Starting phenix.real_space_refine on Sun Jul 5 11:21:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uh9_64159/07_2026/9uh9_64159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uh9_64159/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9uh9_64159/07_2026/9uh9_64159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uh9_64159/07_2026/9uh9_64159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uh9_64159/07_2026/9uh9_64159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uh9_64159/07_2026/9uh9_64159.map" } 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-dev-6108/lib/python3.11/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: 5.00, per 1000 atoms: 0.18 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: 1.94 Conformation dependent library (CDL) restraints added in 860.5 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: 2.85 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: 5.96 Time building geometry restraints manager: 2.67 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=" N1 C A 202 " pdb=" C2 C A 202 " ideal model delta sigma weight residual 1.397 1.418 -0.021 1.00e-02 1.00e+04 4.23e+00 bond pdb=" N9 A A 36 " pdb=" C4 A A 36 " ideal model delta sigma weight residual 1.374 1.385 -0.011 6.00e-03 2.78e+04 3.42e+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 ... (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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 27.590 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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= 0.127 Angle : 0.687 30.541 39362 Z= 0.412 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/Z covalent geometry : bond 0.00240 / 0.13 (28185) covalent geometry : angle 0.68653 / 0.41 (39356) hydrogen bonds : bond 0.16294 / 15.00 ( 1030) hydrogen bonds : angle 5.70581 / 6.81 ( 2927) metal coordination : bond 0.00420 / 0.27 ( 4) metal coordination : angle 2.60275 / 4.24 ( 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 : 0.881 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: 0.1730 time to fit residues: 76.2356 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 : 0.936 ------------------------------------------------------------------------------- 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: 20.0000 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... B 208 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN I 36 ASN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.095272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065310 restraints weight = 99214.350| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.44 r_work: 0.3013 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 28189 Z= 0.235 Angle : 0.603 8.595 39362 Z= 0.317 Chirality : 0.040 0.195 4701 Planarity : 0.005 0.101 4040 Dihedral : 18.974 177.957 7022 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.37 % Allowed : 23.05 % Favored : 72.58 % 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: 0.04 (0.16), residues: 2699 helix: 1.45 (0.16), residues: 1065 sheet: 0.38 (0.21), residues: 555 loop : -1.67 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 147 TYR 0.016 0.002 TYR M 198 PHE 0.013 0.002 PHE H 102 TRP 0.036 0.002 TRP C 33 HIS 0.006 0.001 HIS J 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 (28185) covalent geometry : angle 0.60213 / 0.32 (39356) hydrogen bonds : bond 0.05129 / 4.85 ( 1030) hydrogen bonds : angle 4.90286 / 5.93 ( 2927) metal coordination : bond 0.01010 / 0.59 ( 4) metal coordination : angle 2.66712 / 4.28 ( 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 321 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 216 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8987 (pp30) cc_final: 0.8560 (pp30) REVERT: B 245 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: B 513 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8061 (mtp180) REVERT: C 126 ARG cc_start: 0.7792 (mpp-170) cc_final: 0.7569 (mpp-170) REVERT: D 175 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8339 (mttp) REVERT: E 58 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8592 (pp) REVERT: E 114 LEU cc_start: 0.9420 (mt) cc_final: 0.9205 (mt) REVERT: F 45 LYS cc_start: 0.6722 (mmmt) cc_final: 0.6368 (mmmt) REVERT: F 104 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7535 (pp20) REVERT: G 44 ASP cc_start: 0.8179 (t0) cc_final: 0.7821 (t0) REVERT: H 102 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.9077 (t80) REVERT: I 44 LYS cc_start: 0.8803 (pttm) cc_final: 0.8456 (ttmt) REVERT: I 86 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.6648 (p90) REVERT: K 27 TRP cc_start: 0.9139 (OUTLIER) cc_final: 0.8887 (t60) REVERT: K 54 ASN cc_start: 0.8699 (t0) cc_final: 0.8448 (t0) REVERT: M 78 ARG cc_start: 0.8225 (ptp90) cc_final: 0.7769 (mtm180) REVERT: M 201 LEU cc_start: 0.9210 (mt) cc_final: 0.8838 (tt) outliers start: 105 outliers final: 58 residues processed: 307 average time/residue: 0.1719 time to fit residues: 83.2618 Evaluate side-chains 272 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 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 659 VAL Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 815 LEU 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 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 158 LEU 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 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 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 83 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 99 LYS 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 101 ASP Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 206 LEU 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 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 43 CYS 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 91 CYS Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 195 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: 8.9990 chunk 65 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 234 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 260 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.095865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066041 restraints weight = 98044.457| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.48 r_work: 0.3032 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28189 Z= 0.118 Angle : 0.537 11.102 39362 Z= 0.272 Chirality : 0.037 0.231 4701 Planarity : 0.004 0.069 4040 Dihedral : 18.899 176.597 7020 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.33 % Allowed : 24.26 % Favored : 72.41 % 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: 0.19 (0.16), residues: 2699 helix: 1.63 (0.16), residues: 1061 sheet: 0.40 (0.21), residues: 556 loop : -1.61 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 193 TYR 0.014 0.001 TYR M 198 PHE 0.011 0.001 PHE L 82 TRP 0.012 0.001 TRP K 27 HIS 0.005 0.001 HIS J 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (28185) covalent geometry : angle 0.53592 / 0.27 (39356) hydrogen bonds : bond 0.04259 / 4.10 ( 1030) hydrogen bonds : angle 4.60286 / 5.54 ( 2927) metal coordination : bond 0.00478 / 0.31 ( 4) metal coordination : angle 2.23929 / 3.70 ( 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 310 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 230 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8980 (pp30) cc_final: 0.8536 (pp30) REVERT: B 214 MET cc_start: 0.9270 (mmm) cc_final: 0.9032 (mmm) REVERT: B 245 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: B 304 MET cc_start: 0.8917 (tmm) cc_final: 0.8686 (tmm) REVERT: B 513 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8113 (mtp180) REVERT: D 79 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.5894 (mpp-170) REVERT: E 9 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9083 (pp) REVERT: E 25 ASP cc_start: 0.8732 (t0) cc_final: 0.8521 (t0) REVERT: E 58 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8570 (pp) REVERT: F 45 LYS cc_start: 0.6824 (mmmt) cc_final: 0.6516 (mmmt) REVERT: F 104 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7539 (pp20) REVERT: G 44 ASP cc_start: 0.8122 (t0) cc_final: 0.7716 (t0) REVERT: I 44 LYS cc_start: 0.8889 (pttm) cc_final: 0.8582 (ttmt) REVERT: I 86 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.6533 (p90) REVERT: K 54 ASN cc_start: 0.8876 (t0) cc_final: 0.8651 (t0) REVERT: K 109 ARG cc_start: 0.7093 (mmm160) cc_final: 0.6802 (mmm160) REVERT: M 78 ARG cc_start: 0.8089 (ptp90) cc_final: 0.7635 (mtt180) REVERT: M 104 ILE cc_start: 0.8735 (mm) cc_final: 0.8358 (tp) REVERT: M 201 LEU cc_start: 0.9335 (mt) cc_final: 0.9034 (tp) outliers start: 80 outliers final: 44 residues processed: 300 average time/residue: 0.1669 time to fit residues: 78.7816 Evaluate side-chains 259 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 245 GLN 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 815 LEU Chi-restraints excluded: chain B residue 890 TRP Chi-restraints excluded: chain B residue 891 HIS 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 28 GLU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 9 LEU 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 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 H residue 98 LYS Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 86 HIS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 203 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 K residue 27 TRP Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 65 LEU 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 91 CYS Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 171 ILE 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: 30.0000 chunk 259 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 230 optimal weight: 30.0000 chunk 256 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 HIS B 440 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 205 ASN ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.092640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.062411 restraints weight = 98769.171| |-----------------------------------------------------------------------------| r_work (start): 0.3087 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: 0.8626 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28189 Z= 0.207 Angle : 0.594 10.663 39362 Z= 0.307 Chirality : 0.040 0.223 4701 Planarity : 0.005 0.070 4040 Dihedral : 18.903 178.504 7018 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.49 % Allowed : 23.18 % Favored : 71.33 % 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: 0.02 (0.16), residues: 2699 helix: 1.51 (0.16), residues: 1067 sheet: 0.19 (0.21), residues: 559 loop : -1.67 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 611 TYR 0.015 0.002 TYR L 264 PHE 0.018 0.002 PHE H 102 TRP 0.043 0.002 TRP C 33 HIS 0.006 0.001 HIS J 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (28185) covalent geometry : angle 0.59279 / 0.31 (39356) hydrogen bonds : bond 0.04678 / 4.45 ( 1030) hydrogen bonds : angle 4.71329 / 5.68 ( 2927) metal coordination : bond 0.00877 / 0.56 ( 4) metal coordination : angle 2.69228 / 4.37 ( 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 337 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 205 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8553 (pp30) REVERT: B 245 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8634 (tt0) REVERT: B 331 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9273 (pp) REVERT: B 513 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8032 (mtp180) REVERT: D 42 MET cc_start: 0.5803 (mmm) cc_final: 0.5324 (mmm) REVERT: D 79 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5578 (mpp-170) REVERT: D 175 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8490 (mttm) REVERT: E 25 ASP cc_start: 0.8877 (t0) cc_final: 0.8630 (t0) REVERT: E 58 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8506 (pp) REVERT: E 138 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8787 (mm) REVERT: E 144 ARG cc_start: 0.8379 (tpt90) cc_final: 0.7848 (tpt90) REVERT: F 45 LYS cc_start: 0.6728 (mmmt) cc_final: 0.6508 (mmmt) REVERT: F 104 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7587 (pp20) REVERT: G 44 ASP cc_start: 0.8290 (t0) cc_final: 0.7848 (t0) REVERT: H 84 LYS cc_start: 0.9058 (mttt) cc_final: 0.8661 (mtpt) REVERT: I 44 LYS cc_start: 0.8910 (pttm) cc_final: 0.8545 (ttmt) REVERT: I 86 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.6788 (p90) REVERT: K 54 ASN cc_start: 0.8896 (t0) cc_final: 0.8659 (t0) REVERT: M 201 LEU cc_start: 0.9302 (mt) cc_final: 0.8961 (tt) outliers start: 132 outliers final: 74 residues processed: 316 average time/residue: 0.1679 time to fit residues: 83.1020 Evaluate side-chains 273 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 190 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 129 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 222 LEU 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 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 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 174 LEU 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 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 175 LYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 138 ILE 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 G residue 28 SER 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 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 155 VAL Chi-restraints excluded: chain I residue 187 ILE 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 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 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 K residue 111 VAL 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 311 THR Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain M residue 91 CYS 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: 4.9990 chunk 48 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 4 optimal weight: 40.0000 chunk 275 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 290 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 11 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.092943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.063029 restraints weight = 97029.281| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.38 r_work: 0.2959 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28189 Z= 0.148 Angle : 0.555 8.953 39362 Z= 0.283 Chirality : 0.039 0.249 4701 Planarity : 0.004 0.071 4040 Dihedral : 18.889 177.475 7018 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.99 % Allowed : 23.97 % 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: 0.14 (0.16), residues: 2699 helix: 1.67 (0.16), residues: 1061 sheet: 0.19 (0.21), residues: 560 loop : -1.63 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 147 TYR 0.029 0.001 TYR K 24 PHE 0.016 0.001 PHE H 102 TRP 0.017 0.001 TRP C 33 HIS 0.005 0.001 HIS J 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (28185) covalent geometry : angle 0.55396 / 0.28 (39356) hydrogen bonds : bond 0.04097 / 3.94 ( 1030) hydrogen bonds : angle 4.55867 / 5.46 ( 2927) metal coordination : bond 0.00795 / 0.50 ( 4) metal coordination : angle 2.68849 / 4.41 ( 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 325 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 205 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8508 (pp30) REVERT: B 245 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: B 331 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9275 (pp) REVERT: B 513 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8003 (mtp180) REVERT: D 41 ARG cc_start: 0.7477 (pmt-80) cc_final: 0.7195 (pmt-80) REVERT: D 79 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.5670 (mpp-170) REVERT: E 25 ASP cc_start: 0.8774 (t0) cc_final: 0.8513 (t0) REVERT: E 58 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8434 (pp) REVERT: E 138 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8850 (mm) REVERT: E 144 ARG cc_start: 0.8403 (tpt90) cc_final: 0.7898 (tpt90) REVERT: F 45 LYS cc_start: 0.6739 (mmmt) cc_final: 0.6531 (mmmt) REVERT: F 104 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7597 (pp20) REVERT: G 44 ASP cc_start: 0.8258 (t0) cc_final: 0.7800 (t0) REVERT: I 44 LYS cc_start: 0.8899 (pttm) cc_final: 0.8507 (ttmt) REVERT: I 86 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.6604 (p90) REVERT: J 132 LYS cc_start: 0.8908 (tppt) cc_final: 0.8594 (tptp) REVERT: J 165 MET cc_start: 0.8636 (mmm) cc_final: 0.8068 (mmm) REVERT: K 54 ASN cc_start: 0.8903 (t0) cc_final: 0.8672 (t0) REVERT: M 23 ARG cc_start: 0.6949 (ttt90) cc_final: 0.6701 (ttt90) REVERT: M 137 MET cc_start: 0.9254 (mmm) cc_final: 0.9039 (mmm) REVERT: M 167 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8842 (mm-40) REVERT: M 201 LEU cc_start: 0.9285 (mt) cc_final: 0.8937 (tt) outliers start: 120 outliers final: 75 residues processed: 310 average time/residue: 0.1673 time to fit residues: 82.1946 Evaluate side-chains 274 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 190 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 245 GLN 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 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 849 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 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 35 LEU 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 D residue 167 ILE 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 E residue 138 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 98 LYS Chi-restraints excluded: chain H residue 99 LYS 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 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 187 ILE 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 J residue 33 VAL Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 197 ILE 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 69 ILE 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 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 139 VAL Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 167 GLN 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: 1.9990 chunk 63 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 226 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 156 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 207 optimal weight: 0.0970 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 50 GLN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN F 59 GLN F 93 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 337 HIS ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.091851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.061944 restraints weight = 97592.515| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.40 r_work: 0.2932 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28189 Z= 0.190 Angle : 0.577 11.820 39362 Z= 0.295 Chirality : 0.039 0.297 4701 Planarity : 0.004 0.073 4040 Dihedral : 18.889 178.293 7018 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.29 % Allowed : 23.89 % Favored : 70.83 % 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: 0.09 (0.16), residues: 2699 helix: 1.63 (0.16), residues: 1069 sheet: 0.17 (0.21), residues: 569 loop : -1.70 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 14 TYR 0.012 0.001 TYR I 201 PHE 0.015 0.001 PHE C 189 TRP 0.030 0.001 TRP C 33 HIS 0.005 0.001 HIS K 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (28185) covalent geometry : angle 0.57619 / 0.30 (39356) hydrogen bonds : bond 0.04272 / 4.09 ( 1030) hydrogen bonds : angle 4.58655 / 5.50 ( 2927) metal coordination : bond 0.01142 / 0.73 ( 4) metal coordination : angle 3.14626 / 5.07 ( 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 325 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 198 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8482 (pp30) REVERT: B 245 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8583 (tt0) REVERT: B 331 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9260 (pp) REVERT: B 481 CYS cc_start: 0.9443 (OUTLIER) cc_final: 0.9204 (p) REVERT: B 513 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8002 (mtp180) REVERT: B 686 ARG cc_start: 0.8771 (mtp85) cc_final: 0.8539 (mtp85) REVERT: D 41 ARG cc_start: 0.7603 (pmt-80) cc_final: 0.7191 (pmt-80) REVERT: D 79 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.5508 (mpp-170) REVERT: D 83 GLU cc_start: 0.8781 (pt0) cc_final: 0.8523 (pt0) REVERT: E 25 ASP cc_start: 0.8821 (t0) cc_final: 0.8550 (t0) REVERT: E 39 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.9051 (mmm-85) REVERT: E 58 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8418 (pp) REVERT: E 138 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8853 (mm) REVERT: E 139 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: E 144 ARG cc_start: 0.8370 (tpt90) cc_final: 0.7872 (tpt90) REVERT: F 104 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7581 (pp20) REVERT: G 44 ASP cc_start: 0.8310 (t0) cc_final: 0.7934 (t0) REVERT: I 86 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.6649 (p90) REVERT: J 67 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8060 (mtpp) REVERT: K 73 LEU cc_start: 0.7366 (tp) cc_final: 0.7141 (pp) REVERT: M 78 ARG cc_start: 0.8377 (ptm160) cc_final: 0.7940 (mtm180) REVERT: M 167 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8689 (mm110) REVERT: M 201 LEU cc_start: 0.9293 (mt) cc_final: 0.8957 (tt) outliers start: 127 outliers final: 93 residues processed: 306 average time/residue: 0.1646 time to fit residues: 79.9339 Evaluate side-chains 292 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 186 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 245 GLN 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 540 LEU 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 849 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 C residue 174 LEU 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 35 LEU 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 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 D residue 195 ILE 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 73 PHE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 139 GLN 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 21 THR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 7 THR 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 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 187 ILE 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 215 SER Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 99 LEU 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 197 ILE 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 K residue 111 VAL 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 311 THR Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain M residue 167 GLN 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: 4.9990 chunk 266 optimal weight: 7.9990 chunk 13 optimal weight: 50.0000 chunk 231 optimal weight: 8.9990 chunk 224 optimal weight: 0.3980 chunk 121 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 93 GLN ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN F 93 GLN G 87 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.091509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.061681 restraints weight = 98529.493| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.39 r_work: 0.2927 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28189 Z= 0.181 Angle : 0.590 10.976 39362 Z= 0.301 Chirality : 0.039 0.244 4701 Planarity : 0.004 0.072 4040 Dihedral : 18.902 178.358 7018 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.33 % Allowed : 24.64 % Favored : 70.04 % 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: 0.09 (0.16), residues: 2699 helix: 1.67 (0.16), residues: 1063 sheet: 0.12 (0.21), residues: 559 loop : -1.67 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 122 TYR 0.015 0.001 TYR K 24 PHE 0.014 0.001 PHE B 432 TRP 0.025 0.001 TRP C 33 HIS 0.005 0.001 HIS J 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (28185) covalent geometry : angle 0.58913 / 0.30 (39356) hydrogen bonds : bond 0.04236 / 4.04 ( 1030) hydrogen bonds : angle 4.57607 / 5.49 ( 2927) metal coordination : bond 0.00960 / 0.62 ( 4) metal coordination : angle 2.51261 / 3.99 ( 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 327 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 199 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8453 (pp30) REVERT: B 245 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: B 331 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9263 (pp) REVERT: B 481 CYS cc_start: 0.9448 (OUTLIER) cc_final: 0.9207 (p) REVERT: B 513 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8010 (mtp180) REVERT: B 686 ARG cc_start: 0.8823 (mtp85) cc_final: 0.8570 (mtp85) REVERT: D 42 MET cc_start: 0.7322 (mmm) cc_final: 0.6223 (mmm) REVERT: D 79 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.5421 (mpp-170) REVERT: D 83 GLU cc_start: 0.8812 (pt0) cc_final: 0.8566 (pt0) REVERT: E 25 ASP cc_start: 0.8842 (t0) cc_final: 0.8629 (t0) REVERT: E 39 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.9072 (mmm-85) REVERT: E 58 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8347 (pp) REVERT: E 144 ARG cc_start: 0.8384 (tpt90) cc_final: 0.7888 (tpt90) REVERT: F 104 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7574 (pp20) REVERT: G 44 ASP cc_start: 0.8135 (t0) cc_final: 0.7720 (t0) REVERT: G 87 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: I 44 LYS cc_start: 0.8906 (pttm) cc_final: 0.8501 (ttmt) REVERT: I 86 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.6732 (p90) REVERT: J 67 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8053 (mtpp) REVERT: J 165 MET cc_start: 0.8715 (mmm) cc_final: 0.8165 (mmm) REVERT: K 7 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8638 (mp) REVERT: K 73 LEU cc_start: 0.7363 (tp) cc_final: 0.7141 (pp) REVERT: M 23 ARG cc_start: 0.7003 (ttt90) cc_final: 0.6703 (ttt90) REVERT: M 78 ARG cc_start: 0.8321 (ptm160) cc_final: 0.8005 (mtm180) REVERT: M 137 MET cc_start: 0.9262 (mmm) cc_final: 0.8990 (mmm) REVERT: M 201 LEU cc_start: 0.9299 (mt) cc_final: 0.8950 (tt) REVERT: M 214 MET cc_start: 0.7126 (tmm) cc_final: 0.6596 (ttt) outliers start: 128 outliers final: 92 residues processed: 309 average time/residue: 0.1691 time to fit residues: 82.2054 Evaluate side-chains 288 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 184 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 222 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 245 GLN 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 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 849 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 190 VAL Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 35 LEU 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 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 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 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 137 ILE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 99 LYS 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 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 155 VAL Chi-restraints excluded: chain I residue 187 ILE 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 215 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 197 ILE 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 K residue 111 VAL 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 306 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 312 LEU 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 110 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 139 VAL 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: 7.9990 chunk 183 optimal weight: 9.9990 chunk 10 optimal weight: 40.0000 chunk 23 optimal weight: 20.0000 chunk 196 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 chunk 135 optimal weight: 7.9990 chunk 14 optimal weight: 40.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN F 93 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 255 ASN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.090058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.060209 restraints weight = 99079.827| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.35 r_work: 0.2889 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 28189 Z= 0.248 Angle : 0.632 11.368 39362 Z= 0.326 Chirality : 0.041 0.236 4701 Planarity : 0.005 0.074 4040 Dihedral : 18.959 179.524 7018 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.49 % Allowed : 24.47 % Favored : 70.04 % 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: -0.05 (0.16), residues: 2699 helix: 1.54 (0.16), residues: 1070 sheet: 0.01 (0.22), residues: 547 loop : -1.72 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 126 TYR 0.014 0.002 TYR L 264 PHE 0.018 0.002 PHE B 432 TRP 0.023 0.002 TRP C 33 HIS 0.005 0.001 HIS J 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.25 (28185) covalent geometry : angle 0.63090 / 0.33 (39356) hydrogen bonds : bond 0.04650 / 4.43 ( 1030) hydrogen bonds : angle 4.73601 / 5.69 ( 2927) metal coordination : bond 0.01104 / 0.68 ( 4) metal coordination : angle 2.39088 / 3.90 ( 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 322 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 190 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8469 (pp30) REVERT: B 245 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: B 302 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7769 (mtm-85) REVERT: B 331 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9253 (pp) REVERT: B 493 ILE cc_start: 0.9561 (OUTLIER) cc_final: 0.9353 (mm) REVERT: B 513 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.7994 (mtp180) REVERT: B 686 ARG cc_start: 0.8874 (mtp85) cc_final: 0.8579 (mtp85) REVERT: C 32 ARG cc_start: 0.7022 (mmm160) cc_final: 0.6364 (mmm160) REVERT: D 79 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.5369 (mpp-170) REVERT: D 83 GLU cc_start: 0.8810 (pt0) cc_final: 0.8558 (pt0) REVERT: E 25 ASP cc_start: 0.8881 (t0) cc_final: 0.8659 (t0) REVERT: E 39 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.9131 (mmm-85) REVERT: E 58 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8449 (pp) REVERT: E 144 ARG cc_start: 0.8402 (tpt90) cc_final: 0.7916 (tpt90) REVERT: F 104 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7564 (pp20) REVERT: G 44 ASP cc_start: 0.8116 (t0) cc_final: 0.7739 (t0) REVERT: G 87 GLN cc_start: 0.8209 (mp10) cc_final: 0.7877 (mp10) REVERT: G 110 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7717 (tm-30) REVERT: I 86 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.6658 (p90) REVERT: I 233 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8917 (pt0) REVERT: J 67 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8027 (mtpp) REVERT: J 165 MET cc_start: 0.8813 (mmm) cc_final: 0.8347 (mmm) REVERT: K 7 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8758 (mp) REVERT: K 73 LEU cc_start: 0.7360 (tp) cc_final: 0.7129 (pp) REVERT: M 78 ARG cc_start: 0.8397 (ptm160) cc_final: 0.8164 (mtm180) REVERT: M 137 MET cc_start: 0.9251 (mmm) cc_final: 0.8999 (mmm) REVERT: M 201 LEU cc_start: 0.9314 (mt) cc_final: 0.8915 (tt) outliers start: 132 outliers final: 99 residues processed: 304 average time/residue: 0.1661 time to fit residues: 79.9889 Evaluate side-chains 295 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 183 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 245 GLN 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 493 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 B residue 994 LEU Chi-restraints excluded: chain C residue 174 LEU 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 35 LEU 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 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 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 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 137 ILE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 7 THR 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 102 PHE 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 124 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 187 ILE 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 215 SER 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 81 VAL Chi-restraints excluded: chain J residue 99 LEU 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 J residue 197 ILE Chi-restraints excluded: chain J residue 242 ILE 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 K residue 111 VAL 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 306 LEU Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 353 MET Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 139 VAL 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: 0.5980 chunk 114 optimal weight: 0.9980 chunk 14 optimal weight: 50.0000 chunk 117 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 292 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN F 93 GLN I 86 HIS ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.091340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.061505 restraints weight = 98512.247| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.37 r_work: 0.2930 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28189 Z= 0.137 Angle : 0.580 11.582 39362 Z= 0.294 Chirality : 0.039 0.281 4701 Planarity : 0.004 0.077 4040 Dihedral : 18.949 177.642 7018 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.83 % Allowed : 26.26 % Favored : 69.91 % 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: 0.09 (0.16), residues: 2699 helix: 1.73 (0.16), residues: 1052 sheet: 0.12 (0.21), residues: 569 loop : -1.71 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 126 TYR 0.012 0.001 TYR E 74 PHE 0.012 0.001 PHE C 189 TRP 0.022 0.001 TRP C 33 HIS 0.005 0.001 HIS K 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (28185) covalent geometry : angle 0.57954 / 0.29 (39356) hydrogen bonds : bond 0.03985 / 3.85 ( 1030) hydrogen bonds : angle 4.50152 / 5.41 ( 2927) metal coordination : bond 0.00567 / 0.35 ( 4) metal coordination : angle 2.27192 / 3.54 ( 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 287 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 195 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8442 (pp30) REVERT: B 245 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: B 302 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7580 (mtm-85) REVERT: B 331 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9248 (pp) REVERT: B 513 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8026 (mtp180) REVERT: B 610 ASP cc_start: 0.8731 (m-30) cc_final: 0.8501 (t0) REVERT: D 79 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.5592 (mpp-170) REVERT: E 58 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8336 (pp) REVERT: E 144 ARG cc_start: 0.8376 (tpt90) cc_final: 0.7903 (tpt90) REVERT: F 93 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8184 (pp30) REVERT: F 104 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7603 (pp20) REVERT: G 44 ASP cc_start: 0.8024 (t0) cc_final: 0.7649 (t0) REVERT: G 87 GLN cc_start: 0.8235 (mp10) cc_final: 0.7952 (mp10) REVERT: G 110 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7695 (tm-30) REVERT: I 86 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7236 (p-80) REVERT: J 67 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7912 (mtpp) REVERT: J 132 LYS cc_start: 0.9067 (tppt) cc_final: 0.8697 (tptp) REVERT: J 165 MET cc_start: 0.8633 (mmm) cc_final: 0.8058 (mmm) REVERT: K 7 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8763 (mp) REVERT: K 73 LEU cc_start: 0.7346 (tp) cc_final: 0.7133 (pp) REVERT: M 78 ARG cc_start: 0.8416 (ptm160) cc_final: 0.7951 (mtm180) REVERT: M 137 MET cc_start: 0.9261 (mmm) cc_final: 0.9020 (mmm) REVERT: M 201 LEU cc_start: 0.9321 (mt) cc_final: 0.8963 (tt) outliers start: 92 outliers final: 71 residues processed: 275 average time/residue: 0.1650 time to fit residues: 71.9696 Evaluate side-chains 269 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 187 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 245 GLN 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 435 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 457 GLU 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 B residue 994 LEU Chi-restraints excluded: chain C residue 174 LEU 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 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 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 106 THR Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 75 THR 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 137 ILE Chi-restraints excluded: chain F residue 142 ASP 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 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 187 ILE Chi-restraints excluded: chain I residue 197 ILE 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 99 LEU 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 197 ILE 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 K residue 111 VAL 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 312 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 208 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 18 optimal weight: 30.0000 chunk 274 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 280 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 288 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN F 93 GLN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.090617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060690 restraints weight = 98695.265| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.36 r_work: 0.2909 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28189 Z= 0.184 Angle : 0.600 11.530 39362 Z= 0.306 Chirality : 0.039 0.217 4701 Planarity : 0.004 0.077 4040 Dihedral : 18.938 178.712 7018 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.83 % Allowed : 26.18 % Favored : 70.00 % 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: 0.08 (0.16), residues: 2699 helix: 1.71 (0.16), residues: 1061 sheet: 0.06 (0.21), residues: 561 loop : -1.70 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 126 TYR 0.013 0.001 TYR I 201 PHE 0.013 0.001 PHE B 432 TRP 0.021 0.001 TRP C 33 HIS 0.004 0.001 HIS J 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (28185) covalent geometry : angle 0.59915 / 0.31 (39356) hydrogen bonds : bond 0.04198 / 4.05 ( 1030) hydrogen bonds : angle 4.57669 / 5.52 ( 2927) metal coordination : bond 0.00783 / 0.48 ( 4) metal coordination : angle 2.36989 / 3.95 ( 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 281 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 189 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8447 (pp30) REVERT: B 245 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8516 (tt0) REVERT: B 302 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7715 (mtm-85) REVERT: B 331 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9262 (pp) REVERT: B 513 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8021 (mtp180) REVERT: B 610 ASP cc_start: 0.8783 (m-30) cc_final: 0.8480 (t0) REVERT: B 686 ARG cc_start: 0.8883 (mtp85) cc_final: 0.8565 (mtp85) REVERT: C 32 ARG cc_start: 0.7120 (mmm160) cc_final: 0.6451 (mmm160) REVERT: D 79 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.5609 (mpp-170) REVERT: E 39 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8983 (ttp80) REVERT: E 58 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8339 (pp) REVERT: E 144 ARG cc_start: 0.8386 (tpt90) cc_final: 0.7918 (tpt90) REVERT: F 104 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7648 (pp20) REVERT: G 44 ASP cc_start: 0.8038 (t0) cc_final: 0.7661 (t0) REVERT: G 87 GLN cc_start: 0.8201 (mp10) cc_final: 0.7967 (mp10) REVERT: I 86 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7205 (p-80) REVERT: J 67 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8060 (mtpp) REVERT: J 132 LYS cc_start: 0.9093 (tppt) cc_final: 0.8789 (tptp) REVERT: J 165 MET cc_start: 0.8698 (mmm) cc_final: 0.8167 (mmm) REVERT: K 7 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8772 (mp) REVERT: K 73 LEU cc_start: 0.7289 (tp) cc_final: 0.7071 (pp) REVERT: M 78 ARG cc_start: 0.8420 (ptm160) cc_final: 0.7989 (mtm180) REVERT: M 137 MET cc_start: 0.9273 (mmm) cc_final: 0.9040 (mmm) REVERT: M 201 LEU cc_start: 0.9314 (mt) cc_final: 0.8945 (tt) outliers start: 92 outliers final: 74 residues processed: 269 average time/residue: 0.1713 time to fit residues: 72.2306 Evaluate side-chains 271 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 186 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 129 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 293 VAL Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 457 GLU 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 B residue 994 LEU Chi-restraints excluded: chain C residue 174 LEU 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 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 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 73 PHE 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 102 PHE 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 187 ILE 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 J residue 33 VAL Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 99 LEU 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 J residue 197 ILE 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 K residue 111 VAL 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 312 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 153 optimal weight: 20.0000 chunk 14 optimal weight: 50.0000 chunk 47 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 208 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 233 optimal weight: 0.0770 chunk 291 optimal weight: 10.0000 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN F 93 GLN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.091781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062043 restraints weight = 97583.219| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.38 r_work: 0.2945 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28189 Z= 0.116 Angle : 0.577 11.598 39362 Z= 0.291 Chirality : 0.038 0.222 4701 Planarity : 0.004 0.077 4040 Dihedral : 18.912 177.207 7018 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.04 % Allowed : 27.22 % Favored : 69.75 % 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: 1.77 (0.16), residues: 1056 sheet: 0.14 (0.21), residues: 572 loop : -1.65 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 126 TYR 0.013 0.001 TYR K 24 PHE 0.011 0.001 PHE C 189 TRP 0.020 0.001 TRP C 33 HIS 0.004 0.001 HIS K 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (28185) covalent geometry : angle 0.57661 / 0.29 (39356) hydrogen bonds : bond 0.03764 / 3.66 ( 1030) hydrogen bonds : angle 4.41694 / 5.33 ( 2927) metal coordination : bond 0.00403 / 0.25 ( 4) metal coordination : angle 2.40162 / 3.92 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6675.60 seconds wall clock time: 114 minutes 54.64 seconds (6894.64 seconds total)