 246 TYR 0.025 0.001 TYR D 242 ARG 0.009 0.000 ARG H 138 *********************** 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 213 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 204 time to evaluate : 4.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 208 average time/residue: 0.4288 time to fit residues: 150.2105 Evaluate side-chains 207 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 200 time to evaluate : 3.036 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3123 time to fit residues: 7.5518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 196 optimal weight: 8.9990 chunk 316 optimal weight: 1.9990 chunk 193 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 32811 Z= 0.317 Angle : 0.635 10.460 45845 Z= 0.342 Chirality : 0.040 0.192 4984 Planarity : 0.004 0.045 4812 Dihedral : 22.906 142.004 6532 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.38 % Allowed : 20.97 % Favored : 78.65 % 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: 0.89 (0.15), residues: 1222 sheet: 0.06 (0.22), residues: 612 loop : -1.08 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP a 221 HIS 0.007 0.001 HIS e 13 PHE 0.016 0.001 PHE F 246 TYR 0.025 0.002 TYR D 242 ARG 0.003 0.000 ARG a 262 ********************** 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 216 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 206 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 210 average time/residue: 0.4268 time to fit residues: 150.0328 Evaluate side-chains 205 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 201 time to evaluate : 2.891 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3178 time to fit residues: 6.4619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 209 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 243 optimal weight: 5.9990 chunk 39 optimal weight: 0.0770 chunk 73 optimal weight: 0.9980 chunk 264 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 271 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 39 ASN ** 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** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 HIS ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 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 = 0.3507 r_free = 0.3507 target = 0.068896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.050268 restraints weight = 144479.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.051556 restraints weight = 74497.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.052407 restraints weight = 49768.351| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32811 Z= 0.198 Angle : 0.593 12.738 45845 Z= 0.318 Chirality : 0.039 0.182 4984 Planarity : 0.004 0.048 4812 Dihedral : 22.820 141.660 6532 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.15 % Allowed : 21.35 % Favored : 78.50 % 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: 1.19 (0.15), residues: 1215 sheet: 0.19 (0.22), residues: 608 loop : -0.90 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 221 HIS 0.006 0.001 HIS g 182 PHE 0.012 0.001 PHE F 246 TYR 0.029 0.001 TYR D 242 ARG 0.009 0.000 ARG H 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4878.65 seconds wall clock time: 91 minutes 25.08 seconds (5485.08 seconds total)