Starting phenix.real_space_refine on Tue May 5 06:29:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uh9_64159/05_2026/9uh9_64159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uh9_64159/05_2026/9uh9_64159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uh9_64159/05_2026/9uh9_64159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uh9_64159/05_2026/9uh9_64159.map" model { file = "/net/cci-nas-00/data/ceres_data/9uh9_64159/05_2026/9uh9_64159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uh9_64159/05_2026/9uh9_64159.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 1 6.06 5 P 254 5.49 5 S 121 5.16 5 C 16290 2.51 5 N 4783 2.21 5 O 5662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27111 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 5391 Classifications: {'RNA': 254} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 19, 'rna3p_pur': 101, 'rna3p_pyr': 117} Link IDs: {'rna2p': 36, 'rna3p': 217} Chain breaks: 1 Chain: "B" Number of atoms: 5689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5689 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 47, 'TRANS': 670} Chain breaks: 6 Chain: "C" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1078 Classifications: {'peptide': 137} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 129} Chain breaks: 1 Chain: "D" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1502 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Chain: "E" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1215 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "F" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 869 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain breaks: 1 Chain: "G" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 945 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "I" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1829 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain: "J" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1916 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 12, 'TRANS': 235} Chain: "K" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 963 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2939 Classifications: {'peptide': 362} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 341} Chain: "M" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1828 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 12, 'TRANS': 217} Chain: "K" 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 21720 SG CYS K 43 71.806 90.232 51.402 1.00 92.63 S ATOM 21745 SG CYS K 46 72.142 86.408 52.086 1.00 92.72 S ATOM 22223 SG CYS K 104 69.820 87.651 49.378 1.00114.01 S ATOM 22245 SG CYS K 107 69.093 88.264 53.082 1.00126.46 S Time building chain proxies: 5.52, per 1000 atoms: 0.20 Number of scatterers: 27111 At special positions: 0 Unit cell: (146.3, 163.9, 193.6, 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 1 29.99 S 121 16.00 P 254 15.00 O 5662 8.00 N 4783 7.00 C 16290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 656.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 107 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 46 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 104 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 43 " Number of angles added : 6 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5196 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 18 sheets defined 44.0% alpha, 17.2% beta 19 base pairs and 118 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.836A pdb=" N ARG B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.771A pdb=" N PHE B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.773A pdb=" N LEU B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.632A pdb=" N LYS B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG B 211 " --> pdb=" O TRP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.526A pdb=" N TYR B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 347 Processing helix chain 'B' and resid 439 through 447 Processing helix chain 'B' and resid 464 through 473 removed outlier: 3.745A pdb=" N ILE B 468 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 490 removed outlier: 4.068A pdb=" N VAL B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 542 Processing helix chain 'B' and resid 551 through 554 removed outlier: 4.094A pdb=" N TRP B 554 " --> pdb=" O SER B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 555 through 565 Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.635A pdb=" N ARG B 574 " --> pdb=" O GLN B 570 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET B 575 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.521A pdb=" N PHE B 634 " --> pdb=" O PHE B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 655 Processing helix chain 'B' and resid 666 through 686 Processing helix chain 'B' and resid 694 through 699 removed outlier: 3.753A pdb=" N LEU B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 722 removed outlier: 3.561A pdb=" N TYR B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 820 removed outlier: 3.717A pdb=" N GLN B 814 " --> pdb=" O LYS B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 852 Processing helix chain 'B' and resid 879 through 889 removed outlier: 3.813A pdb=" N GLU B 888 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 904 No H-bonds generated for 'chain 'B' and resid 902 through 904' Processing helix chain 'B' and resid 905 through 919 removed outlier: 4.279A pdb=" N LEU B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS B 910 " --> pdb=" O SER B 906 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 911 " --> pdb=" O LYS B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 959 removed outlier: 4.621A pdb=" N CYS B 959 " --> pdb=" O VAL B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 removed outlier: 3.992A pdb=" N ASP B 992 " --> pdb=" O THR B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 56 Processing helix chain 'C' and resid 106 through 112 removed outlier: 4.136A pdb=" N ARG C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 126 Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.870A pdb=" N HIS C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 164 through 173 removed outlier: 3.735A pdb=" N ILE C 168 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Proline residue: C 170 - end of helix Processing helix chain 'C' and resid 189 through 200 Proline residue: C 198 - end of helix Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 10 through 17 removed outlier: 4.352A pdb=" N ALA D 14 " --> pdb=" O SER D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 43 through 53 removed outlier: 3.652A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 84 removed outlier: 3.596A pdb=" N LEU D 84 " --> pdb=" O GLN D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 99 through 114 removed outlier: 3.677A pdb=" N CYS D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 130 removed outlier: 3.615A pdb=" N ILE D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 74 through 81 removed outlier: 3.585A pdb=" N ALA E 80 " --> pdb=" O LEU E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 126 Processing helix chain 'E' and resid 131 through 139 removed outlier: 4.399A pdb=" N GLN E 139 " --> pdb=" O ARG E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 147 removed outlier: 3.942A pdb=" N CYS E 146 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 147 " --> pdb=" O THR E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 142 through 147' Processing helix chain 'F' and resid 45 through 58 removed outlier: 3.511A pdb=" N LEU F 49 " --> pdb=" O LYS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 removed outlier: 3.549A pdb=" N LEU F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 58 Processing helix chain 'G' and resid 76 through 92 Processing helix chain 'H' and resid 36 through 53 removed outlier: 4.176A pdb=" N LEU H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 58 Processing helix chain 'H' and resid 82 through 92 Processing helix chain 'H' and resid 110 through 116 removed outlier: 3.877A pdb=" N LEU H 114 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 110 through 116' Processing helix chain 'I' and resid 14 through 29 Processing helix chain 'I' and resid 53 through 58 removed outlier: 3.534A pdb=" N LEU I 57 " --> pdb=" O ALA I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 removed outlier: 4.292A pdb=" N LEU I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 100 Processing helix chain 'I' and resid 109 through 117 Processing helix chain 'I' and resid 138 through 149 removed outlier: 3.521A pdb=" N ILE I 142 " --> pdb=" O LYS I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 162 Processing helix chain 'I' and resid 163 through 180 removed outlier: 3.574A pdb=" N ARG I 167 " --> pdb=" O SER I 163 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR I 168 " --> pdb=" O THR I 164 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 211 Processing helix chain 'I' and resid 213 through 219 Processing helix chain 'I' and resid 223 through 238 Processing helix chain 'J' and resid 14 through 29 removed outlier: 3.826A pdb=" N LEU J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 58 removed outlier: 3.597A pdb=" N LEU J 57 " --> pdb=" O ALA J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 92 removed outlier: 4.254A pdb=" N LEU J 90 " --> pdb=" O HIS J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.592A pdb=" N CYS J 117 " --> pdb=" O PHE J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 149 Processing helix chain 'J' and resid 157 through 162 removed outlier: 3.944A pdb=" N LYS J 161 " --> pdb=" O SER J 157 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP J 162 " --> pdb=" O PRO J 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 157 through 162' Processing helix chain 'J' and resid 162 through 180 removed outlier: 4.119A pdb=" N ARG J 166 " --> pdb=" O ASP J 162 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR J 168 " --> pdb=" O THR J 164 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE J 179 " --> pdb=" O ASN J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 197 Processing helix chain 'J' and resid 199 through 211 Processing helix chain 'J' and resid 213 through 219 Processing helix chain 'J' and resid 222 through 238 removed outlier: 3.654A pdb=" N ARG J 226 " --> pdb=" O SER J 222 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA J 238 " --> pdb=" O THR J 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 14 removed outlier: 3.706A pdb=" N LEU K 7 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA K 10 " --> pdb=" O TYR K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 33 removed outlier: 4.003A pdb=" N ALA K 22 " --> pdb=" O CYS K 18 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS K 33 " --> pdb=" O TYR K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 79 removed outlier: 3.617A pdb=" N ARG K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN K 79 " --> pdb=" O ARG K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 95 Processing helix chain 'L' and resid 3 through 8 Processing helix chain 'L' and resid 28 through 36 Processing helix chain 'L' and resid 53 through 62 removed outlier: 3.753A pdb=" N ASN L 62 " --> pdb=" O ASN L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 78 removed outlier: 3.538A pdb=" N ILE L 78 " --> pdb=" O HIS L 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 75 through 78' Processing helix chain 'L' and resid 79 through 86 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 150 through 156 removed outlier: 3.583A pdb=" N LEU L 155 " --> pdb=" O MET L 151 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN L 156 " --> pdb=" O GLU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 Processing helix chain 'L' and resid 192 through 197 Processing helix chain 'L' and resid 236 through 248 Processing helix chain 'L' and resid 286 through 299 Processing helix chain 'M' and resid 10 through 14 Processing helix chain 'M' and resid 32 through 54 Processing helix chain 'M' and resid 55 through 72 removed outlier: 3.609A pdb=" N ASP M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN M 72 " --> pdb=" O VAL M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 98 Processing helix chain 'M' and resid 99 through 113 Processing helix chain 'M' and resid 128 through 164 removed outlier: 3.673A pdb=" N VAL M 132 " --> pdb=" O SER M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 196 removed outlier: 3.525A pdb=" N ASN M 173 " --> pdb=" O PHE M 169 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU M 196 " --> pdb=" O LYS M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 212 removed outlier: 3.859A pdb=" N LEU M 201 " --> pdb=" O LEU M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 231 removed outlier: 3.886A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 239 removed outlier: 3.980A pdb=" N PHE M 235 " --> pdb=" O GLY M 231 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA2, first strand: chain 'B' and resid 502 through 509 removed outlier: 5.139A pdb=" N THR B 503 " --> pdb=" O GLN B 601 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN B 601 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 290 through 295 removed outlier: 6.830A pdb=" N GLY B 290 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR B 309 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU B 292 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 294 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 804 through 805 removed outlier: 7.053A pdb=" N CYS B 804 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N TRP B 858 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE B 875 " --> pdb=" O LEU B 964 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 965 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER B 986 " --> pdb=" O GLY B 965 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL B 967 " --> pdb=" O PHE B 984 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE B 984 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLY B 979 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AA6, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.690A pdb=" N LEU C 131 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL C 132 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL C 161 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL C 134 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 174 through 178 removed outlier: 6.939A pdb=" N ILE D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU D 160 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS D 166 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE D 139 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLU D 187 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 141 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL D 183 " --> pdb=" O THR D 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 54 through 58 removed outlier: 3.989A pdb=" N HIS E 102 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU E 12 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N THR E 100 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL E 14 " --> pdb=" O PHE E 98 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE E 98 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AB1, first strand: chain 'F' and resid 36 through 39 removed outlier: 6.044A pdb=" N VAL F 36 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N SER F 68 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N MET F 38 " --> pdb=" O SER F 68 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N CYS F 70 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN F 93 " --> pdb=" O GLN F 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 20 through 24 Processing sheet with id=AB3, first strand: chain 'H' and resid 9 through 14 removed outlier: 4.411A pdb=" N GLU H 9 " --> pdb=" O LYS L 19 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS L 19 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU L 15 " --> pdb=" O TYR H 13 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR L 311 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR L 40 " --> pdb=" O GLY L 283 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER L 270 " --> pdb=" O PRO L 220 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL L 272 " --> pdb=" O GLN L 218 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN L 218 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA L 274 " --> pdb=" O ASP L 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 62 through 67 removed outlier: 6.061A pdb=" N ILE H 63 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ARG H 76 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N THR H 65 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE H 74 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER H 72 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR H 21 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL H 107 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS H 23 " --> pdb=" O ILE H 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.525A pdb=" N VAL I 102 " --> pdb=" O THR I 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 5 through 10 removed outlier: 4.705A pdb=" N ALA J 5 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA J 34 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU J 7 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASN J 36 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU J 9 " --> pdb=" O ASN J 36 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE J 38 " --> pdb=" O LEU J 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL J 102 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL J 103 " --> pdb=" O LEU J 124 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N CYS J 126 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL J 105 " --> pdb=" O CYS J 126 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE J 152 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N SER J 188 " --> pdb=" O PHE J 152 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU J 154 " --> pdb=" O SER J 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 55 through 60 Processing sheet with id=AB8, first strand: chain 'L' and resid 132 through 133 removed outlier: 6.731A pdb=" N VAL L 107 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA L 94 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE L 179 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LYS L 70 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU L 181 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N PHE L 68 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N TRP L 183 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N TYR L 66 " --> pdb=" O TRP L 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 25 through 29 985 hydrogen bonds defined for protein. 2853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 118 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7862 1.34 - 1.46: 7183 1.46 - 1.58: 12473 1.58 - 1.70: 506 1.70 - 1.82: 161 Bond restraints: 28185 Sorted by residual: bond pdb=" CA ASP D 172 " pdb=" CB ASP D 172 " ideal model delta sigma weight residual 1.534 1.577 -0.043 1.79e-02 3.12e+03 5.66e+00 bond pdb=" N PRO B 301 " pdb=" CD PRO B 301 " ideal model delta sigma weight residual 1.473 1.498 -0.025 1.40e-02 5.10e+03 3.31e+00 bond pdb=" C VAL B 659 " pdb=" N PRO B 660 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.08e-02 8.57e+03 3.21e+00 bond pdb=" CB GLU B 682 " pdb=" CG GLU B 682 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB GLU H 9 " pdb=" CG GLU H 9 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.83e+00 ... (remaining 28180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.11: 39303 6.11 - 12.22: 45 12.22 - 18.32: 5 18.32 - 24.43: 1 24.43 - 30.54: 2 Bond angle restraints: 39356 Sorted by residual: angle pdb=" N ALA B 999 " pdb=" CA ALA B 999 " pdb=" C ALA B 999 " ideal model delta sigma weight residual 111.03 140.02 -28.99 1.11e+00 8.12e-01 6.82e+02 angle pdb=" N ALA B 999 " pdb=" CA ALA B 999 " pdb=" CB ALA B 999 " ideal model delta sigma weight residual 109.98 87.95 22.03 1.45e+00 4.76e-01 2.31e+02 angle pdb=" N PRO B 998 " pdb=" CA PRO B 998 " pdb=" C PRO B 998 " ideal model delta sigma weight residual 112.47 81.93 30.54 2.06e+00 2.36e-01 2.20e+02 angle pdb=" C LYS B 299 " pdb=" CA LYS B 299 " pdb=" CB LYS B 299 " ideal model delta sigma weight residual 110.74 93.09 17.65 1.61e+00 3.86e-01 1.20e+02 angle pdb=" N LYS B 299 " pdb=" CA LYS B 299 " pdb=" C LYS B 299 " ideal model delta sigma weight residual 108.02 123.53 -15.51 1.75e+00 3.27e-01 7.86e+01 ... (remaining 39351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 16509 35.58 - 71.17: 946 71.17 - 106.75: 124 106.75 - 142.34: 0 142.34 - 177.92: 3 Dihedral angle restraints: 17582 sinusoidal: 9588 harmonic: 7994 Sorted by residual: dihedral pdb=" O4' C A 243 " pdb=" C1' C A 243 " pdb=" N1 C A 243 " pdb=" C2 C A 243 " ideal model delta sinusoidal sigma weight residual 232.00 54.08 177.92 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" N ALA B 999 " pdb=" C ALA B 999 " pdb=" CA ALA B 999 " pdb=" CB ALA B 999 " ideal model delta harmonic sigma weight residual 122.90 107.29 15.61 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" C PRO B 998 " pdb=" N PRO B 998 " pdb=" CA PRO B 998 " pdb=" CB PRO B 998 " ideal model delta harmonic sigma weight residual -120.70 -105.48 -15.22 0 2.50e+00 1.60e-01 3.71e+01 ... (remaining 17579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 4531 0.097 - 0.194: 164 0.194 - 0.291: 4 0.291 - 0.388: 0 0.388 - 0.485: 2 Chirality restraints: 4701 Sorted by residual: chirality pdb=" CA ALA B 999 " pdb=" N ALA B 999 " pdb=" C ALA B 999 " pdb=" CB ALA B 999 " both_signs ideal model delta sigma weight residual False 2.48 2.00 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA PRO B 998 " pdb=" N PRO B 998 " pdb=" C PRO B 998 " pdb=" CB PRO B 998 " both_signs ideal model delta sigma weight residual False 2.72 3.19 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" CG LEU J 229 " pdb=" CB LEU J 229 " pdb=" CD1 LEU J 229 " pdb=" CD2 LEU J 229 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4698 not shown) Planarity restraints: 4040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 300 " 0.047 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO B 301 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR K 66 " -0.045 5.00e-02 4.00e+02 6.76e-02 7.31e+00 pdb=" N PRO K 67 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO K 67 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO K 67 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP G 44 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" CG ASP G 44 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP G 44 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP G 44 " -0.013 2.00e-02 2.50e+03 ... (remaining 4037 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 21 2.58 - 3.16: 20328 3.16 - 3.74: 43398 3.74 - 4.32: 56372 4.32 - 4.90: 88698 Nonbonded interactions: 208817 Sorted by model distance: nonbonded pdb=" N PRO B 998 " pdb=" O PRO B 998 " model vdw 1.996 2.496 nonbonded pdb=" C GLN B 997 " pdb=" O PRO B 998 " model vdw 2.181 3.270 nonbonded pdb=" O ASP D 112 " pdb=" OD1 ASP D 112 " model vdw 2.344 3.040 nonbonded pdb=" O ASN K 54 " pdb=" OD1 ASN K 54 " model vdw 2.408 3.040 nonbonded pdb=" N6 A A 122 " pdb=" N1 G A 188 " model vdw 2.474 3.200 ... (remaining 208812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'I' selection = (chain 'J' and resid 2 through 238) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.320 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.002 0.049 28189 Z= 0.118 Angle : 0.687 30.541 39362 Z= 0.367 Chirality : 0.039 0.485 4701 Planarity : 0.004 0.070 4040 Dihedral : 19.811 177.922 12386 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.33 % Allowed : 26.76 % Favored : 72.91 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.16), residues: 2699 helix: 1.36 (0.16), residues: 1042 sheet: 0.39 (0.22), residues: 557 loop : -1.62 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 167 TYR 0.017 0.001 TYR M 187 PHE 0.018 0.001 PHE G 45 TRP 0.017 0.001 TRP L 324 HIS 0.005 0.001 HIS D 7 Details of bonding type rmsd covalent geometry : bond 0.00240 (28185) covalent geometry : angle 0.68643 (39356) hydrogen bonds : bond 0.16294 ( 1030) hydrogen bonds : angle 5.70581 ( 2927) metal coordination : bond 0.00420 ( 4) metal coordination : angle 2.60275 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 276 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8841 (pp30) cc_final: 0.8487 (pp30) REVERT: B 612 LEU cc_start: 0.9050 (mm) cc_final: 0.8846 (mm) REVERT: B 846 LEU cc_start: 0.9216 (tt) cc_final: 0.8782 (pp) REVERT: D 171 GLU cc_start: 0.8306 (pm20) cc_final: 0.8084 (pm20) REVERT: F 104 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7550 (pp20) REVERT: F 107 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7501 (tm-30) REVERT: G 109 ASP cc_start: 0.8392 (m-30) cc_final: 0.7627 (p0) REVERT: I 86 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.6509 (p90) REVERT: J 165 MET cc_start: 0.8478 (mmm) cc_final: 0.7512 (mmm) REVERT: J 196 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8156 (mp0) REVERT: K 73 LEU cc_start: 0.7275 (tp) cc_final: 0.6967 (pp) REVERT: M 201 LEU cc_start: 0.9260 (mt) cc_final: 0.8902 (tp) outliers start: 8 outliers final: 5 residues processed: 283 average time/residue: 0.1845 time to fit residues: 81.5325 Evaluate side-chains 224 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 218 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 TRP Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain I residue 86 HIS Chi-restraints excluded: chain K residue 43 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 111 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: B 205 HIS B 208 HIS B 440 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.093297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.063148 restraints weight = 99640.532| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.49 r_work: 0.2958 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 28189 Z= 0.248 Angle : 0.653 8.131 39362 Z= 0.329 Chirality : 0.041 0.176 4701 Planarity : 0.005 0.071 4040 Dihedral : 18.987 176.517 7022 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.33 % Allowed : 21.85 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2699 helix: 1.37 (0.16), residues: 1063 sheet: 0.24 (0.22), residues: 545 loop : -1.67 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 23 TYR 0.016 0.002 TYR L 264 PHE 0.014 0.002 PHE L 241 TRP 0.045 0.002 TRP C 33 HIS 0.007 0.001 HIS J 86 Details of bonding type rmsd covalent geometry : bond 0.00552 (28185) covalent geometry : angle 0.65160 (39356) hydrogen bonds : bond 0.04921 ( 1030) hydrogen bonds : angle 4.83709 ( 2927) metal coordination : bond 0.00899 ( 4) metal coordination : angle 3.76185 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 209 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8995 (pp30) cc_final: 0.8578 (pp30) REVERT: B 245 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8613 (tt0) REVERT: B 331 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9280 (pp) REVERT: B 513 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.7935 (mtp180) REVERT: B 873 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.9247 (m) REVERT: D 41 ARG cc_start: 0.7210 (pmt-80) cc_final: 0.6894 (pmt-80) REVERT: D 79 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5603 (mpp-170) REVERT: D 175 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8524 (mttp) REVERT: E 58 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8565 (pp) REVERT: F 45 LYS cc_start: 0.6781 (mmmt) cc_final: 0.6458 (mmmt) REVERT: F 104 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7569 (pp20) REVERT: G 44 ASP cc_start: 0.8378 (t0) cc_final: 0.7970 (t0) REVERT: H 102 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8974 (t80) REVERT: I 44 LYS cc_start: 0.8883 (pttm) cc_final: 0.8551 (ttmt) REVERT: I 86 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.6772 (p90) REVERT: K 54 ASN cc_start: 0.8642 (t0) cc_final: 0.8400 (t0) REVERT: K 109 ARG cc_start: 0.7092 (mmm160) cc_final: 0.6833 (mmm160) REVERT: M 78 ARG cc_start: 0.8352 (ptp90) cc_final: 0.7899 (mtt180) REVERT: M 104 ILE cc_start: 0.8777 (mm) cc_final: 0.8547 (tp) REVERT: M 210 ARG cc_start: 0.8574 (tpp80) cc_final: 0.8121 (mmm-85) outliers start: 128 outliers final: 66 residues processed: 318 average time/residue: 0.1768 time to fit residues: 88.5635 Evaluate side-chains 261 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 186 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 58 PHE Chi-restraints excluded: chain I residue 86 HIS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain K residue 27 TRP Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 220 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 107 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 234 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 chunk 214 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 260 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 GLN E 128 ASN I 86 HIS I 205 ASN ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 HIS ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.095234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.065266 restraints weight = 98885.889| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.49 r_work: 0.3016 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28189 Z= 0.101 Angle : 0.541 11.214 39362 Z= 0.265 Chirality : 0.037 0.211 4701 Planarity : 0.004 0.071 4040 Dihedral : 18.851 174.133 7020 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.62 % Allowed : 24.59 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 2699 helix: 1.61 (0.16), residues: 1063 sheet: 0.39 (0.22), residues: 542 loop : -1.61 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 23 TYR 0.012 0.001 TYR I 201 PHE 0.016 0.001 PHE C 189 TRP 0.026 0.001 TRP C 33 HIS 0.004 0.001 HIS J 86 Details of bonding type rmsd covalent geometry : bond 0.00216 (28185) covalent geometry : angle 0.54041 (39356) hydrogen bonds : bond 0.03825 ( 1030) hydrogen bonds : angle 4.50055 ( 2927) metal coordination : bond 0.00406 ( 4) metal coordination : angle 2.37627 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 217 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8499 (pp30) REVERT: B 331 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9207 (pp) REVERT: D 79 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.5553 (mpp-170) REVERT: E 58 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8475 (pp) REVERT: E 138 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8850 (mm) REVERT: E 144 ARG cc_start: 0.8356 (tpt90) cc_final: 0.7818 (tpt90) REVERT: F 45 LYS cc_start: 0.6799 (mmmt) cc_final: 0.6506 (mmmt) REVERT: G 44 ASP cc_start: 0.8210 (t0) cc_final: 0.7791 (t0) REVERT: I 44 LYS cc_start: 0.8907 (pttm) cc_final: 0.8529 (ttmt) REVERT: I 86 HIS cc_start: 0.7768 (OUTLIER) cc_final: 0.7195 (p-80) REVERT: J 165 MET cc_start: 0.8461 (mmm) cc_final: 0.7928 (mmm) REVERT: K 54 ASN cc_start: 0.8879 (t0) cc_final: 0.8647 (t0) REVERT: M 104 ILE cc_start: 0.8520 (mm) cc_final: 0.8245 (tp) REVERT: M 201 LEU cc_start: 0.9280 (mt) cc_final: 0.9011 (tp) REVERT: M 216 TYR cc_start: 0.6957 (t80) cc_final: 0.6517 (t80) outliers start: 87 outliers final: 41 residues processed: 289 average time/residue: 0.1829 time to fit residues: 82.4335 Evaluate side-chains 239 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 86 HIS Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain K residue 27 TRP Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 99 optimal weight: 10.0000 chunk 259 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 230 optimal weight: 30.0000 chunk 256 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN D 11 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 337 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.092548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062271 restraints weight = 98697.577| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.43 r_work: 0.2944 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28189 Z= 0.183 Angle : 0.582 10.379 39362 Z= 0.290 Chirality : 0.039 0.199 4701 Planarity : 0.004 0.069 4040 Dihedral : 18.854 177.582 7018 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.70 % Allowed : 24.05 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2699 helix: 1.70 (0.16), residues: 1060 sheet: 0.22 (0.21), residues: 560 loop : -1.61 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 122 TYR 0.012 0.001 TYR M 216 PHE 0.013 0.001 PHE C 189 TRP 0.028 0.001 TRP C 33 HIS 0.006 0.001 HIS J 86 Details of bonding type rmsd covalent geometry : bond 0.00406 (28185) covalent geometry : angle 0.58049 (39356) hydrogen bonds : bond 0.04168 ( 1030) hydrogen bonds : angle 4.54873 ( 2927) metal coordination : bond 0.00813 ( 4) metal coordination : angle 2.90307 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 204 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8498 (pp30) REVERT: B 331 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9265 (pp) REVERT: B 513 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.7999 (mtp180) REVERT: C 154 ARG cc_start: 0.6715 (mmt-90) cc_final: 0.6497 (mmt-90) REVERT: D 79 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.5675 (mpp-170) REVERT: D 171 GLU cc_start: 0.8828 (pm20) cc_final: 0.8537 (pm20) REVERT: E 39 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8991 (mmm-85) REVERT: E 58 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8410 (pp) REVERT: E 144 ARG cc_start: 0.8428 (tpt90) cc_final: 0.7924 (tpt90) REVERT: G 44 ASP cc_start: 0.8096 (t0) cc_final: 0.7611 (t0) REVERT: I 86 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7287 (p-80) REVERT: J 67 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8065 (mtpp) REVERT: J 132 LYS cc_start: 0.8972 (tppt) cc_final: 0.8623 (tptp) REVERT: K 54 ASN cc_start: 0.8908 (t0) cc_final: 0.8708 (t0) REVERT: M 78 ARG cc_start: 0.8322 (ptm160) cc_final: 0.7826 (mtm180) REVERT: M 201 LEU cc_start: 0.9264 (mt) cc_final: 0.8914 (tt) REVERT: M 214 MET cc_start: 0.7160 (tmm) cc_final: 0.6594 (ttt) outliers start: 113 outliers final: 65 residues processed: 300 average time/residue: 0.2013 time to fit residues: 93.9550 Evaluate side-chains 255 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 182 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 86 HIS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 215 SER Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 27 TRP Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 133 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 275 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 290 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN J 143 ASN M 114 ASN M 129 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.093280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.063264 restraints weight = 98433.353| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.41 r_work: 0.2972 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28189 Z= 0.120 Angle : 0.543 12.323 39362 Z= 0.269 Chirality : 0.037 0.201 4701 Planarity : 0.004 0.068 4040 Dihedral : 18.818 176.072 7018 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.12 % Allowed : 24.59 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 2699 helix: 1.75 (0.16), residues: 1068 sheet: 0.37 (0.21), residues: 564 loop : -1.58 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 147 TYR 0.031 0.001 TYR K 24 PHE 0.014 0.001 PHE C 189 TRP 0.028 0.001 TRP C 33 HIS 0.004 0.001 HIS J 86 Details of bonding type rmsd covalent geometry : bond 0.00263 (28185) covalent geometry : angle 0.54201 (39356) hydrogen bonds : bond 0.03680 ( 1030) hydrogen bonds : angle 4.37990 ( 2927) metal coordination : bond 0.00594 ( 4) metal coordination : angle 3.06580 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 200 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8455 (pp30) REVERT: B 331 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9243 (pp) REVERT: B 481 CYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9188 (p) REVERT: B 513 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8015 (mtp180) REVERT: B 686 ARG cc_start: 0.8781 (mtp85) cc_final: 0.8528 (mtp85) REVERT: C 32 ARG cc_start: 0.6987 (mmm160) cc_final: 0.5449 (mmm160) REVERT: D 79 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.5721 (mpp-170) REVERT: E 39 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.9001 (mmm-85) REVERT: E 58 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8421 (pp) REVERT: E 144 ARG cc_start: 0.8379 (tpt90) cc_final: 0.7865 (tpt90) REVERT: G 44 ASP cc_start: 0.8048 (t0) cc_final: 0.7643 (t0) REVERT: I 86 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7161 (p-80) REVERT: K 7 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8429 (mp) REVERT: K 54 ASN cc_start: 0.8891 (t0) cc_final: 0.8669 (t0) REVERT: M 78 ARG cc_start: 0.8280 (ptm160) cc_final: 0.7904 (mtm180) REVERT: M 137 MET cc_start: 0.9289 (mmm) cc_final: 0.9070 (mmm) REVERT: M 201 LEU cc_start: 0.9280 (mt) cc_final: 0.8943 (tt) outliers start: 99 outliers final: 58 residues processed: 286 average time/residue: 0.2003 time to fit residues: 89.3689 Evaluate side-chains 254 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 187 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 86 HIS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 27 TRP Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 239 GLU Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 175 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 107 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 226 optimal weight: 20.0000 chunk 235 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 207 optimal weight: 0.0670 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN E 128 ASN F 93 GLN ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.092968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.063164 restraints weight = 98661.109| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.39 r_work: 0.2966 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28189 Z= 0.127 Angle : 0.550 10.661 39362 Z= 0.272 Chirality : 0.037 0.200 4701 Planarity : 0.004 0.067 4040 Dihedral : 18.794 176.520 7018 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.79 % Allowed : 24.97 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2699 helix: 1.80 (0.16), residues: 1065 sheet: 0.39 (0.21), residues: 566 loop : -1.58 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 14 TYR 0.011 0.001 TYR M 216 PHE 0.011 0.001 PHE C 189 TRP 0.026 0.001 TRP C 33 HIS 0.005 0.001 HIS K 15 Details of bonding type rmsd covalent geometry : bond 0.00283 (28185) covalent geometry : angle 0.54987 (39356) hydrogen bonds : bond 0.03628 ( 1030) hydrogen bonds : angle 4.36687 ( 2927) metal coordination : bond 0.00431 ( 4) metal coordination : angle 1.73449 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 199 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8526 (pp30) REVERT: B 331 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9239 (pp) REVERT: B 481 CYS cc_start: 0.9442 (OUTLIER) cc_final: 0.9201 (p) REVERT: B 513 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8007 (mtp180) REVERT: B 610 ASP cc_start: 0.8792 (m-30) cc_final: 0.8562 (t70) REVERT: B 686 ARG cc_start: 0.8762 (mtp85) cc_final: 0.8530 (mtp85) REVERT: C 32 ARG cc_start: 0.7072 (mmm160) cc_final: 0.5534 (mmm160) REVERT: D 41 ARG cc_start: 0.7055 (pmt-80) cc_final: 0.6299 (pmt-80) REVERT: D 42 MET cc_start: 0.6991 (mmm) cc_final: 0.6673 (mmm) REVERT: D 79 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.5724 (mpp-170) REVERT: D 171 GLU cc_start: 0.8744 (pm20) cc_final: 0.8462 (pm20) REVERT: E 39 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8970 (mmm-85) REVERT: E 58 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8410 (pp) REVERT: E 144 ARG cc_start: 0.8356 (tpt90) cc_final: 0.7873 (tpt90) REVERT: G 44 ASP cc_start: 0.8082 (t0) cc_final: 0.7565 (t0) REVERT: I 86 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7176 (p-80) REVERT: K 7 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8502 (mp) REVERT: K 54 ASN cc_start: 0.8912 (t0) cc_final: 0.8681 (t0) REVERT: M 78 ARG cc_start: 0.8305 (ptm160) cc_final: 0.7943 (mtm180) REVERT: M 201 LEU cc_start: 0.9275 (mt) cc_final: 0.8909 (tt) REVERT: M 214 MET cc_start: 0.7554 (tmm) cc_final: 0.7336 (tmm) outliers start: 91 outliers final: 66 residues processed: 276 average time/residue: 0.2006 time to fit residues: 86.3135 Evaluate side-chains 262 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 187 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 86 HIS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 27 TRP Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 239 GLU Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 125 optimal weight: 5.9990 chunk 266 optimal weight: 0.0040 chunk 13 optimal weight: 40.0000 chunk 231 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 90 optimal weight: 0.0980 chunk 257 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN E 128 ASN F 93 GLN G 87 GLN ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.092820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.063074 restraints weight = 97551.443| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.35 r_work: 0.2967 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28189 Z= 0.125 Angle : 0.552 10.127 39362 Z= 0.273 Chirality : 0.037 0.215 4701 Planarity : 0.004 0.066 4040 Dihedral : 18.775 176.584 7018 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.87 % Allowed : 24.89 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.16), residues: 2699 helix: 1.83 (0.16), residues: 1066 sheet: 0.35 (0.21), residues: 556 loop : -1.52 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 14 TYR 0.015 0.001 TYR K 45 PHE 0.011 0.001 PHE C 189 TRP 0.021 0.001 TRP C 33 HIS 0.005 0.001 HIS K 15 Details of bonding type rmsd covalent geometry : bond 0.00280 (28185) covalent geometry : angle 0.55174 (39356) hydrogen bonds : bond 0.03541 ( 1030) hydrogen bonds : angle 4.31194 ( 2927) metal coordination : bond 0.00652 ( 4) metal coordination : angle 2.11480 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 200 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 118 MET cc_start: 0.8939 (tpt) cc_final: 0.8556 (tpt) REVERT: B 124 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8467 (pp30) REVERT: B 331 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9269 (pp) REVERT: B 481 CYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9182 (p) REVERT: B 513 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.7991 (mtp180) REVERT: B 610 ASP cc_start: 0.8778 (m-30) cc_final: 0.8563 (t70) REVERT: B 686 ARG cc_start: 0.8772 (mtp85) cc_final: 0.8536 (mtp85) REVERT: C 32 ARG cc_start: 0.7120 (mmm160) cc_final: 0.6063 (mmm160) REVERT: D 41 ARG cc_start: 0.7053 (pmt-80) cc_final: 0.6342 (pmt-80) REVERT: D 42 MET cc_start: 0.6809 (mmm) cc_final: 0.6602 (mmm) REVERT: D 79 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.5860 (mpt180) REVERT: D 83 GLU cc_start: 0.8742 (pt0) cc_final: 0.8498 (pt0) REVERT: E 39 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8953 (mmm-85) REVERT: E 58 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8397 (pp) REVERT: E 144 ARG cc_start: 0.8389 (tpt90) cc_final: 0.7895 (tpt90) REVERT: F 93 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8236 (pp30) REVERT: G 44 ASP cc_start: 0.8045 (t0) cc_final: 0.7612 (t0) REVERT: G 70 TYR cc_start: 0.8014 (m-80) cc_final: 0.7556 (m-80) REVERT: I 86 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7015 (p-80) REVERT: I 177 MET cc_start: 0.9285 (tpp) cc_final: 0.8822 (mtt) REVERT: I 233 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8841 (pt0) REVERT: J 67 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8046 (mtpp) REVERT: J 165 MET cc_start: 0.8554 (mmm) cc_final: 0.7984 (mmm) REVERT: K 7 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8610 (mp) REVERT: K 54 ASN cc_start: 0.8901 (t0) cc_final: 0.8663 (t0) REVERT: K 73 LEU cc_start: 0.7396 (tp) cc_final: 0.7148 (pp) REVERT: M 78 ARG cc_start: 0.8333 (ptm160) cc_final: 0.7967 (mtm180) REVERT: M 201 LEU cc_start: 0.9284 (mt) cc_final: 0.8911 (tt) REVERT: M 214 MET cc_start: 0.7581 (tmm) cc_final: 0.7314 (tmm) outliers start: 93 outliers final: 65 residues processed: 280 average time/residue: 0.1993 time to fit residues: 87.2147 Evaluate side-chains 265 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 188 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 86 HIS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 27 TRP Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 132 optimal weight: 0.0970 chunk 183 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 135 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN G 87 GLN ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 HIS M 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.091674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.061731 restraints weight = 98630.759| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.41 r_work: 0.2933 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28189 Z= 0.174 Angle : 0.580 9.928 39362 Z= 0.288 Chirality : 0.038 0.238 4701 Planarity : 0.004 0.067 4040 Dihedral : 18.802 177.989 7018 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.12 % Allowed : 24.84 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 2699 helix: 1.83 (0.16), residues: 1059 sheet: 0.33 (0.21), residues: 558 loop : -1.58 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 147 TYR 0.015 0.001 TYR K 45 PHE 0.025 0.001 PHE G 45 TRP 0.019 0.001 TRP C 33 HIS 0.005 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00385 (28185) covalent geometry : angle 0.57974 (39356) hydrogen bonds : bond 0.03846 ( 1030) hydrogen bonds : angle 4.38504 ( 2927) metal coordination : bond 0.00516 ( 4) metal coordination : angle 1.74390 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 192 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 MET cc_start: 0.9004 (tpt) cc_final: 0.8617 (tpt) REVERT: B 124 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8499 (pp30) REVERT: B 331 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9276 (pp) REVERT: B 481 CYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9210 (p) REVERT: B 513 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8008 (mtp180) REVERT: B 610 ASP cc_start: 0.8800 (m-30) cc_final: 0.8561 (t70) REVERT: C 32 ARG cc_start: 0.7060 (mmm160) cc_final: 0.5996 (mmm160) REVERT: D 41 ARG cc_start: 0.7117 (pmt-80) cc_final: 0.6414 (pmt-80) REVERT: D 42 MET cc_start: 0.6721 (mmm) cc_final: 0.6494 (mmm) REVERT: D 79 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.5335 (mpp-170) REVERT: D 83 GLU cc_start: 0.8801 (pt0) cc_final: 0.8565 (pt0) REVERT: E 39 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.9001 (mmm-85) REVERT: E 58 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8381 (pp) REVERT: E 144 ARG cc_start: 0.8363 (tpt90) cc_final: 0.7899 (tpt90) REVERT: G 44 ASP cc_start: 0.8159 (t0) cc_final: 0.7734 (t0) REVERT: I 86 HIS cc_start: 0.8042 (OUTLIER) cc_final: 0.7015 (p-80) REVERT: I 177 MET cc_start: 0.9305 (tpp) cc_final: 0.8922 (mtt) REVERT: I 233 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8837 (pt0) REVERT: J 67 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8110 (mtpp) REVERT: K 7 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8645 (mp) REVERT: K 45 TYR cc_start: 0.8621 (m-80) cc_final: 0.8204 (m-80) REVERT: K 54 ASN cc_start: 0.8862 (t0) cc_final: 0.8635 (t0) REVERT: K 73 LEU cc_start: 0.7339 (tp) cc_final: 0.7104 (pp) REVERT: L 141 ILE cc_start: 0.9239 (mm) cc_final: 0.9023 (mm) REVERT: M 78 ARG cc_start: 0.8418 (ptm160) cc_final: 0.8074 (mtm180) REVERT: M 137 MET cc_start: 0.9270 (mmm) cc_final: 0.9058 (mmm) REVERT: M 201 LEU cc_start: 0.9279 (mt) cc_final: 0.8897 (tt) REVERT: M 214 MET cc_start: 0.7624 (tmm) cc_final: 0.7356 (tmm) outliers start: 99 outliers final: 74 residues processed: 280 average time/residue: 0.1964 time to fit residues: 86.6022 Evaluate side-chains 270 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 185 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 86 HIS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 40 ASP Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 27 TRP Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 239 GLU Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 75 optimal weight: 0.0870 chunk 114 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 117 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 247 optimal weight: 8.9990 chunk 225 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.092092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062270 restraints weight = 98236.260| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.38 r_work: 0.2956 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28189 Z= 0.131 Angle : 0.564 11.716 39362 Z= 0.279 Chirality : 0.038 0.257 4701 Planarity : 0.004 0.067 4040 Dihedral : 18.802 176.897 7018 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.45 % Allowed : 25.47 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2699 helix: 1.82 (0.16), residues: 1065 sheet: 0.37 (0.21), residues: 568 loop : -1.59 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 147 TYR 0.032 0.001 TYR K 24 PHE 0.025 0.001 PHE G 45 TRP 0.018 0.001 TRP C 33 HIS 0.004 0.001 HIS K 15 Details of bonding type rmsd covalent geometry : bond 0.00293 (28185) covalent geometry : angle 0.56398 (39356) hydrogen bonds : bond 0.03567 ( 1030) hydrogen bonds : angle 4.32005 ( 2927) metal coordination : bond 0.00338 ( 4) metal coordination : angle 1.54150 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 196 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 MET cc_start: 0.8989 (tpt) cc_final: 0.8584 (tpt) REVERT: B 124 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8479 (pp30) REVERT: B 304 MET cc_start: 0.8932 (tmm) cc_final: 0.8423 (tmm) REVERT: B 331 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9261 (pp) REVERT: B 481 CYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9191 (p) REVERT: B 513 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8003 (mtp180) REVERT: B 610 ASP cc_start: 0.8797 (m-30) cc_final: 0.8551 (t70) REVERT: B 686 ARG cc_start: 0.8812 (mtp85) cc_final: 0.8559 (mtp85) REVERT: C 32 ARG cc_start: 0.7107 (mmm160) cc_final: 0.6019 (mmm160) REVERT: D 41 ARG cc_start: 0.7206 (pmt-80) cc_final: 0.6596 (pmt-80) REVERT: D 42 MET cc_start: 0.6638 (mmm) cc_final: 0.6426 (mmm) REVERT: D 79 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.5242 (mpp-170) REVERT: D 83 GLU cc_start: 0.8791 (pt0) cc_final: 0.8541 (pt0) REVERT: E 58 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8391 (pp) REVERT: E 144 ARG cc_start: 0.8400 (tpt90) cc_final: 0.7936 (tpt90) REVERT: G 44 ASP cc_start: 0.8139 (t0) cc_final: 0.7712 (t0) REVERT: G 87 GLN cc_start: 0.9222 (tp40) cc_final: 0.8818 (mp10) REVERT: G 110 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7653 (tm-30) REVERT: I 86 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7016 (p-80) REVERT: I 177 MET cc_start: 0.9289 (tpp) cc_final: 0.9001 (mtt) REVERT: I 233 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8861 (pt0) REVERT: J 67 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8049 (mtpp) REVERT: J 165 MET cc_start: 0.8586 (mmm) cc_final: 0.7992 (mmm) REVERT: K 7 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8698 (mp) REVERT: K 54 ASN cc_start: 0.8906 (t0) cc_final: 0.8667 (t0) REVERT: K 73 LEU cc_start: 0.7355 (tp) cc_final: 0.7113 (pp) REVERT: K 109 ARG cc_start: 0.6767 (mtp85) cc_final: 0.6405 (mtp85) REVERT: M 104 ILE cc_start: 0.8531 (mm) cc_final: 0.8181 (tp) REVERT: M 137 MET cc_start: 0.9296 (mmm) cc_final: 0.9084 (mmm) REVERT: M 201 LEU cc_start: 0.9290 (mt) cc_final: 0.8925 (tt) REVERT: M 214 MET cc_start: 0.7576 (tmm) cc_final: 0.7282 (tmm) outliers start: 83 outliers final: 64 residues processed: 269 average time/residue: 0.1974 time to fit residues: 83.2955 Evaluate side-chains 262 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 188 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 86 HIS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 27 TRP Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 208 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 274 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 280 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN M 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.091210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.061354 restraints weight = 98850.855| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.41 r_work: 0.2928 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28189 Z= 0.166 Angle : 0.589 10.459 39362 Z= 0.292 Chirality : 0.038 0.277 4701 Planarity : 0.004 0.067 4040 Dihedral : 18.824 178.117 7018 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.45 % Allowed : 25.51 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 2699 helix: 1.83 (0.16), residues: 1059 sheet: 0.33 (0.21), residues: 566 loop : -1.62 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 210 TYR 0.013 0.001 TYR I 201 PHE 0.023 0.001 PHE G 45 TRP 0.016 0.001 TRP C 33 HIS 0.004 0.001 HIS J 86 Details of bonding type rmsd covalent geometry : bond 0.00371 (28185) covalent geometry : angle 0.58876 (39356) hydrogen bonds : bond 0.03848 ( 1030) hydrogen bonds : angle 4.40635 ( 2927) metal coordination : bond 0.00466 ( 4) metal coordination : angle 1.73341 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 188 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 MET cc_start: 0.9019 (tpt) cc_final: 0.8634 (tpt) REVERT: B 124 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8447 (pp30) REVERT: B 331 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9244 (pp) REVERT: B 481 CYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9204 (p) REVERT: B 513 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8012 (mtp180) REVERT: B 610 ASP cc_start: 0.8804 (m-30) cc_final: 0.8549 (t70) REVERT: C 32 ARG cc_start: 0.7196 (mmm160) cc_final: 0.6097 (mmm160) REVERT: D 41 ARG cc_start: 0.7309 (pmt-80) cc_final: 0.6673 (pmt-80) REVERT: D 42 MET cc_start: 0.6690 (mmm) cc_final: 0.6471 (mmm) REVERT: D 79 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.5093 (mpp-170) REVERT: D 83 GLU cc_start: 0.8838 (pt0) cc_final: 0.8602 (pt0) REVERT: E 58 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8371 (pp) REVERT: E 144 ARG cc_start: 0.8444 (tpt90) cc_final: 0.7999 (tpt90) REVERT: G 44 ASP cc_start: 0.8142 (t0) cc_final: 0.7747 (t0) REVERT: G 87 GLN cc_start: 0.9224 (tp40) cc_final: 0.8825 (mp10) REVERT: I 86 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.6798 (p-80) REVERT: I 177 MET cc_start: 0.9242 (tpp) cc_final: 0.8999 (mtt) REVERT: I 233 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.8874 (pt0) REVERT: J 67 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8093 (mtpp) REVERT: J 165 MET cc_start: 0.8701 (mmm) cc_final: 0.8196 (mmm) REVERT: K 7 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8734 (mp) REVERT: K 54 ASN cc_start: 0.8835 (t0) cc_final: 0.8591 (t0) REVERT: K 73 LEU cc_start: 0.7310 (tp) cc_final: 0.7092 (pp) REVERT: M 78 ARG cc_start: 0.8435 (ptm160) cc_final: 0.8014 (mtm180) REVERT: M 137 MET cc_start: 0.9306 (mmm) cc_final: 0.9080 (mmm) REVERT: M 201 LEU cc_start: 0.9299 (mt) cc_final: 0.8914 (tt) REVERT: M 214 MET cc_start: 0.7627 (tmm) cc_final: 0.7340 (tmm) outliers start: 83 outliers final: 69 residues processed: 260 average time/residue: 0.1978 time to fit residues: 81.0679 Evaluate side-chains 263 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 184 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 86 HIS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 27 TRP Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 221 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 153 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 54 optimal weight: 0.0770 chunk 46 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 chunk 291 optimal weight: 10.0000 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.092550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.063015 restraints weight = 97972.614| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.39 r_work: 0.2970 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28189 Z= 0.105 Angle : 0.565 11.265 39362 Z= 0.278 Chirality : 0.037 0.259 4701 Planarity : 0.004 0.067 4040 Dihedral : 18.800 175.733 7018 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.54 % Allowed : 26.59 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2699 helix: 1.82 (0.16), residues: 1075 sheet: 0.43 (0.21), residues: 563 loop : -1.56 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 147 TYR 0.021 0.001 TYR K 24 PHE 0.025 0.001 PHE G 45 TRP 0.015 0.001 TRP C 33 HIS 0.004 0.001 HIS K 15 Details of bonding type rmsd covalent geometry : bond 0.00230 (28185) covalent geometry : angle 0.56448 (39356) hydrogen bonds : bond 0.03395 ( 1030) hydrogen bonds : angle 4.26125 ( 2927) metal coordination : bond 0.00191 ( 4) metal coordination : angle 1.57263 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7601.37 seconds wall clock time: 130 minutes 51.63 seconds (7851.63 seconds total)