Starting phenix.real_space_refine on Sat Dec 16 12:26:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gov_0043/12_2023/6gov_0043.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gov_0043/12_2023/6gov_0043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gov_0043/12_2023/6gov_0043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gov_0043/12_2023/6gov_0043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gov_0043/12_2023/6gov_0043.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gov_0043/12_2023/6gov_0043.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 116 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 21567 2.51 5 N 6234 2.21 5 O 6990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35040 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3288 Classifications: {'peptide': 420} Link IDs: {'CIS': 2, 'PTRANS': 13, 'TRANS': 404} Chain: "B" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1106 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "E" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "G" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1377 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 159} Chain breaks: 1 Chain: "N" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 882 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "U" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "V" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1699 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Chain: "W" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "X" Number of atoms: 10575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10575 Classifications: {'peptide': 1341} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "Y" Number of atoms: 10410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10410 Classifications: {'peptide': 1339} Link IDs: {'PTRANS': 55, 'TRANS': 1283} Chain breaks: 2 Chain: "K" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 657 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 748 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain: "R" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1029 Classifications: {'RNA': 48} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 25, 'rna3p_pyr': 13} Link IDs: {'rna2p': 10, 'rna3p': 37} Chain breaks: 2 Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22658 SG CYS Y 70 113.048 104.962 82.522 1.00159.16 S ATOM 22672 SG CYS Y 72 113.505 104.924 80.503 1.00165.16 S ATOM 22780 SG CYS Y 85 115.289 107.016 81.506 1.00154.68 S ATOM 22804 SG CYS Y 88 111.976 106.062 82.925 1.00160.92 S ATOM 28492 SG CYS Y 814 98.618 98.416 149.340 1.00113.28 S ATOM 29057 SG CYS Y 888 97.093 98.342 146.184 1.00109.86 S ATOM 29108 SG CYS Y 895 98.323 97.059 147.264 1.00 98.95 S ATOM 29129 SG CYS Y 898 96.851 96.699 148.578 1.00 98.91 S Time building chain proxies: 18.87, per 1000 atoms: 0.54 Number of scatterers: 35040 At special positions: 0 Unit cell: (202.5, 172.8, 190.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 130 16.00 P 116 15.00 Mg 1 11.99 O 6990 8.00 N 6234 7.00 C 21567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.94 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y1502 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 72 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 85 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 88 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 70 " pdb=" ZN Y1503 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 888 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 814 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 898 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 895 " Number of angles added : 12 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7726 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 53 sheets defined 39.2% alpha, 14.9% beta 35 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 10.75 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 20 through 37 removed outlier: 3.574A pdb=" N PHE A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.785A pdb=" N ALA A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 133 removed outlier: 4.460A pdb=" N GLU A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 213 removed outlier: 3.901A pdb=" N LEU A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 4.373A pdb=" N GLY A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.812A pdb=" N ALA A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 314 through 319 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 340 through 362 Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.805A pdb=" N ALA A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.278A pdb=" N ALA A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 399 through 419 Processing helix chain 'B' and resid 3 through 24 removed outlier: 4.118A pdb=" N ARG B 7 " --> pdb=" O PRO B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.632A pdb=" N GLN B 38 " --> pdb=" O PHE B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 58 Processing helix chain 'B' and resid 58 through 67 Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.563A pdb=" N LYS B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 119 through 135 Proline residue: B 132 - end of helix Processing helix chain 'E' and resid 14 through 31 Processing helix chain 'E' and resid 80 through 87 Processing helix chain 'G' and resid 18 through 33 removed outlier: 3.561A pdb=" N VAL G 22 " --> pdb=" O PHE G 18 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA G 23 " --> pdb=" O GLU G 19 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR G 24 " --> pdb=" O GLY G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 104 through 114 Processing helix chain 'G' and resid 138 through 142 removed outlier: 3.782A pdb=" N PHE G 141 " --> pdb=" O ASP G 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 11 Processing helix chain 'N' and resid 11 through 19 removed outlier: 3.656A pdb=" N LYS N 19 " --> pdb=" O GLN N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 35 removed outlier: 3.735A pdb=" N ASN N 34 " --> pdb=" O LYS N 31 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG N 35 " --> pdb=" O PRO N 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 31 through 35' Processing helix chain 'N' and resid 46 through 53 Processing helix chain 'N' and resid 57 through 82 Processing helix chain 'U' and resid 34 through 50 removed outlier: 4.108A pdb=" N THR U 38 " --> pdb=" O GLY U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 86 removed outlier: 3.502A pdb=" N ILE U 81 " --> pdb=" O ASP U 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 115 No H-bonds generated for 'chain 'U' and resid 113 through 115' Processing helix chain 'U' and resid 154 through 163 removed outlier: 4.035A pdb=" N ARG U 158 " --> pdb=" O PRO U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 233 removed outlier: 4.166A pdb=" N ASP U 233 " --> pdb=" O GLU U 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 50 removed outlier: 3.878A pdb=" N LEU V 39 " --> pdb=" O PHE V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 87 removed outlier: 3.967A pdb=" N GLY V 87 " --> pdb=" O LEU V 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 115 No H-bonds generated for 'chain 'V' and resid 113 through 115' Processing helix chain 'V' and resid 212 through 233 removed outlier: 4.090A pdb=" N ALA V 216 " --> pdb=" O ASP V 212 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE V 217 " --> pdb=" O PRO V 213 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG V 218 " --> pdb=" O GLU V 214 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA V 230 " --> pdb=" O GLU V 226 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE V 231 " --> pdb=" O GLN V 227 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP V 233 " --> pdb=" O GLU V 229 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 32 removed outlier: 3.675A pdb=" N LEU W 21 " --> pdb=" O PHE W 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 56 removed outlier: 3.537A pdb=" N ILE W 49 " --> pdb=" O LYS W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 60 through 91 Processing helix chain 'X' and resid 28 through 39 removed outlier: 3.753A pdb=" N LEU X 32 " --> pdb=" O LEU X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 57 removed outlier: 3.602A pdb=" N ALA X 52 " --> pdb=" O GLY X 48 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE X 57 " --> pdb=" O PHE X 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 89 Processing helix chain 'X' and resid 206 through 212 Processing helix chain 'X' and resid 216 through 225 Processing helix chain 'X' and resid 242 through 247 Processing helix chain 'X' and resid 270 through 281 Processing helix chain 'X' and resid 288 through 293 Processing helix chain 'X' and resid 318 through 328 Processing helix chain 'X' and resid 346 through 354 removed outlier: 3.559A pdb=" N THR X 350 " --> pdb=" O TYR X 346 " (cutoff:3.500A) Processing helix chain 'X' and resid 358 through 371 removed outlier: 3.595A pdb=" N ARG X 371 " --> pdb=" O TYR X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 377 through 390 removed outlier: 3.868A pdb=" N PHE X 389 " --> pdb=" O PHE X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 398 through 408 Processing helix chain 'X' and resid 421 through 438 removed outlier: 3.690A pdb=" N ILE X 425 " --> pdb=" O SER X 421 " (cutoff:3.500A) Processing helix chain 'X' and resid 455 through 480 removed outlier: 3.941A pdb=" N MET X 459 " --> pdb=" O SER X 455 " (cutoff:3.500A) Processing helix chain 'X' and resid 495 through 508 removed outlier: 3.815A pdb=" N SER X 499 " --> pdb=" O ALA X 495 " (cutoff:3.500A) Processing helix chain 'X' and resid 519 through 528 removed outlier: 3.688A pdb=" N ARG X 528 " --> pdb=" O ILE X 524 " (cutoff:3.500A) Processing helix chain 'X' and resid 609 through 613 removed outlier: 3.535A pdb=" N ASN X 613 " --> pdb=" O GLU X 610 " (cutoff:3.500A) Processing helix chain 'X' and resid 670 through 674 removed outlier: 3.604A pdb=" N HIS X 673 " --> pdb=" O PHE X 670 " (cutoff:3.500A) Processing helix chain 'X' and resid 675 through 686 Processing helix chain 'X' and resid 687 through 689 No H-bonds generated for 'chain 'X' and resid 687 through 689' Processing helix chain 'X' and resid 704 through 712 Processing helix chain 'X' and resid 738 through 741 removed outlier: 3.703A pdb=" N MET X 741 " --> pdb=" O GLU X 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 738 through 741' Processing helix chain 'X' and resid 820 through 825 Processing helix chain 'X' and resid 859 through 863 Processing helix chain 'X' and resid 898 through 904 Processing helix chain 'X' and resid 942 through 981 removed outlier: 3.906A pdb=" N ASP X 959 " --> pdb=" O GLN X 955 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU X 960 " --> pdb=" O ALA X 956 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA X 969 " --> pdb=" O GLN X 965 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY X 970 " --> pdb=" O ILE X 966 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU X 971 " --> pdb=" O LEU X 967 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA X 981 " --> pdb=" O ALA X 977 " (cutoff:3.500A) Processing helix chain 'X' and resid 985 through 990 Processing helix chain 'X' and resid 993 through 999 Processing helix chain 'X' and resid 1005 through 1038 removed outlier: 3.582A pdb=" N LYS X1035 " --> pdb=" O ALA X1031 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN X1038 " --> pdb=" O ARG X1034 " (cutoff:3.500A) Processing helix chain 'X' and resid 1101 through 1106 removed outlier: 4.093A pdb=" N SER X1105 " --> pdb=" O LEU X1101 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG X1106 " --> pdb=" O GLY X1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 1101 through 1106' Processing helix chain 'X' and resid 1109 through 1134 removed outlier: 3.896A pdb=" N LEU X1113 " --> pdb=" O ILE X1109 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS X1127 " --> pdb=" O GLY X1123 " (cutoff:3.500A) Processing helix chain 'X' and resid 1137 through 1151 removed outlier: 4.012A pdb=" N LEU X1151 " --> pdb=" O ARG X1147 " (cutoff:3.500A) Processing helix chain 'X' and resid 1167 through 1177 Processing helix chain 'X' and resid 1191 through 1202 removed outlier: 3.653A pdb=" N ILE X1195 " --> pdb=" O LYS X1191 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY X1202 " --> pdb=" O LEU X1198 " (cutoff:3.500A) Processing helix chain 'X' and resid 1238 through 1242 Processing helix chain 'X' and resid 1271 through 1281 Processing helix chain 'X' and resid 1284 through 1292 Processing helix chain 'X' and resid 1297 through 1311 Processing helix chain 'X' and resid 1320 through 1331 removed outlier: 3.645A pdb=" N ASN X1324 " --> pdb=" O PRO X1320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 34 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.857A pdb=" N ARG Y 81 " --> pdb=" O LEU Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 100 Processing helix chain 'Y' and resid 114 through 119 Processing helix chain 'Y' and resid 122 through 129 Processing helix chain 'Y' and resid 131 through 140 Processing helix chain 'Y' and resid 161 through 172 Processing helix chain 'Y' and resid 181 through 192 removed outlier: 3.578A pdb=" N ILE Y 185 " --> pdb=" O GLY Y 181 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS Y 190 " --> pdb=" O GLN Y 186 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET Y 192 " --> pdb=" O LEU Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 207 Processing helix chain 'Y' and resid 210 through 230 Processing helix chain 'Y' and resid 246 through 250 removed outlier: 3.818A pdb=" N ARG Y 250 " --> pdb=" O PRO Y 247 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 285 Processing helix chain 'Y' and resid 288 through 308 removed outlier: 3.617A pdb=" N ASP Y 308 " --> pdb=" O ASP Y 304 " (cutoff:3.500A) Processing helix chain 'Y' and resid 327 through 331 removed outlier: 3.537A pdb=" N ILE Y 331 " --> pdb=" O ALA Y 328 " (cutoff:3.500A) Processing helix chain 'Y' and resid 370 through 377 Processing helix chain 'Y' and resid 377 through 388 Processing helix chain 'Y' and resid 393 through 404 removed outlier: 3.808A pdb=" N ALA Y 397 " --> pdb=" O THR Y 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 405 through 417 removed outlier: 4.074A pdb=" N TRP Y 409 " --> pdb=" O GLU Y 405 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP Y 410 " --> pdb=" O ALA Y 406 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG Y 417 " --> pdb=" O ASP Y 413 " (cutoff:3.500A) Processing helix chain 'Y' and resid 453 through 458 Processing helix chain 'Y' and resid 473 through 483 removed outlier: 3.769A pdb=" N GLN Y 477 " --> pdb=" O THR Y 473 " (cutoff:3.500A) Processing helix chain 'Y' and resid 485 through 489 removed outlier: 3.941A pdb=" N ASN Y 489 " --> pdb=" O SER Y 486 " (cutoff:3.500A) Processing helix chain 'Y' and resid 503 through 514 Processing helix chain 'Y' and resid 529 through 539 removed outlier: 3.738A pdb=" N ALA Y 533 " --> pdb=" O GLY Y 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 574 through 580 Processing helix chain 'Y' and resid 581 through 583 No H-bonds generated for 'chain 'Y' and resid 581 through 583' Processing helix chain 'Y' and resid 588 through 592 Processing helix chain 'Y' and resid 597 through 612 removed outlier: 3.835A pdb=" N ILE Y 601 " --> pdb=" O GLY Y 597 " (cutoff:3.500A) Processing helix chain 'Y' and resid 614 through 636 removed outlier: 3.947A pdb=" N GLY Y 636 " --> pdb=" O ALA Y 632 " (cutoff:3.500A) Processing helix chain 'Y' and resid 640 through 644 removed outlier: 4.055A pdb=" N MET Y 644 " --> pdb=" O ILE Y 641 " (cutoff:3.500A) Processing helix chain 'Y' and resid 649 through 670 Processing helix chain 'Y' and resid 674 through 703 removed outlier: 4.139A pdb=" N THR Y 703 " --> pdb=" O ASP Y 699 " (cutoff:3.500A) Processing helix chain 'Y' and resid 720 through 728 Processing helix chain 'Y' and resid 733 through 742 removed outlier: 3.613A pdb=" N ILE Y 737 " --> pdb=" O SER Y 733 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA Y 741 " --> pdb=" O ILE Y 737 " (cutoff:3.500A) Processing helix chain 'Y' and resid 768 through 804 removed outlier: 4.250A pdb=" N HIS Y 777 " --> pdb=" O PHE Y 773 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY Y 778 " --> pdb=" O ILE Y 774 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA Y 791 " --> pdb=" O ALA Y 787 " (cutoff:3.500A) Processing helix chain 'Y' and resid 805 through 807 No H-bonds generated for 'chain 'Y' and resid 805 through 807' Processing helix chain 'Y' and resid 834 through 839 removed outlier: 3.700A pdb=" N ARG Y 838 " --> pdb=" O PRO Y 834 " (cutoff:3.500A) Processing helix chain 'Y' and resid 865 through 874 Processing helix chain 'Y' and resid 914 through 925 removed outlier: 3.540A pdb=" N ILE Y 918 " --> pdb=" O ALA Y 914 " (cutoff:3.500A) Processing helix chain 'Y' and resid 926 through 930 removed outlier: 3.678A pdb=" N LEU Y 930 " --> pdb=" O GLY Y 927 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1137 through 1146 removed outlier: 3.706A pdb=" N VAL Y1141 " --> pdb=" O GLY Y1137 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1216 through 1225 removed outlier: 3.789A pdb=" N ILE Y1220 " --> pdb=" O ALA Y1216 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1226 through 1244 removed outlier: 3.734A pdb=" N THR Y1230 " --> pdb=" O VAL Y1226 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN Y1244 " --> pdb=" O VAL Y1240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1249 through 1259 removed outlier: 4.410A pdb=" N ILE Y1253 " --> pdb=" O ASN Y1249 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN Y1259 " --> pdb=" O VAL Y1255 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1282 through 1295 removed outlier: 3.597A pdb=" N ASN Y1295 " --> pdb=" O GLU Y1291 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1308 through 1315 Processing helix chain 'Y' and resid 1327 through 1339 removed outlier: 3.645A pdb=" N VAL Y1331 " --> pdb=" O GLU Y1327 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1346 through 1354 removed outlier: 4.025A pdb=" N ASN Y1350 " --> pdb=" O GLY Y1346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1362 through 1375 removed outlier: 3.746A pdb=" N ASP Y1368 " --> pdb=" O ALA Y1364 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG Y1372 " --> pdb=" O ASP Y1368 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA Y1375 " --> pdb=" O ARG Y1371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 145 removed outlier: 4.386A pdb=" N VAL A 141 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP A 153 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N SER A 151 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL A 145 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASN A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU A 163 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE A 196 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 229 removed outlier: 7.007A pdb=" N ALA A 237 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA A 226 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS A 235 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ARG A 228 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG A 233 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA A 234 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL A 274 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 236 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 293 through 299 removed outlier: 3.654A pdb=" N SER A 295 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 12 Processing sheet with id=AA6, first strand: chain 'G' and resid 8 through 13 Processing sheet with id=AA7, first strand: chain 'G' and resid 46 through 49 Processing sheet with id=AA8, first strand: chain 'G' and resid 167 through 173 removed outlier: 7.347A pdb=" N ARG G 157 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL G 151 " --> pdb=" O ARG G 157 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS G 159 " --> pdb=" O GLU G 149 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN G 145 " --> pdb=" O SER G 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 14 through 18 removed outlier: 4.791A pdb=" N ILE U 16 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS U 25 " --> pdb=" O ILE U 16 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP U 199 " --> pdb=" O PRO U 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 97 through 105 removed outlier: 3.797A pdb=" N GLU U 58 " --> pdb=" O LYS U 145 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN U 147 " --> pdb=" O VAL U 56 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL U 56 " --> pdb=" O GLN U 147 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY U 149 " --> pdb=" O CYS U 54 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N CYS U 54 " --> pdb=" O GLY U 149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 90 through 91 Processing sheet with id=AB3, first strand: chain 'U' and resid 108 through 111 removed outlier: 3.859A pdb=" N CYS U 131 " --> pdb=" O VAL U 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'V' and resid 16 through 17 removed outlier: 6.460A pdb=" N ASP V 199 " --> pdb=" O PRO V 30 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU V 198 " --> pdb=" O ALA V 189 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA V 189 " --> pdb=" O LEU V 198 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS V 200 " --> pdb=" O VAL V 187 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL V 187 " --> pdb=" O LYS V 200 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL V 202 " --> pdb=" O TYR V 185 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR V 185 " --> pdb=" O VAL V 202 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU V 204 " --> pdb=" O ILE V 183 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE V 183 " --> pdb=" O GLU V 204 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU V 206 " --> pdb=" O GLU V 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'V' and resid 97 through 105 removed outlier: 3.995A pdb=" N GLU V 58 " --> pdb=" O LYS V 145 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN V 147 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL V 56 " --> pdb=" O GLN V 147 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY V 149 " --> pdb=" O CYS V 54 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS V 54 " --> pdb=" O GLY V 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'V' and resid 90 through 91 Processing sheet with id=AB7, first strand: chain 'V' and resid 108 through 111 Processing sheet with id=AB8, first strand: chain 'V' and resid 152 through 153 Processing sheet with id=AB9, first strand: chain 'X' and resid 13 through 14 removed outlier: 6.260A pdb=" N LYS X 13 " --> pdb=" O ALA X1183 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 59 through 60 removed outlier: 6.989A pdb=" N LYS X 99 " --> pdb=" O VAL X 71 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR X 73 " --> pdb=" O ARG X 97 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG X 97 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU X 75 " --> pdb=" O PRO X 95 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA X 94 " --> pdb=" O GLU X 126 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU X 126 " --> pdb=" O ALA X 94 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU X 96 " --> pdb=" O MET X 124 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET X 124 " --> pdb=" O LEU X 96 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP X 116 " --> pdb=" O ILE X 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 136 through 137 Processing sheet with id=AC3, first strand: chain 'X' and resid 451 through 454 Processing sheet with id=AC4, first strand: chain 'X' and resid 154 through 158 removed outlier: 3.596A pdb=" N LEU X 184 " --> pdb=" O ILE X 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'X' and resid 284 through 285 removed outlier: 4.032A pdb=" N GLU X 231 " --> pdb=" O GLN X 238 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE X 229 " --> pdb=" O GLU X 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 255 through 257 removed outlier: 6.680A pdb=" N ALA X 257 " --> pdb=" O VAL X 261 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL X 261 " --> pdb=" O ALA X 257 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 296 through 297 removed outlier: 3.635A pdb=" N MET X 315 " --> pdb=" O VAL X 297 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 301 through 302 Processing sheet with id=AC9, first strand: chain 'X' and resid 580 through 581 removed outlier: 5.185A pdb=" N GLU X 602 " --> pdb=" O LYS X 593 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 580 through 581 Processing sheet with id=AD2, first strand: chain 'X' and resid 716 through 717 removed outlier: 6.541A pdb=" N ALA X 716 " --> pdb=" O LEU X 783 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 748 through 752 removed outlier: 6.087A pdb=" N LYS X 735 " --> pdb=" O VAL X 724 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL X 724 " --> pdb=" O LYS X 735 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 757 through 758 removed outlier: 3.525A pdb=" N THR X 757 " --> pdb=" O ILE X 765 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 1066 through 1067 removed outlier: 4.294A pdb=" N THR X1226 " --> pdb=" O PHE X 804 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE X 816 " --> pdb=" O SER X1077 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE X1079 " --> pdb=" O ILE X 816 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL X 818 " --> pdb=" O ILE X1079 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 1066 through 1067 removed outlier: 3.522A pdb=" N VAL X1225 " --> pdb=" O ILE X1210 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 830 through 841 removed outlier: 6.287A pdb=" N THR X 830 " --> pdb=" O LYS X1057 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS X1057 " --> pdb=" O THR X 830 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS X 832 " --> pdb=" O ALA X1055 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA X1055 " --> pdb=" O HIS X 832 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN X 834 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR X1053 " --> pdb=" O GLN X 834 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU X 836 " --> pdb=" O LYS X1051 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LYS X1051 " --> pdb=" O LEU X 836 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS X 838 " --> pdb=" O ILE X1049 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE X1049 " --> pdb=" O CYS X 838 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER X 840 " --> pdb=" O LEU X1047 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP X 930 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA X1055 " --> pdb=" O VAL X 928 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL X 928 " --> pdb=" O ALA X1055 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 882 through 884 removed outlier: 6.972A pdb=" N LEU X 918 " --> pdb=" O LEU X 883 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 887 through 889 Processing sheet with id=AE1, first strand: chain 'X' and resid 1244 through 1246 removed outlier: 7.657A pdb=" N ILE Y 447 " --> pdb=" O ARG Y 352 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL Y 354 " --> pdb=" O ILE Y 447 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 1268 through 1269 removed outlier: 3.950A pdb=" N GLN X1268 " --> pdb=" O VAL Y 347 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 1335 through 1339 removed outlier: 3.649A pdb=" N LYS Y 21 " --> pdb=" O GLU X1338 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Y' and resid 103 through 112 removed outlier: 10.420A pdb=" N LEU Y 107 " --> pdb=" O PRO Y 243 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N SER Y 109 " --> pdb=" O VAL Y 241 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL Y 241 " --> pdb=" O SER Y 109 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Y' and resid 145 through 146 removed outlier: 3.524A pdb=" N LYS Y 179 " --> pdb=" O VAL Y 145 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 316 through 317 removed outlier: 3.712A pdb=" N THR Y 317 " --> pdb=" O ASN Y 320 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN Y 320 " --> pdb=" O THR Y 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'Y' and resid 547 through 556 Processing sheet with id=AE8, first strand: chain 'Y' and resid 809 through 811 Processing sheet with id=AE9, first strand: chain 'Y' and resid 820 through 822 Processing sheet with id=AF1, first strand: chain 'Y' and resid 825 through 826 removed outlier: 6.966A pdb=" N VAL Y 825 " --> pdb=" O LYS Y 832 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 957 through 961 removed outlier: 6.530A pdb=" N LEU Y 982 " --> pdb=" O SER Y 994 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER Y 994 " --> pdb=" O LEU Y 982 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU Y 984 " --> pdb=" O LYS Y 992 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 965 through 967 Processing sheet with id=AF4, first strand: chain 'Y' and resid 1002 through 1003 Processing sheet with id=AF5, first strand: chain 'Y' and resid 1035 through 1038 Processing sheet with id=AF6, first strand: chain 'Y' and resid 1046 through 1050 Processing sheet with id=AF7, first strand: chain 'Y' and resid 1187 through 1190 removed outlier: 3.836A pdb=" N GLY Y1161 " --> pdb=" O VAL Y1204 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL Y1204 " --> pdb=" O GLY Y1161 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 1280 through 1281 1333 hydrogen bonds defined for protein. 3774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 180 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 16.81 Time building geometry restraints manager: 14.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11321 1.34 - 1.46: 7909 1.46 - 1.59: 16122 1.59 - 1.71: 225 1.71 - 1.83: 229 Bond restraints: 35806 Sorted by residual: bond pdb=" C ASP X1084 " pdb=" N MET X1085 " ideal model delta sigma weight residual 1.327 1.273 0.053 1.71e-02 3.42e+03 9.75e+00 bond pdb=" C CYS Y 58 " pdb=" N ALA Y 59 " ideal model delta sigma weight residual 1.332 1.291 0.041 1.40e-02 5.10e+03 8.76e+00 bond pdb=" CG1 ILE U 183 " pdb=" CD1 ILE U 183 " ideal model delta sigma weight residual 1.513 1.430 0.083 3.90e-02 6.57e+02 4.51e+00 bond pdb=" CG1 ILE V 183 " pdb=" CD1 ILE V 183 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.23e+00 bond pdb=" CG ARG X 637 " pdb=" CD ARG X 637 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.20e+00 ... (remaining 35801 not shown) Histogram of bond angle deviations from ideal: 95.23 - 103.29: 568 103.29 - 111.34: 15097 111.34 - 119.39: 15624 119.39 - 127.45: 17157 127.45 - 135.50: 436 Bond angle restraints: 48882 Sorted by residual: angle pdb=" C GLU X 825 " pdb=" N ASP X 826 " pdb=" CA ASP X 826 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.53e+01 angle pdb=" N VAL A 12 " pdb=" CA VAL A 12 " pdb=" C VAL A 12 " ideal model delta sigma weight residual 112.29 107.69 4.60 9.40e-01 1.13e+00 2.40e+01 angle pdb=" CA ARG Y 250 " pdb=" CB ARG Y 250 " pdb=" CG ARG Y 250 " ideal model delta sigma weight residual 114.10 123.88 -9.78 2.00e+00 2.50e-01 2.39e+01 angle pdb=" C ARG Y 709 " pdb=" N ASP Y 710 " pdb=" CA ASP Y 710 " ideal model delta sigma weight residual 125.66 134.63 -8.97 1.85e+00 2.92e-01 2.35e+01 angle pdb=" CA TYR X1018 " pdb=" CB TYR X1018 " pdb=" CG TYR X1018 " ideal model delta sigma weight residual 113.90 122.24 -8.34 1.80e+00 3.09e-01 2.14e+01 ... (remaining 48877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.64: 21134 29.64 - 59.27: 674 59.27 - 88.91: 65 88.91 - 118.54: 1 118.54 - 148.18: 3 Dihedral angle restraints: 21877 sinusoidal: 9905 harmonic: 11972 Sorted by residual: dihedral pdb=" CA LEU Y 120 " pdb=" C LEU Y 120 " pdb=" N PRO Y 121 " pdb=" CA PRO Y 121 " ideal model delta harmonic sigma weight residual 180.00 103.03 76.97 0 5.00e+00 4.00e-02 2.37e+02 dihedral pdb=" O4' U R 6 " pdb=" C1' U R 6 " pdb=" N1 U R 6 " pdb=" C2 U R 6 " ideal model delta sinusoidal sigma weight residual 200.00 51.82 148.18 1 1.50e+01 4.44e-03 7.89e+01 dihedral pdb=" CA ILE Y 416 " pdb=" C ILE Y 416 " pdb=" N ARG Y 417 " pdb=" CA ARG Y 417 " ideal model delta harmonic sigma weight residual -180.00 -140.12 -39.88 0 5.00e+00 4.00e-02 6.36e+01 ... (remaining 21874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 5448 0.129 - 0.257: 162 0.257 - 0.386: 2 0.386 - 0.515: 0 0.515 - 0.643: 1 Chirality restraints: 5613 Sorted by residual: chirality pdb=" CB ILE X1079 " pdb=" CA ILE X1079 " pdb=" CG1 ILE X1079 " pdb=" CG2 ILE X1079 " both_signs ideal model delta sigma weight residual False 2.64 2.00 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CB ILE Y 754 " pdb=" CA ILE Y 754 " pdb=" CG1 ILE Y 754 " pdb=" CG2 ILE Y 754 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CB VAL X 690 " pdb=" CA VAL X 690 " pdb=" CG1 VAL X 690 " pdb=" CG2 VAL X 690 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 5610 not shown) Planarity restraints: 5988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Y 120 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO Y 121 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO Y 121 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO Y 121 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU Y 438 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.90e+00 pdb=" N PRO Y 439 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO Y 439 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO Y 439 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR X1229 " 0.017 2.00e-02 2.50e+03 2.12e-02 9.02e+00 pdb=" CG TYR X1229 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR X1229 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR X1229 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR X1229 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR X1229 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR X1229 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR X1229 " -0.002 2.00e-02 2.50e+03 ... (remaining 5985 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 203 2.55 - 3.14: 25981 3.14 - 3.73: 52671 3.73 - 4.31: 70777 4.31 - 4.90: 115360 Nonbonded interactions: 264992 Sorted by model distance: nonbonded pdb=" N CYS Y 88 " pdb="ZN ZN Y1502 " model vdw 1.963 2.310 nonbonded pdb=" OD1 ASP Y 462 " pdb="MG MG Y1501 " model vdw 1.969 2.170 nonbonded pdb=" OD2 ASP Y 460 " pdb="MG MG Y1501 " model vdw 2.061 2.170 nonbonded pdb=" CB ASP Y 460 " pdb="MG MG Y1501 " model vdw 2.107 2.570 nonbonded pdb=" OE2 GLU A 21 " pdb=" NH1 ARG A 51 " model vdw 2.112 2.520 ... (remaining 264987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'U' and (resid 6 through 158 or resid 170 through 234)) selection = (chain 'V' and resid 6 through 234) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.990 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 105.850 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 35806 Z= 0.492 Angle : 0.931 11.303 48882 Z= 0.505 Chirality : 0.056 0.643 5613 Planarity : 0.007 0.101 5988 Dihedral : 13.385 148.178 14151 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.73 % Favored : 92.20 % Rotamer: Outliers : 0.25 % Allowed : 2.69 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.11), residues: 4127 helix: -2.26 (0.10), residues: 1446 sheet: -1.73 (0.21), residues: 566 loop : -2.92 (0.11), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP X 807 HIS 0.008 0.002 HIS Y 113 PHE 0.039 0.003 PHE X 812 TYR 0.047 0.003 TYR X1229 ARG 0.009 0.001 ARG X 452 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 467 time to evaluate : 4.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 470 average time/residue: 0.5621 time to fit residues: 405.2073 Evaluate side-chains 274 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 271 time to evaluate : 4.167 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3127 time to fit residues: 7.5205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 357 optimal weight: 0.9980 chunk 320 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 109 optimal weight: 0.5980 chunk 216 optimal weight: 0.7980 chunk 171 optimal weight: 7.9990 chunk 331 optimal weight: 0.7980 chunk 128 optimal weight: 9.9990 chunk 201 optimal weight: 0.8980 chunk 246 optimal weight: 5.9990 chunk 384 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 133 HIS A 313 ASN B 105 ASN E 3 ASN G 34 ASN V 37 HIS V 103 ASN V 132 HIS X 69 GLN X 517 GLN X1023 HIS ** X1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1312 ASN Y 80 HIS Y 164 GLN Y 875 ASN Y1350 ASN Y1366 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35806 Z= 0.169 Angle : 0.570 11.264 48882 Z= 0.298 Chirality : 0.041 0.265 5613 Planarity : 0.005 0.078 5988 Dihedral : 15.122 155.350 5976 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.41 % Allowed : 7.04 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.12), residues: 4127 helix: -0.22 (0.13), residues: 1492 sheet: -1.30 (0.21), residues: 537 loop : -2.44 (0.12), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 115 HIS 0.005 0.001 HIS X1023 PHE 0.028 0.001 PHE A 24 TYR 0.029 0.001 TYR X1018 ARG 0.007 0.000 ARG X 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 333 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 23 residues processed: 366 average time/residue: 0.5189 time to fit residues: 308.7092 Evaluate side-chains 280 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 257 time to evaluate : 3.914 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3377 time to fit residues: 19.7872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 213 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 319 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 384 optimal weight: 10.0000 chunk 415 optimal weight: 10.0000 chunk 342 optimal weight: 3.9990 chunk 381 optimal weight: 9.9990 chunk 131 optimal weight: 0.5980 chunk 308 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS V 66 HIS V 103 ASN V 117 HIS X 343 HIS X 517 GLN ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35806 Z= 0.281 Angle : 0.606 11.006 48882 Z= 0.312 Chirality : 0.042 0.164 5613 Planarity : 0.004 0.075 5988 Dihedral : 14.942 157.017 5976 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.67 % Allowed : 9.19 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.12), residues: 4127 helix: 0.60 (0.13), residues: 1491 sheet: -1.14 (0.21), residues: 551 loop : -2.26 (0.12), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 334 HIS 0.010 0.001 HIS V 117 PHE 0.018 0.002 PHE A 24 TYR 0.028 0.002 TYR X1018 ARG 0.007 0.000 ARG X 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 265 time to evaluate : 4.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 34 residues processed: 312 average time/residue: 0.5214 time to fit residues: 263.7063 Evaluate side-chains 282 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 248 time to evaluate : 3.945 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3409 time to fit residues: 27.1671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 380 optimal weight: 9.9990 chunk 289 optimal weight: 7.9990 chunk 199 optimal weight: 0.0000 chunk 42 optimal weight: 40.0000 chunk 183 optimal weight: 0.7980 chunk 258 optimal weight: 0.9980 chunk 386 optimal weight: 9.9990 chunk 408 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 366 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 37 HIS X 86 GLN X 618 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 35806 Z= 0.164 Angle : 0.538 11.397 48882 Z= 0.275 Chirality : 0.040 0.164 5613 Planarity : 0.004 0.073 5988 Dihedral : 14.807 156.024 5976 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.13 % Allowed : 10.26 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 4127 helix: 1.08 (0.13), residues: 1508 sheet: -0.89 (0.22), residues: 544 loop : -2.11 (0.12), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y1193 HIS 0.003 0.001 HIS Y 430 PHE 0.018 0.001 PHE A 24 TYR 0.024 0.001 TYR X1018 ARG 0.005 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 289 time to evaluate : 3.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 14 residues processed: 313 average time/residue: 0.5193 time to fit residues: 260.0176 Evaluate side-chains 276 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 262 time to evaluate : 4.207 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3463 time to fit residues: 14.9850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 340 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 5 optimal weight: 30.0000 chunk 304 optimal weight: 0.0870 chunk 168 optimal weight: 0.8980 chunk 348 optimal weight: 0.9990 chunk 282 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 208 optimal weight: 5.9990 chunk 366 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 35806 Z= 0.150 Angle : 0.525 11.007 48882 Z= 0.267 Chirality : 0.040 0.193 5613 Planarity : 0.004 0.071 5988 Dihedral : 14.709 156.914 5976 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.93 % Allowed : 10.91 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 4127 helix: 1.38 (0.14), residues: 1507 sheet: -0.64 (0.22), residues: 545 loop : -2.00 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y1193 HIS 0.003 0.000 HIS Y 430 PHE 0.024 0.001 PHE G 39 TYR 0.022 0.001 TYR X1018 ARG 0.005 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 288 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 13 residues processed: 305 average time/residue: 0.5289 time to fit residues: 259.0180 Evaluate side-chains 278 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 265 time to evaluate : 4.005 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3255 time to fit residues: 13.4158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 137 optimal weight: 0.2980 chunk 368 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 409 optimal weight: 0.6980 chunk 339 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35806 Z= 0.148 Angle : 0.518 10.951 48882 Z= 0.264 Chirality : 0.040 0.188 5613 Planarity : 0.004 0.071 5988 Dihedral : 14.648 157.842 5976 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.59 % Allowed : 11.98 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4127 helix: 1.50 (0.14), residues: 1512 sheet: -0.50 (0.22), residues: 572 loop : -1.91 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y1193 HIS 0.003 0.001 HIS Y 430 PHE 0.016 0.001 PHE A 24 TYR 0.026 0.001 TYR U 185 ARG 0.005 0.000 ARG X 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 277 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 287 average time/residue: 0.5406 time to fit residues: 246.1052 Evaluate side-chains 266 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 258 time to evaluate : 3.990 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3868 time to fit residues: 11.1716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 394 optimal weight: 6.9990 chunk 46 optimal weight: 30.0000 chunk 233 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 chunk 231 optimal weight: 0.3980 chunk 344 optimal weight: 0.8980 chunk 228 optimal weight: 0.9990 chunk 407 optimal weight: 0.5980 chunk 255 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 188 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 35806 Z= 0.136 Angle : 0.516 10.850 48882 Z= 0.261 Chirality : 0.040 0.166 5613 Planarity : 0.004 0.082 5988 Dihedral : 14.595 158.318 5976 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.76 % Allowed : 12.30 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 4127 helix: 1.64 (0.14), residues: 1517 sheet: -0.39 (0.22), residues: 572 loop : -1.84 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y1193 HIS 0.002 0.000 HIS Y 430 PHE 0.014 0.001 PHE A 24 TYR 0.025 0.001 TYR X1018 ARG 0.013 0.000 ARG E 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 278 time to evaluate : 3.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 8 residues processed: 295 average time/residue: 0.5371 time to fit residues: 253.6248 Evaluate side-chains 272 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 264 time to evaluate : 3.842 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3673 time to fit residues: 12.2784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 252 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 80 optimal weight: 50.0000 chunk 78 optimal weight: 40.0000 chunk 259 optimal weight: 2.9990 chunk 277 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 320 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 86 GLN ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35806 Z= 0.276 Angle : 0.591 12.557 48882 Z= 0.300 Chirality : 0.042 0.168 5613 Planarity : 0.004 0.072 5988 Dihedral : 14.648 158.237 5976 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.62 % Allowed : 12.58 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.13), residues: 4127 helix: 1.54 (0.14), residues: 1506 sheet: -0.39 (0.22), residues: 572 loop : -1.85 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y1193 HIS 0.005 0.001 HIS Y 545 PHE 0.025 0.002 PHE Y1325 TYR 0.028 0.001 TYR X1018 ARG 0.011 0.000 ARG E 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 257 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 273 average time/residue: 0.5353 time to fit residues: 235.1636 Evaluate side-chains 260 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 249 time to evaluate : 4.082 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3522 time to fit residues: 13.2147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 370 optimal weight: 0.9980 chunk 390 optimal weight: 0.5980 chunk 356 optimal weight: 0.6980 chunk 379 optimal weight: 20.0000 chunk 228 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 298 optimal weight: 0.0870 chunk 116 optimal weight: 8.9990 chunk 343 optimal weight: 0.2980 chunk 359 optimal weight: 0.9980 chunk 378 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35806 Z= 0.138 Angle : 0.537 13.103 48882 Z= 0.268 Chirality : 0.040 0.172 5613 Planarity : 0.003 0.069 5988 Dihedral : 14.574 157.231 5976 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.34 % Allowed : 12.55 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 4127 helix: 1.73 (0.14), residues: 1512 sheet: -0.29 (0.22), residues: 582 loop : -1.75 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y1193 HIS 0.003 0.001 HIS Y 430 PHE 0.016 0.001 PHE Y1325 TYR 0.027 0.001 TYR U 185 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 269 time to evaluate : 3.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 274 average time/residue: 0.5469 time to fit residues: 237.9168 Evaluate side-chains 266 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 259 time to evaluate : 3.641 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3186 time to fit residues: 9.1945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 249 optimal weight: 6.9990 chunk 401 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 190 optimal weight: 0.0980 chunk 279 optimal weight: 0.9990 chunk 421 optimal weight: 50.0000 chunk 387 optimal weight: 4.9990 chunk 335 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 86 GLN ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35806 Z= 0.239 Angle : 0.582 13.335 48882 Z= 0.291 Chirality : 0.041 0.188 5613 Planarity : 0.004 0.071 5988 Dihedral : 14.601 157.453 5976 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.23 % Allowed : 12.97 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.13), residues: 4127 helix: 1.71 (0.14), residues: 1508 sheet: -0.34 (0.22), residues: 583 loop : -1.76 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y1193 HIS 0.004 0.001 HIS X 447 PHE 0.014 0.001 PHE Y1325 TYR 0.027 0.001 TYR X1018 ARG 0.008 0.000 ARG E 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 252 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 255 average time/residue: 0.5308 time to fit residues: 217.8743 Evaluate side-chains 252 residues out of total 3538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 248 time to evaluate : 3.709 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3633 time to fit residues: 7.7832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 266 optimal weight: 0.9990 chunk 357 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 309 optimal weight: 6.9990 chunk 49 optimal weight: 40.0000 chunk 93 optimal weight: 5.9990 chunk 336 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 345 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 618 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.168162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.116520 restraints weight = 63026.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111640 restraints weight = 54819.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112888 restraints weight = 58626.733| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35806 Z= 0.226 Angle : 0.576 12.766 48882 Z= 0.289 Chirality : 0.041 0.180 5613 Planarity : 0.004 0.070 5988 Dihedral : 14.601 157.629 5976 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.17 % Allowed : 13.20 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.10 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4127 helix: 1.73 (0.14), residues: 1506 sheet: -0.25 (0.22), residues: 573 loop : -1.73 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y1193 HIS 0.004 0.001 HIS Y 545 PHE 0.014 0.001 PHE A 24 TYR 0.027 0.001 TYR X1018 ARG 0.007 0.000 ARG E 7 =============================================================================== Job complete usr+sys time: 6325.32 seconds wall clock time: 116 minutes 20.50 seconds (6980.50 seconds total)