Starting phenix.real_space_refine on Mon May 26 11:39:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pid_17681/05_2025/8pid_17681.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pid_17681/05_2025/8pid_17681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pid_17681/05_2025/8pid_17681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pid_17681/05_2025/8pid_17681.map" model { file = "/net/cci-nas-00/data/ceres_data/8pid_17681/05_2025/8pid_17681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pid_17681/05_2025/8pid_17681.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.047 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 89 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 17460 2.51 5 N 5013 2.21 5 O 5620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28297 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1294 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 150} Chain: "I" Number of atoms: 10450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 bond proxies already assigned to first conformer: 10558 Chain: "J" Number of atoms: 10450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10450 Classifications: {'peptide': 1343} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1287} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "G" Number of atoms: 1807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Conformer: "B" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} bond proxies already assigned to first conformer: 1812 Chain: "H" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 784 Classifications: {'DNA': 38} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 37} Chain: "R" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 303 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "J" 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 12193 SG CYS J 70 24.334 70.291 85.576 1.00 90.31 S ATOM 12207 SG CYS J 72 23.326 66.614 85.192 1.00 91.52 S ATOM 12315 SG CYS J 85 21.696 68.777 87.827 1.00 90.44 S ATOM 12339 SG CYS J 88 25.403 67.813 88.170 1.00 87.37 S ATOM 18027 SG CYS J 814 56.468 126.456 93.755 1.00 74.29 S ATOM 18592 SG CYS J 888 58.541 123.452 93.071 1.00 72.59 S ATOM 18643 SG CYS J 895 57.575 126.019 90.253 1.00 67.71 S ATOM 18664 SG CYS J 898 60.271 126.753 92.762 1.00 68.41 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE I 156 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE I 156 " occ=0.50 Time building chain proxies: 23.10, per 1000 atoms: 0.82 Number of scatterers: 28297 At special positions: 0 Unit cell: (139.776, 169.728, 158.912, 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 112 16.00 P 89 15.00 Mg 1 11.99 O 5620 8.00 N 5013 7.00 C 17460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.42 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " Number of angles added : 12 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6244 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 50 sheets defined 38.9% alpha, 18.1% beta 40 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 10.77 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 71 Processing helix chain 'P' and resid 89 through 100 removed outlier: 3.552A pdb=" N ILE P 93 " --> pdb=" O PRO P 89 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL P 98 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 124 removed outlier: 3.704A pdb=" N PHE P 123 " --> pdb=" O GLU P 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.639A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.990A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.708A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.983A pdb=" N SER I 166 " --> pdb=" O LYS I 163 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 163 through 167' Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 removed outlier: 3.775A pdb=" N ILE I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 295 removed outlier: 3.738A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.950A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.552A pdb=" N MET I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.782A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 612 removed outlier: 4.020A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 624 through 628 removed outlier: 3.849A pdb=" N HIS I 628 " --> pdb=" O GLU I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.514A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.133A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 942 through 983 Processing helix chain 'I' and resid 985 through 991 Processing helix chain 'I' and resid 993 through 998 removed outlier: 3.534A pdb=" N TRP I 997 " --> pdb=" O ARG I 994 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.582A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 4.322A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.566A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 4.117A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 removed outlier: 3.591A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.747A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.570A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.661A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.702A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.556A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.502A pdb=" N ILE J 416 " --> pdb=" O LEU J 412 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.722A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.955A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.936A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 4.041A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.936A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.066A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.653A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 915 through 925 Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.537A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.347A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1296 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.730A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN J1326 " --> pdb=" O ALA J1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.730A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1360 through 1375 removed outlier: 4.169A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA J1375 " --> pdb=" O ARG J1371 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.557A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.609A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 removed outlier: 4.136A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.566A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.169A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.576A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 160 removed outlier: 3.609A pdb=" N ARG H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 166 removed outlier: 3.767A pdb=" N ASP H 164 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG H 166 " --> pdb=" O GLU H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'H' and resid 228 through 232 Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'P' and resid 149 through 155 removed outlier: 3.543A pdb=" N SER P 139 " --> pdb=" O VAL P 154 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N MET P 140 " --> pdb=" O THR P 131 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR P 131 " --> pdb=" O MET P 140 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE P 129 " --> pdb=" O LEU P 142 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASN P 144 " --> pdb=" O GLN P 127 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN P 127 " --> pdb=" O ASN P 144 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE P 126 " --> pdb=" O ILE P 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.608A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.805A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA7, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.307A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 154 through 159 removed outlier: 4.951A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB1, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB2, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.020A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.559A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.811A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB6, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.671A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.239A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 755 through 758 Processing sheet with id=AB9, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.371A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 830 through 841 removed outlier: 4.024A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.589A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.224A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC6, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC7, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AC8, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.713A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.261A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.807A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 253 through 254 Processing sheet with id=AD2, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD3, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AD4, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD6, first strand: chain 'J' and resid 825 through 827 removed outlier: 7.261A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP J 830 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 842 through 843 removed outlier: 4.009A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.528A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.851A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.362A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 6.262A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE4, first strand: chain 'J' and resid 1046 through 1050 Processing sheet with id=AE5, first strand: chain 'J' and resid 1188 through 1191 removed outlier: 6.946A pdb=" N LYS J1172 " --> pdb=" O GLU J1168 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU J1168 " --> pdb=" O LYS J1172 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG J1174 " --> pdb=" O GLY J1166 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.673A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.781A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.585A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AF1, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.948A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AF3, first strand: chain 'H' and resid 15 through 20 removed outlier: 6.662A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 98 through 105 removed outlier: 3.899A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.605A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) 1141 hydrogen bonds defined for protein. 3188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 14.94 Time building geometry restraints manager: 8.63 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: 9135 1.34 - 1.46: 4057 1.46 - 1.58: 15362 1.58 - 1.70: 176 1.70 - 1.81: 194 Bond restraints: 28924 Sorted by residual: bond pdb=" CD GLU K 76 " pdb=" OE1 GLU K 76 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.35e+00 bond pdb=" CB ASN H 137 " pdb=" CG ASN H 137 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.18e+00 bond pdb=" CB LYS J 964 " pdb=" CG LYS J 964 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CB GLU K 76 " pdb=" CG GLU K 76 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CB LYS J1151 " pdb=" CG LYS J1151 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 ... (remaining 28919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 39013 1.73 - 3.46: 399 3.46 - 5.20: 42 5.20 - 6.93: 17 6.93 - 8.66: 6 Bond angle restraints: 39477 Sorted by residual: angle pdb=" CA GLU K 76 " pdb=" CB GLU K 76 " pdb=" CG GLU K 76 " ideal model delta sigma weight residual 114.10 121.99 -7.89 2.00e+00 2.50e-01 1.56e+01 angle pdb=" C GLN K 75 " pdb=" N GLU K 76 " pdb=" CA GLU K 76 " ideal model delta sigma weight residual 121.14 114.91 6.23 1.75e+00 3.27e-01 1.27e+01 angle pdb=" CB ARG I 996 " pdb=" CG ARG I 996 " pdb=" CD ARG I 996 " ideal model delta sigma weight residual 111.30 119.29 -7.99 2.30e+00 1.89e-01 1.21e+01 angle pdb=" N GLY H 108 " pdb=" CA GLY H 108 " pdb=" C GLY H 108 " ideal model delta sigma weight residual 112.34 118.99 -6.65 2.04e+00 2.40e-01 1.06e+01 angle pdb=" CB LYS J1151 " pdb=" CG LYS J1151 " pdb=" CD LYS J1151 " ideal model delta sigma weight residual 111.30 118.51 -7.21 2.30e+00 1.89e-01 9.83e+00 ... (remaining 39472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 16733 35.09 - 70.17: 829 70.17 - 105.26: 39 105.26 - 140.35: 0 140.35 - 175.43: 2 Dihedral angle restraints: 17603 sinusoidal: 7899 harmonic: 9704 Sorted by residual: dihedral pdb=" C4' DC B 28 " pdb=" C3' DC B 28 " pdb=" O3' DC B 28 " pdb=" P DC B 29 " ideal model delta sinusoidal sigma weight residual 220.00 44.57 175.43 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC A 39 " pdb=" C3' DC A 39 " pdb=" O3' DC A 39 " pdb=" P DC A 40 " ideal model delta sinusoidal sigma weight residual 220.00 74.24 145.76 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA ASN I 314 " pdb=" C ASN I 314 " pdb=" N MET I 315 " pdb=" CA MET I 315 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 17600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2913 0.027 - 0.055: 955 0.055 - 0.082: 342 0.082 - 0.109: 231 0.109 - 0.137: 67 Chirality restraints: 4508 Sorted by residual: chirality pdb=" CA LYS I 236 " pdb=" N LYS I 236 " pdb=" C LYS I 236 " pdb=" CB LYS I 236 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE J1190 " pdb=" N ILE J1190 " pdb=" C ILE J1190 " pdb=" CB ILE J1190 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE J1090 " pdb=" N ILE J1090 " pdb=" C ILE J1090 " pdb=" CB ILE J1090 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 4505 not shown) Planarity restraints: 4852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO I 190 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET I 488 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO I 489 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 489 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 489 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 153 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO G 154 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO G 154 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 154 " 0.020 5.00e-02 4.00e+02 ... (remaining 4849 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 200 2.53 - 3.12: 20579 3.12 - 3.71: 45657 3.71 - 4.31: 61162 4.31 - 4.90: 103643 Nonbonded interactions: 231241 Sorted by model distance: nonbonded pdb=" OD2 ASP J 460 " pdb=" OP1 U R 17 " model vdw 1.935 3.040 nonbonded pdb=" P U R 17 " pdb="MG MG J1503 " model vdw 2.054 2.530 nonbonded pdb=" OP1 U R 17 " pdb="MG MG J1503 " model vdw 2.067 2.170 nonbonded pdb=" OD2 ASP J 462 " pdb="MG MG J1503 " model vdw 2.081 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.086 2.170 ... (remaining 231236 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 'G' and (resid 4 through 218 or resid 220 through 233)) selection = (chain 'H' and (resid 4 through 218 or resid 220 through 233)) } 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 5.270 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: 1.400 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 88.430 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.130 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 0.040 28932 Z= 0.095 Angle : 0.461 8.659 39489 Z= 0.242 Chirality : 0.038 0.137 4508 Planarity : 0.003 0.045 4852 Dihedral : 18.104 175.432 11359 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 0.28 % Allowed : 18.47 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 3359 helix: 2.38 (0.16), residues: 1138 sheet: 0.38 (0.24), residues: 510 loop : -0.16 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 997 HIS 0.003 0.000 HIS P 152 PHE 0.005 0.001 PHE I1025 TYR 0.009 0.001 TYR J 631 ARG 0.012 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.13424 ( 1243) hydrogen bonds : angle 5.15562 ( 3392) metal coordination : bond 0.00333 ( 8) metal coordination : angle 3.26912 ( 12) covalent geometry : bond 0.00208 (28924) covalent geometry : angle 0.45727 (39477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.6867 (tmm) cc_final: 0.6463 (tmm) REVERT: I 741 MET cc_start: 0.8463 (mmt) cc_final: 0.8141 (mmt) REVERT: J 1034 PHE cc_start: 0.8380 (m-80) cc_final: 0.7999 (m-80) REVERT: J 1040 MET cc_start: 0.6087 (ptt) cc_final: 0.5314 (pmt) REVERT: G 93 GLN cc_start: 0.8244 (pp30) cc_final: 0.7921 (pp30) outliers start: 5 outliers final: 2 residues processed: 187 average time/residue: 1.4590 time to fit residues: 319.9401 Evaluate side-chains 170 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain G residue 90 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 311 optimal weight: 0.4980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1116 HIS K 15 ASN G 117 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.077840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.052606 restraints weight = 164861.822| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.67 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28932 Z= 0.165 Angle : 0.518 9.291 39489 Z= 0.269 Chirality : 0.041 0.172 4508 Planarity : 0.004 0.065 4852 Dihedral : 15.660 174.220 4749 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 1.98 % Allowed : 18.51 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3359 helix: 2.30 (0.16), residues: 1164 sheet: 0.25 (0.23), residues: 524 loop : -0.18 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 997 HIS 0.011 0.001 HIS G 117 PHE 0.012 0.001 PHE I1164 TYR 0.014 0.001 TYR J 631 ARG 0.013 0.000 ARG I 996 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 1243) hydrogen bonds : angle 4.12785 ( 3392) metal coordination : bond 0.01004 ( 8) metal coordination : angle 5.27767 ( 12) covalent geometry : bond 0.00378 (28924) covalent geometry : angle 0.50963 (39477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 174 time to evaluate : 3.022 Fit side-chains revert: symmetry clash REVERT: P 95 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8495 (tm-30) REVERT: I 562 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: I 741 MET cc_start: 0.8783 (mmt) cc_final: 0.8388 (mmt) REVERT: J 136 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: J 372 MET cc_start: 0.9076 (ttm) cc_final: 0.8866 (mtp) REVERT: J 902 ASP cc_start: 0.8337 (t0) cc_final: 0.8060 (t0) REVERT: J 913 GLU cc_start: 0.7912 (pp20) cc_final: 0.7659 (pp20) REVERT: J 1040 MET cc_start: 0.7061 (ptt) cc_final: 0.6080 (pmt) REVERT: G 93 GLN cc_start: 0.8380 (pp30) cc_final: 0.7843 (pp30) REVERT: H 66 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.8679 (m-70) outliers start: 54 outliers final: 18 residues processed: 217 average time/residue: 1.3297 time to fit residues: 341.5825 Evaluate side-chains 183 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 104 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 153 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 241 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 504 GLN K 15 ASN G 117 HIS H 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.077702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.052762 restraints weight = 142465.101| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.30 r_work: 0.2737 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28932 Z= 0.131 Angle : 0.496 8.509 39489 Z= 0.257 Chirality : 0.040 0.166 4508 Planarity : 0.004 0.054 4852 Dihedral : 15.651 174.634 4747 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.46 % Rotamer: Outliers : 1.91 % Allowed : 19.17 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3359 helix: 2.27 (0.16), residues: 1164 sheet: 0.27 (0.23), residues: 518 loop : -0.21 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 997 HIS 0.011 0.001 HIS G 117 PHE 0.011 0.001 PHE I 405 TYR 0.014 0.001 TYR J 631 ARG 0.016 0.000 ARG I 996 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 1243) hydrogen bonds : angle 3.98078 ( 3392) metal coordination : bond 0.00813 ( 8) metal coordination : angle 5.13915 ( 12) covalent geometry : bond 0.00300 (28924) covalent geometry : angle 0.48827 (39477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 95 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8652 (tm-30) REVERT: I 1 MET cc_start: 0.7732 (tmm) cc_final: 0.7522 (tmm) REVERT: I 562 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8769 (tp30) REVERT: I 741 MET cc_start: 0.8805 (mmt) cc_final: 0.8416 (mmt) REVERT: J 136 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: J 902 ASP cc_start: 0.8520 (t0) cc_final: 0.8237 (t0) REVERT: J 913 GLU cc_start: 0.8166 (pp20) cc_final: 0.7868 (pp20) REVERT: J 1040 MET cc_start: 0.7209 (ptt) cc_final: 0.6248 (pmt) REVERT: G 93 GLN cc_start: 0.8655 (pp30) cc_final: 0.8085 (pp30) REVERT: H 66 HIS cc_start: 0.9125 (OUTLIER) cc_final: 0.8810 (m-70) REVERT: H 205 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8249 (ttm) outliers start: 52 outliers final: 19 residues processed: 206 average time/residue: 1.3285 time to fit residues: 324.9188 Evaluate side-chains 182 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 205 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 88 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 285 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 251 optimal weight: 30.0000 chunk 282 optimal weight: 0.0020 chunk 266 optimal weight: 4.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 762 ASN K 15 ASN G 117 HIS H 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.077898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.053355 restraints weight = 123400.128| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.87 r_work: 0.2763 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28932 Z= 0.116 Angle : 0.492 9.154 39489 Z= 0.255 Chirality : 0.040 0.171 4508 Planarity : 0.003 0.060 4852 Dihedral : 15.626 174.924 4747 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 2.05 % Allowed : 19.34 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3359 helix: 2.27 (0.16), residues: 1166 sheet: 0.25 (0.23), residues: 496 loop : -0.20 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 997 HIS 0.011 0.001 HIS G 117 PHE 0.011 0.001 PHE I 405 TYR 0.013 0.001 TYR J 631 ARG 0.016 0.000 ARG I 996 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 1243) hydrogen bonds : angle 3.90102 ( 3392) metal coordination : bond 0.00686 ( 8) metal coordination : angle 5.00686 ( 12) covalent geometry : bond 0.00266 (28924) covalent geometry : angle 0.48458 (39477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 169 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 95 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8675 (tm-30) REVERT: I 562 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8736 (tp30) REVERT: I 741 MET cc_start: 0.8823 (mmt) cc_final: 0.8423 (mmt) REVERT: J 136 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: J 902 ASP cc_start: 0.8491 (t0) cc_final: 0.8206 (t0) REVERT: J 913 GLU cc_start: 0.8132 (pp20) cc_final: 0.7863 (pp20) REVERT: J 1040 MET cc_start: 0.7264 (ptt) cc_final: 0.6292 (pmt) REVERT: G 93 GLN cc_start: 0.8649 (pp30) cc_final: 0.8057 (pp30) REVERT: H 65 LEU cc_start: 0.9612 (mm) cc_final: 0.9334 (tt) outliers start: 56 outliers final: 29 residues processed: 211 average time/residue: 1.2984 time to fit residues: 326.2261 Evaluate side-chains 189 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 92 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 19 optimal weight: 3.9990 chunk 329 optimal weight: 0.0980 chunk 167 optimal weight: 20.0000 chunk 252 optimal weight: 0.0770 chunk 105 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 337 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 187 optimal weight: 0.3980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS H 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.077948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.053122 restraints weight = 142118.039| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.24 r_work: 0.2750 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28932 Z= 0.114 Angle : 0.501 10.511 39489 Z= 0.257 Chirality : 0.040 0.159 4508 Planarity : 0.004 0.065 4852 Dihedral : 15.613 175.156 4747 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.44 % Rotamer: Outliers : 2.12 % Allowed : 19.58 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.15), residues: 3359 helix: 2.28 (0.16), residues: 1166 sheet: 0.22 (0.23), residues: 496 loop : -0.19 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 997 HIS 0.012 0.001 HIS G 117 PHE 0.011 0.001 PHE I 405 TYR 0.012 0.001 TYR J 631 ARG 0.017 0.000 ARG I 996 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 1243) hydrogen bonds : angle 3.84103 ( 3392) metal coordination : bond 0.00651 ( 8) metal coordination : angle 4.94001 ( 12) covalent geometry : bond 0.00265 (28924) covalent geometry : angle 0.49338 (39477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 95 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8674 (tm-30) REVERT: I 562 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8760 (tp30) REVERT: I 741 MET cc_start: 0.8835 (mmt) cc_final: 0.8434 (mmt) REVERT: J 136 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: J 875 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.8053 (t0) REVERT: J 902 ASP cc_start: 0.8529 (t0) cc_final: 0.8239 (t0) REVERT: J 913 GLU cc_start: 0.8207 (pp20) cc_final: 0.7942 (pp20) REVERT: J 1040 MET cc_start: 0.7337 (ptt) cc_final: 0.6402 (pmt) REVERT: K 15 ASN cc_start: 0.8418 (t0) cc_final: 0.8200 (t0) REVERT: G 93 GLN cc_start: 0.8625 (pp30) cc_final: 0.7999 (pp30) REVERT: H 65 LEU cc_start: 0.9612 (mm) cc_final: 0.9341 (tt) outliers start: 58 outliers final: 30 residues processed: 213 average time/residue: 1.2906 time to fit residues: 328.9499 Evaluate side-chains 194 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 131 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 281 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 257 optimal weight: 30.0000 chunk 0 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.074911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.050127 restraints weight = 129568.402| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 4.03 r_work: 0.2667 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 28932 Z= 0.243 Angle : 0.587 10.928 39489 Z= 0.303 Chirality : 0.042 0.164 4508 Planarity : 0.004 0.059 4852 Dihedral : 15.762 172.282 4747 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 2.36 % Allowed : 19.58 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3359 helix: 2.08 (0.16), residues: 1166 sheet: 0.01 (0.23), residues: 518 loop : -0.29 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 409 HIS 0.012 0.001 HIS G 117 PHE 0.017 0.001 PHE I1221 TYR 0.018 0.001 TYR J 631 ARG 0.016 0.001 ARG I 996 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 1243) hydrogen bonds : angle 4.06985 ( 3392) metal coordination : bond 0.01540 ( 8) metal coordination : angle 6.12593 ( 12) covalent geometry : bond 0.00561 (28924) covalent geometry : angle 0.57762 (39477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 170 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 95 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8709 (tm-30) REVERT: I 562 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8815 (tp30) REVERT: J 29 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8817 (tpp) REVERT: J 136 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: J 603 LYS cc_start: 0.8942 (tmmt) cc_final: 0.8641 (tppp) REVERT: J 762 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8396 (m-40) REVERT: J 875 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8024 (t0) REVERT: J 902 ASP cc_start: 0.8557 (t0) cc_final: 0.8343 (t0) REVERT: J 1040 MET cc_start: 0.7494 (ptt) cc_final: 0.6621 (pmt) REVERT: K 15 ASN cc_start: 0.8626 (t0) cc_final: 0.8419 (t0) REVERT: G 93 GLN cc_start: 0.8772 (pp30) cc_final: 0.8152 (pp30) REVERT: G 156 SER cc_start: 0.9408 (m) cc_final: 0.9132 (t) REVERT: H 65 LEU cc_start: 0.9634 (mm) cc_final: 0.9143 (tt) REVERT: H 66 HIS cc_start: 0.9182 (OUTLIER) cc_final: 0.8611 (m-70) outliers start: 65 outliers final: 28 residues processed: 222 average time/residue: 1.3072 time to fit residues: 344.6507 Evaluate side-chains 197 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 144 optimal weight: 0.9980 chunk 258 optimal weight: 5.9990 chunk 14 optimal weight: 0.0970 chunk 151 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.076096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.051218 restraints weight = 132274.134| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 4.13 r_work: 0.2698 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28932 Z= 0.147 Angle : 0.550 12.470 39489 Z= 0.280 Chirality : 0.041 0.157 4508 Planarity : 0.004 0.056 4852 Dihedral : 15.705 174.045 4747 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.01 % Allowed : 20.49 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3359 helix: 2.10 (0.16), residues: 1166 sheet: -0.02 (0.23), residues: 511 loop : -0.28 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 997 HIS 0.012 0.001 HIS G 117 PHE 0.011 0.001 PHE I 405 TYR 0.015 0.001 TYR I1053 ARG 0.018 0.000 ARG I 996 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 1243) hydrogen bonds : angle 3.95025 ( 3392) metal coordination : bond 0.00914 ( 8) metal coordination : angle 5.72904 ( 12) covalent geometry : bond 0.00341 (28924) covalent geometry : angle 0.54139 (39477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 95 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8612 (tm-30) REVERT: I 562 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8803 (tp30) REVERT: J 29 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8873 (tpp) REVERT: J 603 LYS cc_start: 0.8924 (tmmt) cc_final: 0.8616 (tppp) REVERT: J 762 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8280 (m-40) REVERT: J 875 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7979 (t0) REVERT: J 902 ASP cc_start: 0.8518 (t0) cc_final: 0.8175 (t0) REVERT: J 964 LYS cc_start: 0.9420 (mmmt) cc_final: 0.8951 (mtmt) REVERT: J 1040 MET cc_start: 0.7564 (ptt) cc_final: 0.6733 (pmt) REVERT: J 1109 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7563 (pp) REVERT: G 93 GLN cc_start: 0.8771 (pp30) cc_final: 0.8155 (pp30) REVERT: H 65 LEU cc_start: 0.9631 (mm) cc_final: 0.9361 (tt) outliers start: 55 outliers final: 31 residues processed: 213 average time/residue: 1.2924 time to fit residues: 327.1561 Evaluate side-chains 195 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1109 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 13 optimal weight: 20.0000 chunk 289 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 335 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 109 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 HIS ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 910 ASN J1366 HIS K 15 ASN G 117 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.075185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.050416 restraints weight = 128424.733| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 4.08 r_work: 0.2675 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 28932 Z= 0.208 Angle : 0.580 12.871 39489 Z= 0.295 Chirality : 0.042 0.145 4508 Planarity : 0.004 0.064 4852 Dihedral : 15.739 173.394 4747 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.98 % Allowed : 20.38 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.15), residues: 3359 helix: 2.03 (0.15), residues: 1166 sheet: -0.10 (0.23), residues: 511 loop : -0.30 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 997 HIS 0.012 0.001 HIS G 117 PHE 0.012 0.001 PHE I1323 TYR 0.016 0.001 TYR I1053 ARG 0.019 0.000 ARG I 996 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 1243) hydrogen bonds : angle 4.01860 ( 3392) metal coordination : bond 0.01281 ( 8) metal coordination : angle 5.91665 ( 12) covalent geometry : bond 0.00482 (28924) covalent geometry : angle 0.57078 (39477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 95 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8692 (tm-30) REVERT: I 562 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8811 (tp30) REVERT: J 29 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8899 (ttp) REVERT: J 136 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: J 603 LYS cc_start: 0.8945 (tmmt) cc_final: 0.8646 (tppp) REVERT: J 762 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8330 (m-40) REVERT: J 875 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.7996 (t0) REVERT: J 964 LYS cc_start: 0.9439 (mmmt) cc_final: 0.8991 (mttt) REVERT: J 1040 MET cc_start: 0.7561 (ptt) cc_final: 0.6725 (pmt) REVERT: J 1109 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7557 (pp) REVERT: J 1196 LEU cc_start: 0.8915 (mp) cc_final: 0.8270 (tp) REVERT: K 4 VAL cc_start: 0.9468 (p) cc_final: 0.9266 (p) REVERT: G 93 GLN cc_start: 0.8786 (pp30) cc_final: 0.8165 (pp30) REVERT: H 65 LEU cc_start: 0.9633 (mm) cc_final: 0.9360 (tt) outliers start: 54 outliers final: 33 residues processed: 204 average time/residue: 1.3926 time to fit residues: 337.2509 Evaluate side-chains 200 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1109 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 195 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 283 optimal weight: 0.3980 chunk 255 optimal weight: 2.9990 chunk 291 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 334 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 273 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS G 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.051459 restraints weight = 124969.262| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 4.02 r_work: 0.2713 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28932 Z= 0.136 Angle : 0.554 13.443 39489 Z= 0.281 Chirality : 0.040 0.173 4508 Planarity : 0.004 0.065 4852 Dihedral : 15.692 174.410 4747 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.81 % Allowed : 20.80 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3359 helix: 2.09 (0.16), residues: 1166 sheet: -0.08 (0.23), residues: 510 loop : -0.29 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 997 HIS 0.012 0.001 HIS G 117 PHE 0.011 0.001 PHE I 812 TYR 0.013 0.001 TYR J 631 ARG 0.019 0.000 ARG I 996 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 1243) hydrogen bonds : angle 3.92217 ( 3392) metal coordination : bond 0.00820 ( 8) metal coordination : angle 5.73202 ( 12) covalent geometry : bond 0.00316 (28924) covalent geometry : angle 0.54455 (39477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 95 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8642 (tm-30) REVERT: I 562 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8778 (tp30) REVERT: J 29 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8884 (tpp) REVERT: J 136 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: J 603 LYS cc_start: 0.8920 (tmmt) cc_final: 0.8622 (tppp) REVERT: J 762 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8225 (m-40) REVERT: J 875 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8049 (t0) REVERT: J 964 LYS cc_start: 0.9452 (mmmt) cc_final: 0.9019 (mttt) REVERT: J 1040 MET cc_start: 0.7537 (ptt) cc_final: 0.6641 (pmt) REVERT: J 1109 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7569 (pp) REVERT: J 1196 LEU cc_start: 0.8927 (mp) cc_final: 0.8273 (tp) REVERT: K 69 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8104 (ttp80) REVERT: G 93 GLN cc_start: 0.8771 (pp30) cc_final: 0.8153 (pp30) REVERT: H 65 LEU cc_start: 0.9622 (mm) cc_final: 0.9363 (tt) outliers start: 49 outliers final: 34 residues processed: 208 average time/residue: 1.3617 time to fit residues: 334.4120 Evaluate side-chains 203 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1109 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 171 optimal weight: 1.9990 chunk 151 optimal weight: 0.0370 chunk 325 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 309 optimal weight: 3.9990 chunk 277 optimal weight: 0.8980 chunk 241 optimal weight: 9.9990 chunk 319 optimal weight: 0.9980 chunk 329 optimal weight: 8.9990 chunk 328 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS G 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.051426 restraints weight = 136491.196| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.22 r_work: 0.2703 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28932 Z= 0.126 Angle : 0.557 14.311 39489 Z= 0.282 Chirality : 0.040 0.192 4508 Planarity : 0.004 0.057 4852 Dihedral : 15.680 174.662 4747 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.60 % Allowed : 21.15 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3359 helix: 2.10 (0.16), residues: 1167 sheet: -0.07 (0.23), residues: 510 loop : -0.27 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 997 HIS 0.012 0.001 HIS G 117 PHE 0.011 0.001 PHE I 405 TYR 0.013 0.001 TYR I1053 ARG 0.020 0.000 ARG I 996 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 1243) hydrogen bonds : angle 3.90679 ( 3392) metal coordination : bond 0.00743 ( 8) metal coordination : angle 5.61196 ( 12) covalent geometry : bond 0.00294 (28924) covalent geometry : angle 0.54811 (39477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 95 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8634 (tm-30) REVERT: I 562 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8793 (tp30) REVERT: I 1080 ASN cc_start: 0.9216 (t0) cc_final: 0.8995 (t0) REVERT: J 29 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8882 (tpp) REVERT: J 603 LYS cc_start: 0.8926 (tmmt) cc_final: 0.8618 (tppp) REVERT: J 762 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8230 (m-40) REVERT: J 875 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.7981 (t0) REVERT: J 964 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9020 (mttt) REVERT: J 1040 MET cc_start: 0.7566 (ptt) cc_final: 0.6668 (pmt) REVERT: J 1109 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7549 (pp) REVERT: J 1196 LEU cc_start: 0.8912 (mp) cc_final: 0.8256 (tp) REVERT: G 93 GLN cc_start: 0.8787 (pp30) cc_final: 0.8170 (pp30) REVERT: H 65 LEU cc_start: 0.9637 (mm) cc_final: 0.9373 (tt) outliers start: 43 outliers final: 29 residues processed: 198 average time/residue: 1.4037 time to fit residues: 328.9121 Evaluate side-chains 197 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1109 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 195 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 151 optimal weight: 0.0670 chunk 11 optimal weight: 8.9990 chunk 309 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 chunk 213 optimal weight: 8.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS G 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.075137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.049807 restraints weight = 168290.842| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 4.69 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28932 Z= 0.201 Angle : 0.595 14.546 39489 Z= 0.301 Chirality : 0.041 0.170 4508 Planarity : 0.004 0.068 4852 Dihedral : 15.741 173.500 4747 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.63 % Allowed : 21.22 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3359 helix: 1.99 (0.16), residues: 1172 sheet: -0.16 (0.23), residues: 518 loop : -0.33 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 997 HIS 0.012 0.001 HIS G 117 PHE 0.013 0.001 PHE I1221 TYR 0.017 0.001 TYR I1053 ARG 0.020 0.000 ARG I 996 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 1243) hydrogen bonds : angle 4.00877 ( 3392) metal coordination : bond 0.01281 ( 8) metal coordination : angle 5.91860 ( 12) covalent geometry : bond 0.00466 (28924) covalent geometry : angle 0.58592 (39477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19619.52 seconds wall clock time: 339 minutes 32.83 seconds (20372.83 seconds total)