Starting phenix.real_space_refine on Sat Feb 7 02:20:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xui_33470/02_2026/7xui_33470.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xui_33470/02_2026/7xui_33470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xui_33470/02_2026/7xui_33470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xui_33470/02_2026/7xui_33470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xui_33470/02_2026/7xui_33470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xui_33470/02_2026/7xui_33470.map" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 111 5.49 5 Mg 1 5.21 5 S 117 5.16 5 C 18149 2.51 5 N 5238 2.21 5 O 5992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29610 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1743 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1704 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10575 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 10380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10380 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2213 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 5, 'TRANS': 263} Chain breaks: 2 Chain: "B" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "R" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2162 Classifications: {'RNA': 101} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 45, 'rna3p_pyr': 38} Link IDs: {'rna2p': 18, 'rna3p': 82} Chain breaks: 1 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 14480 SG CYS J 70 37.658 115.182 86.636 1.00137.00 S ATOM 14494 SG CYS J 72 37.750 118.432 86.065 1.00151.28 S ATOM 14602 SG CYS J 85 36.171 116.187 83.395 1.00147.83 S ATOM 14626 SG CYS J 88 40.026 115.919 84.020 1.00143.76 S ATOM 20314 SG CYS J 814 47.531 52.329 76.712 1.00 66.40 S ATOM 20879 SG CYS J 888 50.282 54.546 77.915 1.00 58.00 S ATOM 20930 SG CYS J 895 47.634 53.291 80.462 1.00 52.85 S ATOM 20951 SG CYS J 898 49.986 51.032 79.285 1.00 55.70 S Time building chain proxies: 6.49, per 1000 atoms: 0.22 Number of scatterers: 29610 At special positions: 0 Unit cell: (147.34, 157.94, 179.14, 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 117 16.00 P 111 15.00 Mg 1 11.99 O 5992 8.00 N 5238 7.00 C 18149 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: 2.91 Conformation dependent library (CDL) restraints added in 1.3 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 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " 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 814 " Number of angles added : 12 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6434 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 45 sheets defined 40.9% alpha, 12.6% beta 37 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'G' and resid 35 through 50 Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 111 through 115 removed outlier: 3.597A pdb=" N ASP G 114 " --> pdb=" O THR G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 4.130A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.635A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) 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 212 through 228 removed outlier: 3.960A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 49 through 57 Processing helix chain 'I' and resid 81 through 89 removed outlier: 4.312A pdb=" N ILE I 87 " --> pdb=" O GLN I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.219A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 4.061A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 291 through 295 Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 391 removed outlier: 3.828A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE I 390 " --> pdb=" O GLU I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.693A pdb=" N ASN I 462 " --> pdb=" O GLU I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.539A pdb=" N SER I 508 " --> pdb=" O GLU I 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.884A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 544 through 549 Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 663 through 667 removed outlier: 3.674A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 685 Processing helix chain 'I' and resid 705 through 712 Processing helix chain 'I' and resid 820 through 825 removed outlier: 3.546A pdb=" N GLU I 825 " --> pdb=" O ARG I 821 " (cutoff:3.500A) Processing helix chain 'I' and resid 860 through 865 removed outlier: 3.872A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU I 865 " --> pdb=" O LEU I 862 " (cutoff:3.500A) Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 942 through 981 removed outlier: 3.801A pdb=" N GLU I 963 " --> pdb=" O ASP I 959 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.764A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 998 removed outlier: 3.603A pdb=" N ARG I 996 " --> pdb=" O PRO I 993 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1007 No H-bonds generated for 'chain 'I' and resid 1005 through 1007' Processing helix chain 'I' and resid 1008 through 1038 removed outlier: 3.520A pdb=" N ASP I1019 " --> pdb=" O ALA I1015 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLU I1020 " --> pdb=" O GLU I1016 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS I1022 " --> pdb=" O TYR I1018 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN I1038 " --> pdb=" O ARG I1034 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.614A pdb=" N ASP I1084 " --> pdb=" O PRO I1081 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1081 through 1085' Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 4.264A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 4.033A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.508A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.673A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.718A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.591A pdb=" N LEU I1333 " --> pdb=" O GLU I1329 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 removed outlier: 3.572A pdb=" N SER J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.541A pdb=" N ARG J 81 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 100 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 141 removed outlier: 4.264A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 172 Processing helix chain 'J' and resid 180 through 192 removed outlier: 3.916A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.966A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 238 Processing helix chain 'J' and resid 264 through 286 removed outlier: 3.764A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.554A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 331 Processing helix chain 'J' and resid 338 through 342 removed outlier: 3.601A pdb=" N ASN J 341 " --> 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 389 removed outlier: 3.654A pdb=" N ILE J 381 " --> pdb=" O PHE J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 403 Processing helix chain 'J' and resid 407 through 416 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 453 through 458 Processing helix chain 'J' and resid 473 through 483 removed outlier: 3.673A pdb=" N GLN J 477 " --> pdb=" O THR J 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.821A 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: 3.892A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 593 Processing helix chain 'J' and resid 598 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.658A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.054A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 729 removed outlier: 3.559A pdb=" N GLY J 729 " --> pdb=" O MET J 725 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.939A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.774A pdb=" N CYS J 888 " --> pdb=" O VAL J 885 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.579A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1068 through 1074 Processing helix chain 'J' and resid 1137 through 1147 removed outlier: 3.589A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1226 through 1243 Processing helix chain 'J' and resid 1250 through 1261 Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.670A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1324 Processing helix chain 'J' and resid 1327 through 1338 removed outlier: 3.803A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA J1338 " --> pdb=" O GLU J1334 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1360 through 1373 Processing helix chain 'K' and resid 7 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.702A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 78 removed outlier: 5.005A pdb=" N GLN K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 137 Processing helix chain 'L' and resid 137 through 152 removed outlier: 3.625A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 234 Processing helix chain 'L' and resid 244 through 257 removed outlier: 3.583A pdb=" N LYS L 257 " --> pdb=" O SER L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 290 Processing helix chain 'L' and resid 298 through 307 Processing helix chain 'L' and resid 318 through 323 removed outlier: 4.003A pdb=" N MET L 322 " --> pdb=" O ALA L 318 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN L 323 " --> pdb=" O ALA L 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 318 through 323' Processing helix chain 'L' and resid 330 through 352 removed outlier: 4.193A pdb=" N GLU L 335 " --> pdb=" O HIS L 331 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU L 336 " --> pdb=" O ASP L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 392 removed outlier: 4.730A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 417 Processing helix chain 'L' and resid 426 through 430 Processing helix chain 'L' and resid 431 through 447 Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 18 removed outlier: 8.458A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'G' and resid 97 through 98 removed outlier: 7.657A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA6, first strand: chain 'G' and resid 108 through 110 removed outlier: 3.876A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 152 through 153 removed outlier: 3.629A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 182 through 184 Processing sheet with id=AA9, first strand: chain 'H' and resid 26 through 27 removed outlier: 4.079A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 99 through 101 removed outlier: 6.665A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 109 through 111 removed outlier: 3.695A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.844A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 59 through 61 removed outlier: 4.394A pdb=" N SER I 66 " --> pdb=" O SER I 61 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB7, first strand: chain 'I' and resid 148 through 151 Processing sheet with id=AB8, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB9, first strand: chain 'I' and resid 284 through 285 removed outlier: 3.632A pdb=" N GLN I 238 " --> pdb=" O GLU I 231 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU I 231 " --> pdb=" O GLN I 238 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU I 240 " --> pdb=" O ILE I 229 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.690A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS I 593 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.690A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 633 through 637 Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.591A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 722 through 728 removed outlier: 6.890A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 3.983A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 830 through 831 Processing sheet with id=AC9, first strand: chain 'I' and resid 846 through 847 removed outlier: 6.326A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 removed outlier: 3.774A pdb=" N VAL I 884 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.319A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD5, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD6, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.779A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL J 244 " --> pdb=" O GLY J 103 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 143 through 145 removed outlier: 3.730A pdb=" N LEU J 160 " --> pdb=" O TYR J 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.646A pdb=" N ILE J 552 " --> pdb=" O SER J 568 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'J' and resid 809 through 811 removed outlier: 7.227A pdb=" N VAL J 894 " --> pdb=" O THR J 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 821 Processing sheet with id=AE3, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.151A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 949 through 952 removed outlier: 4.025A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL J 952 " --> pdb=" O THR J1016 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR J1016 " --> pdb=" O VAL J 952 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA J1001 " --> pdb=" O ILE J 975 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 991 through 996 removed outlier: 4.188A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1047 through 1048 removed outlier: 3.973A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG J1123 " --> pdb=" O ILE J1106 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1155 through 1156 removed outlier: 6.533A pdb=" N ILE J1155 " --> pdb=" O ILE J1210 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AE9, first strand: chain 'J' and resid 1279 through 1281 1141 hydrogen bonds defined for protein. 3219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 7.14 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5401 1.32 - 1.45: 7584 1.45 - 1.57: 16877 1.57 - 1.69: 219 1.69 - 1.82: 203 Bond restraints: 30284 Sorted by residual: bond pdb=" CB ASN I 519 " pdb=" CG ASN I 519 " ideal model delta sigma weight residual 1.516 1.446 0.070 2.50e-02 1.60e+03 7.83e+00 bond pdb=" N GLU K 71 " pdb=" CA GLU K 71 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.67e+00 bond pdb=" CE2 TYR J 457 " pdb=" CZ TYR J 457 " ideal model delta sigma weight residual 1.378 1.320 0.058 2.40e-02 1.74e+03 5.87e+00 bond pdb=" CD2 TYR J 457 " pdb=" CE2 TYR J 457 " ideal model delta sigma weight residual 1.382 1.310 0.072 3.00e-02 1.11e+03 5.74e+00 bond pdb=" CB VAL I 733 " pdb=" CG2 VAL I 733 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.26e+00 ... (remaining 30279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 39647 1.92 - 3.83: 1465 3.83 - 5.75: 270 5.75 - 7.67: 27 7.67 - 9.58: 12 Bond angle restraints: 41421 Sorted by residual: angle pdb=" N VAL J 407 " pdb=" CA VAL J 407 " pdb=" C VAL J 407 " ideal model delta sigma weight residual 112.96 106.32 6.64 1.00e+00 1.00e+00 4.40e+01 angle pdb=" N GLN K 72 " pdb=" CA GLN K 72 " pdb=" C GLN K 72 " ideal model delta sigma weight residual 113.43 106.53 6.90 1.26e+00 6.30e-01 3.00e+01 angle pdb=" N GLN L 406 " pdb=" CA GLN L 406 " pdb=" CB GLN L 406 " ideal model delta sigma weight residual 110.16 116.97 -6.81 1.48e+00 4.57e-01 2.12e+01 angle pdb=" CA ARG J1036 " pdb=" CB ARG J1036 " pdb=" CG ARG J1036 " ideal model delta sigma weight residual 114.10 122.68 -8.58 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CA GLU H 193 " pdb=" CB GLU H 193 " pdb=" CG GLU H 193 " ideal model delta sigma weight residual 114.10 122.32 -8.22 2.00e+00 2.50e-01 1.69e+01 ... (remaining 41416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.09: 17380 25.09 - 50.18: 1078 50.18 - 75.27: 271 75.27 - 100.36: 28 100.36 - 125.45: 3 Dihedral angle restraints: 18760 sinusoidal: 8771 harmonic: 9989 Sorted by residual: dihedral pdb=" CA MET I 800 " pdb=" C MET I 800 " pdb=" N ARG I 801 " pdb=" CA ARG I 801 " ideal model delta harmonic sigma weight residual -180.00 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU J 342 " pdb=" C LEU J 342 " pdb=" N LEU J 343 " pdb=" CA LEU J 343 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA PRO J 584 " pdb=" C PRO J 584 " pdb=" N LYS J 585 " pdb=" CA LYS J 585 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 18757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3261 0.046 - 0.093: 1155 0.093 - 0.139: 329 0.139 - 0.186: 46 0.186 - 0.232: 7 Chirality restraints: 4798 Sorted by residual: chirality pdb=" CB VAL J 592 " pdb=" CA VAL J 592 " pdb=" CG1 VAL J 592 " pdb=" CG2 VAL J 592 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA GLU H 193 " pdb=" N GLU H 193 " pdb=" C GLU H 193 " pdb=" CB GLU H 193 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CG LEU I1233 " pdb=" CB LEU I1233 " pdb=" CD1 LEU I1233 " pdb=" CD2 LEU I1233 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 4795 not shown) Planarity restraints: 5001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN I 766 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" CG ASN I 766 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN I 766 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN I 766 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 358 " 0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO J 359 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO J 359 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO J 359 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN K 70 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C GLN K 70 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN K 70 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU K 71 " -0.019 2.00e-02 2.50e+03 ... (remaining 4998 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 274 2.49 - 3.09: 23528 3.09 - 3.69: 45916 3.69 - 4.30: 63320 4.30 - 4.90: 103076 Nonbonded interactions: 236114 Sorted by model distance: nonbonded pdb=" O3' G R 105 " pdb="MG MG J1503 " model vdw 1.885 2.170 nonbonded pdb=" OE2 GLU J 479 " pdb=" OG1 THR J1361 " model vdw 1.923 3.040 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 1.935 2.170 nonbonded pdb=" O LYS J 964 " pdb=" OG1 THR J 976 " model vdw 2.002 3.040 nonbonded pdb=" OG SER I 421 " pdb=" OD1 ASP I 423 " model vdw 2.010 3.040 ... (remaining 236109 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 5 through 159 or resid 169 through 233 or (resid 234 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 5 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 234)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 32.950 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.009 0.091 30292 Z= 0.420 Angle : 0.889 17.033 41433 Z= 0.480 Chirality : 0.051 0.232 4798 Planarity : 0.005 0.083 5001 Dihedral : 17.021 125.450 12326 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.68 % Favored : 88.29 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.13), residues: 3449 helix: -0.69 (0.14), residues: 1270 sheet: -2.51 (0.24), residues: 402 loop : -2.43 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 133 TYR 0.030 0.002 TYR J 140 PHE 0.022 0.003 PHE I 464 TRP 0.008 0.002 TRP L 315 HIS 0.016 0.002 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00947 (30284) covalent geometry : angle 0.87947 (41421) hydrogen bonds : bond 0.15532 ( 1226) hydrogen bonds : angle 6.88654 ( 3395) metal coordination : bond 0.03263 ( 8) metal coordination : angle 7.51852 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.7766 (tpp80) cc_final: 0.7235 (tpp80) REVERT: G 186 ASN cc_start: 0.8681 (t0) cc_final: 0.8110 (t0) REVERT: H 174 ASP cc_start: 0.8273 (m-30) cc_final: 0.7941 (m-30) REVERT: H 197 ASP cc_start: 0.6812 (p0) cc_final: 0.6406 (p0) REVERT: I 193 ASN cc_start: 0.8297 (m110) cc_final: 0.7868 (m-40) REVERT: I 790 ASP cc_start: 0.8420 (t70) cc_final: 0.8107 (t70) REVERT: I 1088 ASP cc_start: 0.7792 (p0) cc_final: 0.7516 (p0) REVERT: I 1325 VAL cc_start: 0.8742 (t) cc_final: 0.8340 (t) REVERT: I 1329 GLU cc_start: 0.7999 (mp0) cc_final: 0.7792 (mp0) REVERT: J 160 LEU cc_start: 0.7868 (mm) cc_final: 0.7477 (mp) REVERT: J 201 LEU cc_start: 0.9547 (mt) cc_final: 0.9209 (mt) REVERT: J 868 TRP cc_start: 0.8567 (m100) cc_final: 0.8348 (m100) REVERT: J 1177 ILE cc_start: 0.9329 (mm) cc_final: 0.9045 (tp) REVERT: J 1193 TRP cc_start: 0.7870 (p90) cc_final: 0.7604 (p90) REVERT: K 35 LYS cc_start: 0.7774 (ttpt) cc_final: 0.7012 (tttt) REVERT: K 63 ILE cc_start: 0.8396 (mm) cc_final: 0.8189 (mm) REVERT: K 69 ARG cc_start: 0.9172 (mmm160) cc_final: 0.8850 (mmm160) REVERT: L 288 MET cc_start: 0.9341 (pmm) cc_final: 0.8916 (pmm) REVERT: L 379 MET cc_start: 0.8543 (tmm) cc_final: 0.8230 (tmm) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.1919 time to fit residues: 132.2721 Evaluate side-chains 359 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 ASN G 137 ASN I 450 ASN J 158 GLN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.160538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104568 restraints weight = 48566.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103202 restraints weight = 30852.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103287 restraints weight = 25757.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103954 restraints weight = 24795.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103980 restraints weight = 21318.059| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 30292 Z= 0.149 Angle : 0.694 12.938 41433 Z= 0.358 Chirality : 0.044 0.218 4798 Planarity : 0.005 0.075 5001 Dihedral : 15.188 121.189 5504 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.08 % Allowed : 9.61 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.14), residues: 3449 helix: 0.15 (0.14), residues: 1308 sheet: -2.03 (0.26), residues: 372 loop : -2.13 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 368 TYR 0.016 0.001 TYR J 140 PHE 0.012 0.001 PHE J1034 TRP 0.008 0.001 TRP J 580 HIS 0.003 0.001 HIS J1023 Details of bonding type rmsd covalent geometry : bond 0.00330 (30284) covalent geometry : angle 0.68916 (41421) hydrogen bonds : bond 0.05125 ( 1226) hydrogen bonds : angle 5.15963 ( 3395) metal coordination : bond 0.01328 ( 8) metal coordination : angle 5.06019 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 462 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 186 ASN cc_start: 0.8515 (t0) cc_final: 0.7920 (t0) REVERT: H 41 ASN cc_start: 0.8924 (t0) cc_final: 0.8430 (t0) REVERT: H 95 LYS cc_start: 0.8648 (pttm) cc_final: 0.8361 (pttm) REVERT: I 183 TRP cc_start: 0.8482 (m-90) cc_final: 0.8164 (m-90) REVERT: I 193 ASN cc_start: 0.8541 (m110) cc_final: 0.8230 (m110) REVERT: I 346 TYR cc_start: 0.6709 (m-80) cc_final: 0.6329 (m-80) REVERT: I 461 GLU cc_start: 0.7005 (tt0) cc_final: 0.6701 (tt0) REVERT: I 516 ASP cc_start: 0.8256 (t0) cc_final: 0.7974 (t0) REVERT: I 600 THR cc_start: 0.8542 (m) cc_final: 0.7926 (p) REVERT: I 681 MET cc_start: 0.7877 (mtt) cc_final: 0.7647 (mtp) REVERT: I 685 MET cc_start: 0.7929 (mtm) cc_final: 0.7722 (mtm) REVERT: I 848 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8117 (mt-10) REVERT: I 949 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8052 (tp30) REVERT: I 1030 GLU cc_start: 0.8257 (tp30) cc_final: 0.6986 (tp30) REVERT: I 1033 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8232 (tmm160) REVERT: I 1034 ARG cc_start: 0.8971 (ptm-80) cc_final: 0.7967 (ptm-80) REVERT: I 1036 ILE cc_start: 0.9513 (pt) cc_final: 0.9274 (pt) REVERT: I 1119 MET cc_start: 0.8252 (tpt) cc_final: 0.7891 (tpt) REVERT: I 1292 THR cc_start: 0.9551 (m) cc_final: 0.9172 (p) REVERT: I 1325 VAL cc_start: 0.8915 (t) cc_final: 0.7834 (p) REVERT: J 180 MET cc_start: 0.5506 (tmm) cc_final: 0.5083 (tmm) REVERT: J 201 LEU cc_start: 0.9600 (mt) cc_final: 0.9248 (mt) REVERT: J 307 LEU cc_start: 0.8536 (mp) cc_final: 0.8023 (mp) REVERT: J 500 ILE cc_start: 0.8994 (tt) cc_final: 0.8706 (tt) REVERT: J 728 SER cc_start: 0.9152 (p) cc_final: 0.8933 (p) REVERT: J 1177 ILE cc_start: 0.9186 (mm) cc_final: 0.8952 (tp) REVERT: K 42 GLU cc_start: 0.6484 (pt0) cc_final: 0.6248 (pt0) REVERT: K 63 ILE cc_start: 0.8231 (mm) cc_final: 0.7973 (mm) REVERT: K 69 ARG cc_start: 0.9145 (mmm160) cc_final: 0.8743 (mmm160) REVERT: L 379 MET cc_start: 0.8576 (tmm) cc_final: 0.8070 (tmm) outliers start: 32 outliers final: 19 residues processed: 471 average time/residue: 0.1789 time to fit residues: 135.5258 Evaluate side-chains 401 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 382 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 344 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 93 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 333 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 197 optimal weight: 20.0000 chunk 160 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 338 optimal weight: 9.9990 chunk 137 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 66 HIS I 20 GLN I1017 GLN J 158 GLN J 979 ASN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 70 GLN ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.160100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.103612 restraints weight = 48742.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.102012 restraints weight = 30733.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.102307 restraints weight = 27450.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102764 restraints weight = 26083.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103027 restraints weight = 22160.798| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30292 Z= 0.156 Angle : 0.666 12.802 41433 Z= 0.341 Chirality : 0.043 0.205 4798 Planarity : 0.005 0.178 5001 Dihedral : 15.013 118.969 5504 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.40 % Allowed : 12.62 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.14), residues: 3449 helix: 0.38 (0.14), residues: 1307 sheet: -1.64 (0.25), residues: 397 loop : -2.01 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 122 TYR 0.021 0.001 TYR G 185 PHE 0.011 0.001 PHE I 15 TRP 0.036 0.001 TRP J1193 HIS 0.004 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00354 (30284) covalent geometry : angle 0.66255 (41421) hydrogen bonds : bond 0.04744 ( 1226) hydrogen bonds : angle 4.89154 ( 3395) metal coordination : bond 0.01264 ( 8) metal coordination : angle 4.22212 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 415 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.7357 (tpp80) cc_final: 0.7151 (tpp80) REVERT: G 186 ASN cc_start: 0.8493 (t0) cc_final: 0.7935 (t0) REVERT: H 41 ASN cc_start: 0.8980 (t0) cc_final: 0.8463 (t0) REVERT: H 95 LYS cc_start: 0.8583 (pttm) cc_final: 0.8371 (pttm) REVERT: H 114 ASP cc_start: 0.8549 (t0) cc_final: 0.8243 (t0) REVERT: H 141 SER cc_start: 0.8876 (t) cc_final: 0.8564 (t) REVERT: H 143 ARG cc_start: 0.8357 (mpp80) cc_final: 0.7953 (mpp80) REVERT: I 193 ASN cc_start: 0.8515 (m110) cc_final: 0.7488 (m110) REVERT: I 343 HIS cc_start: 0.8093 (m90) cc_final: 0.7677 (m90) REVERT: I 516 ASP cc_start: 0.8287 (t0) cc_final: 0.8018 (t0) REVERT: I 600 THR cc_start: 0.8516 (m) cc_final: 0.8011 (p) REVERT: I 848 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7939 (mp0) REVERT: I 1034 ARG cc_start: 0.8923 (ptm-80) cc_final: 0.8628 (ptm-80) REVERT: I 1292 THR cc_start: 0.9551 (m) cc_final: 0.9178 (p) REVERT: I 1325 VAL cc_start: 0.8982 (t) cc_final: 0.8172 (p) REVERT: J 180 MET cc_start: 0.5533 (tmm) cc_final: 0.5098 (tmm) REVERT: J 201 LEU cc_start: 0.9588 (mt) cc_final: 0.9340 (mt) REVERT: J 307 LEU cc_start: 0.8489 (mp) cc_final: 0.7983 (mp) REVERT: J 414 GLU cc_start: 0.7788 (tt0) cc_final: 0.7437 (tt0) REVERT: J 500 ILE cc_start: 0.9019 (tt) cc_final: 0.8742 (tt) REVERT: J 728 SER cc_start: 0.9179 (p) cc_final: 0.8969 (p) REVERT: J 1177 ILE cc_start: 0.9163 (mm) cc_final: 0.8943 (tp) REVERT: K 8 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7622 (p0) REVERT: K 42 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: K 67 ARG cc_start: 0.9032 (mmt90) cc_final: 0.8733 (tpp80) REVERT: K 69 ARG cc_start: 0.9055 (mmm160) cc_final: 0.8683 (mmm160) REVERT: L 278 ASP cc_start: 0.9315 (m-30) cc_final: 0.8863 (m-30) REVERT: L 379 MET cc_start: 0.8516 (tmm) cc_final: 0.8018 (tmm) outliers start: 71 outliers final: 37 residues processed: 454 average time/residue: 0.1948 time to fit residues: 143.3126 Evaluate side-chains 415 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 376 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 479 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 140 TYR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 322 optimal weight: 6.9990 chunk 69 optimal weight: 0.0470 chunk 239 optimal weight: 2.9990 chunk 299 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 158 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 272 optimal weight: 20.0000 chunk 254 optimal weight: 2.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 208 ASN I 60 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN K 70 GLN ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.162487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108503 restraints weight = 48563.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105022 restraints weight = 35106.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106658 restraints weight = 30645.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106676 restraints weight = 23503.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106700 restraints weight = 21934.487| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30292 Z= 0.159 Angle : 0.653 13.646 41433 Z= 0.333 Chirality : 0.042 0.266 4798 Planarity : 0.005 0.137 5001 Dihedral : 14.908 117.563 5504 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.64 % Allowed : 14.61 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.14), residues: 3449 helix: 0.49 (0.14), residues: 1317 sheet: -1.37 (0.26), residues: 373 loop : -1.91 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 122 TYR 0.021 0.001 TYR G 185 PHE 0.014 0.001 PHE I 464 TRP 0.035 0.002 TRP J1193 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00365 (30284) covalent geometry : angle 0.65036 (41421) hydrogen bonds : bond 0.04546 ( 1226) hydrogen bonds : angle 4.70260 ( 3395) metal coordination : bond 0.01209 ( 8) metal coordination : angle 3.80763 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 406 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 186 ASN cc_start: 0.8491 (t0) cc_final: 0.8017 (t0) REVERT: H 41 ASN cc_start: 0.8940 (t0) cc_final: 0.8464 (t0) REVERT: H 95 LYS cc_start: 0.8480 (pttm) cc_final: 0.8261 (pttm) REVERT: I 343 HIS cc_start: 0.7750 (m90) cc_final: 0.7350 (m90) REVERT: I 516 ASP cc_start: 0.8322 (t0) cc_final: 0.8104 (t0) REVERT: I 1016 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7280 (pt0) REVERT: I 1033 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8200 (tmm160) REVERT: I 1292 THR cc_start: 0.9544 (m) cc_final: 0.9244 (p) REVERT: I 1325 VAL cc_start: 0.8928 (t) cc_final: 0.8280 (p) REVERT: J 180 MET cc_start: 0.5646 (tmm) cc_final: 0.5199 (tmm) REVERT: J 201 LEU cc_start: 0.9437 (mt) cc_final: 0.9197 (mt) REVERT: J 307 LEU cc_start: 0.8657 (mp) cc_final: 0.8245 (mp) REVERT: J 414 GLU cc_start: 0.7618 (tt0) cc_final: 0.7403 (tt0) REVERT: K 69 ARG cc_start: 0.8689 (mmm160) cc_final: 0.8446 (mmm160) REVERT: L 373 ARG cc_start: 0.8257 (mmp-170) cc_final: 0.7811 (mmp80) REVERT: L 379 MET cc_start: 0.8417 (tmm) cc_final: 0.7950 (tmm) outliers start: 78 outliers final: 53 residues processed: 454 average time/residue: 0.1863 time to fit residues: 136.7185 Evaluate side-chains 427 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 373 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 479 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1016 GLU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 140 TYR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 GLN Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 289 LYS Chi-restraints excluded: chain L residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 32 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 175 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 351 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 271 optimal weight: 40.0000 chunk 150 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 193 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.161615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119382 restraints weight = 48673.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116582 restraints weight = 76100.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118221 restraints weight = 60357.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119925 restraints weight = 33536.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119967 restraints weight = 31022.615| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 30292 Z= 0.192 Angle : 0.668 12.797 41433 Z= 0.341 Chirality : 0.043 0.275 4798 Planarity : 0.005 0.113 5001 Dihedral : 14.867 116.615 5504 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.77 % Allowed : 16.17 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3449 helix: 0.51 (0.14), residues: 1318 sheet: -1.31 (0.26), residues: 394 loop : -1.83 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 122 TYR 0.022 0.001 TYR G 185 PHE 0.012 0.001 PHE I 15 TRP 0.034 0.001 TRP J1193 HIS 0.004 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00447 (30284) covalent geometry : angle 0.66543 (41421) hydrogen bonds : bond 0.04598 ( 1226) hydrogen bonds : angle 4.65546 ( 3395) metal coordination : bond 0.01370 ( 8) metal coordination : angle 3.67682 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 401 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 186 ASN cc_start: 0.8405 (t0) cc_final: 0.8025 (t0) REVERT: H 41 ASN cc_start: 0.8802 (t0) cc_final: 0.8321 (t0) REVERT: I 516 ASP cc_start: 0.8386 (t0) cc_final: 0.8137 (t0) REVERT: I 704 MET cc_start: 0.8216 (ppp) cc_final: 0.7975 (tmm) REVERT: I 1027 LYS cc_start: 0.8269 (ptpp) cc_final: 0.8013 (ptpp) REVERT: I 1292 THR cc_start: 0.9501 (m) cc_final: 0.9196 (p) REVERT: I 1325 VAL cc_start: 0.8753 (t) cc_final: 0.8552 (p) REVERT: J 180 MET cc_start: 0.5744 (tmm) cc_final: 0.5312 (tmm) REVERT: J 307 LEU cc_start: 0.8725 (mp) cc_final: 0.8358 (mp) REVERT: J 624 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.9005 (tt) REVERT: K 8 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7386 (p0) REVERT: K 63 ILE cc_start: 0.8598 (mm) cc_final: 0.8146 (mm) REVERT: L 379 MET cc_start: 0.7976 (tmm) cc_final: 0.7575 (tmm) outliers start: 82 outliers final: 63 residues processed: 450 average time/residue: 0.1816 time to fit residues: 132.5247 Evaluate side-chains 441 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 376 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 186 PHE Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 479 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 GLN Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 289 LYS Chi-restraints excluded: chain L residue 406 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 285 optimal weight: 0.0030 chunk 157 optimal weight: 3.9990 chunk 326 optimal weight: 50.0000 chunk 204 optimal weight: 10.0000 chunk 299 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 321 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 142 optimal weight: 0.0870 chunk 110 optimal weight: 2.9990 overall best weight: 0.9170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 951 GLN K 70 GLN ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.163406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110408 restraints weight = 48320.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107340 restraints weight = 35760.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108580 restraints weight = 33555.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.108805 restraints weight = 25596.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108898 restraints weight = 22703.872| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30292 Z= 0.136 Angle : 0.656 13.348 41433 Z= 0.331 Chirality : 0.042 0.312 4798 Planarity : 0.004 0.092 5001 Dihedral : 14.777 116.049 5504 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.88 % Allowed : 17.52 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3449 helix: 0.60 (0.14), residues: 1317 sheet: -1.20 (0.27), residues: 400 loop : -1.72 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 69 TYR 0.023 0.001 TYR G 185 PHE 0.011 0.001 PHE J 461 TRP 0.032 0.001 TRP J1193 HIS 0.003 0.001 HIS J 430 Details of bonding type rmsd covalent geometry : bond 0.00309 (30284) covalent geometry : angle 0.65302 (41421) hydrogen bonds : bond 0.04275 ( 1226) hydrogen bonds : angle 4.57112 ( 3395) metal coordination : bond 0.01027 ( 8) metal coordination : angle 3.53731 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 404 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ASN cc_start: 0.8832 (t0) cc_final: 0.8369 (t0) REVERT: I 414 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8591 (tp) REVERT: I 516 ASP cc_start: 0.8241 (t0) cc_final: 0.8009 (t0) REVERT: I 848 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: I 1016 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7321 (pt0) REVERT: I 1027 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8178 (ptpp) REVERT: I 1292 THR cc_start: 0.9509 (m) cc_final: 0.9244 (p) REVERT: I 1325 VAL cc_start: 0.8918 (t) cc_final: 0.8677 (p) REVERT: J 307 LEU cc_start: 0.8689 (mp) cc_final: 0.8274 (mp) REVERT: J 414 GLU cc_start: 0.7633 (tt0) cc_final: 0.7419 (tt0) REVERT: J 1027 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8189 (p) REVERT: K 63 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7936 (mm) REVERT: K 64 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8505 (mm) REVERT: K 70 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8058 (pp30) REVERT: L 379 MET cc_start: 0.8235 (tmm) cc_final: 0.7819 (tmm) outliers start: 85 outliers final: 58 residues processed: 453 average time/residue: 0.1777 time to fit residues: 130.4497 Evaluate side-chains 452 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 387 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 479 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 848 GLU Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1016 GLU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 140 TYR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 289 LYS Chi-restraints excluded: chain L residue 406 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 0 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 271 optimal weight: 8.9990 chunk 232 optimal weight: 0.0010 chunk 10 optimal weight: 5.9990 chunk 293 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 326 optimal weight: 50.0000 chunk 291 optimal weight: 5.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 193 ASN I 604 HIS J 45 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.161710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119227 restraints weight = 48479.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117532 restraints weight = 73686.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119607 restraints weight = 59378.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119172 restraints weight = 35218.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120458 restraints weight = 31453.240| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 30292 Z= 0.197 Angle : 0.689 13.672 41433 Z= 0.349 Chirality : 0.043 0.342 4798 Planarity : 0.004 0.077 5001 Dihedral : 14.779 115.269 5504 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.15 % Allowed : 18.17 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3449 helix: 0.56 (0.14), residues: 1320 sheet: -1.15 (0.27), residues: 395 loop : -1.72 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 69 TYR 0.021 0.001 TYR G 185 PHE 0.012 0.001 PHE I 15 TRP 0.029 0.001 TRP J1193 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00462 (30284) covalent geometry : angle 0.68636 (41421) hydrogen bonds : bond 0.04450 ( 1226) hydrogen bonds : angle 4.58072 ( 3395) metal coordination : bond 0.01410 ( 8) metal coordination : angle 3.62989 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 388 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ASN cc_start: 0.8798 (t0) cc_final: 0.8324 (t0) REVERT: I 516 ASP cc_start: 0.8344 (t0) cc_final: 0.8102 (t0) REVERT: I 1016 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6997 (pt0) REVERT: I 1027 LYS cc_start: 0.8345 (ptpp) cc_final: 0.8045 (ptpp) REVERT: I 1292 THR cc_start: 0.9488 (m) cc_final: 0.9215 (p) REVERT: I 1325 VAL cc_start: 0.8840 (t) cc_final: 0.8545 (p) REVERT: J 307 LEU cc_start: 0.8731 (mp) cc_final: 0.8333 (mp) REVERT: J 335 GLN cc_start: 0.7801 (mm110) cc_final: 0.7369 (mm-40) REVERT: J 624 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.9018 (tt) REVERT: J 1027 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7724 (p) REVERT: K 64 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8469 (mm) REVERT: L 379 MET cc_start: 0.7882 (tmm) cc_final: 0.7528 (tmm) outliers start: 93 outliers final: 71 residues processed: 449 average time/residue: 0.1749 time to fit residues: 128.9643 Evaluate side-chains 448 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 373 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 479 LEU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1016 GLU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 140 TYR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 289 LYS Chi-restraints excluded: chain L residue 406 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 243 optimal weight: 0.0970 chunk 182 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 223 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 658 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120362 restraints weight = 48794.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118311 restraints weight = 79327.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120763 restraints weight = 61849.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120263 restraints weight = 39360.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121409 restraints weight = 34942.606| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 30292 Z= 0.185 Angle : 0.695 14.170 41433 Z= 0.351 Chirality : 0.043 0.356 4798 Planarity : 0.004 0.068 5001 Dihedral : 14.764 114.754 5504 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.18 % Allowed : 18.37 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3449 helix: 0.60 (0.15), residues: 1310 sheet: -1.18 (0.26), residues: 403 loop : -1.70 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 69 TYR 0.031 0.001 TYR J 144 PHE 0.016 0.001 PHE I 464 TRP 0.031 0.001 TRP J1193 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00434 (30284) covalent geometry : angle 0.69278 (41421) hydrogen bonds : bond 0.04407 ( 1226) hydrogen bonds : angle 4.58602 ( 3395) metal coordination : bond 0.01314 ( 8) metal coordination : angle 3.44573 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 387 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ASN cc_start: 0.8767 (t0) cc_final: 0.8297 (t0) REVERT: I 516 ASP cc_start: 0.8332 (t0) cc_final: 0.8088 (t0) REVERT: I 600 THR cc_start: 0.8165 (m) cc_final: 0.7848 (p) REVERT: I 1027 LYS cc_start: 0.8280 (ptpp) cc_final: 0.8041 (ptpp) REVERT: I 1033 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7192 (tmm160) REVERT: I 1035 LYS cc_start: 0.8579 (pttp) cc_final: 0.8156 (tttt) REVERT: I 1292 THR cc_start: 0.9476 (m) cc_final: 0.9223 (p) REVERT: J 136 GLU cc_start: 0.7016 (tm-30) cc_final: 0.5226 (tp30) REVERT: J 307 LEU cc_start: 0.8736 (mp) cc_final: 0.8347 (mp) REVERT: J 335 GLN cc_start: 0.7807 (mm110) cc_final: 0.7397 (mm-40) REVERT: J 624 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8927 (tt) REVERT: J 1027 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7625 (p) REVERT: J 1189 MET cc_start: 0.7373 (tmm) cc_final: 0.6899 (mmm) REVERT: K 63 ILE cc_start: 0.8543 (mm) cc_final: 0.8132 (mm) REVERT: K 64 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8536 (mm) REVERT: L 322 MET cc_start: 0.5973 (pmm) cc_final: 0.5662 (pmm) outliers start: 94 outliers final: 74 residues processed: 447 average time/residue: 0.1801 time to fit residues: 132.3642 Evaluate side-chains 452 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 375 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 479 LEU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1016 GLU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1056 LEU Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 289 LYS Chi-restraints excluded: chain L residue 406 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 127 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 273 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 334 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1126 GLN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.163802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120623 restraints weight = 48252.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.117008 restraints weight = 45837.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118857 restraints weight = 45293.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118794 restraints weight = 27652.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119865 restraints weight = 24045.307| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 30292 Z= 0.136 Angle : 0.692 14.689 41433 Z= 0.348 Chirality : 0.042 0.313 4798 Planarity : 0.004 0.064 5001 Dihedral : 14.695 114.254 5504 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.47 % Allowed : 19.25 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3449 helix: 0.69 (0.15), residues: 1311 sheet: -1.09 (0.26), residues: 405 loop : -1.61 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I1033 TYR 0.022 0.001 TYR G 185 PHE 0.017 0.001 PHE I 464 TRP 0.027 0.001 TRP J1193 HIS 0.003 0.001 HIS J 430 Details of bonding type rmsd covalent geometry : bond 0.00313 (30284) covalent geometry : angle 0.69059 (41421) hydrogen bonds : bond 0.04099 ( 1226) hydrogen bonds : angle 4.51255 ( 3395) metal coordination : bond 0.00893 ( 8) metal coordination : angle 3.05585 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 412 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ASN cc_start: 0.8718 (t0) cc_final: 0.8261 (t0) REVERT: H 125 LYS cc_start: 0.7928 (tppt) cc_final: 0.6901 (tppt) REVERT: I 516 ASP cc_start: 0.8298 (t0) cc_final: 0.7990 (t0) REVERT: I 600 THR cc_start: 0.8227 (m) cc_final: 0.7869 (p) REVERT: I 1027 LYS cc_start: 0.8680 (ptpp) cc_final: 0.8218 (ptpp) REVERT: I 1035 LYS cc_start: 0.8895 (pttp) cc_final: 0.8368 (tttt) REVERT: I 1292 THR cc_start: 0.9490 (m) cc_final: 0.9223 (p) REVERT: J 307 LEU cc_start: 0.8662 (mp) cc_final: 0.8224 (mp) REVERT: J 335 GLN cc_start: 0.8031 (mm110) cc_final: 0.7725 (mm-40) REVERT: J 414 GLU cc_start: 0.7695 (tt0) cc_final: 0.7439 (tt0) REVERT: J 624 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8947 (tt) REVERT: J 1027 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8164 (p) REVERT: J 1189 MET cc_start: 0.7661 (tmm) cc_final: 0.7438 (mmm) REVERT: K 56 GLU cc_start: 0.6614 (pp20) cc_final: 0.5736 (pp20) REVERT: K 61 ASN cc_start: 0.8241 (t0) cc_final: 0.7829 (t0) REVERT: K 67 ARG cc_start: 0.9053 (mmt90) cc_final: 0.8502 (mmm-85) REVERT: L 254 GLU cc_start: 0.5837 (pp20) cc_final: 0.5533 (pp20) REVERT: L 322 MET cc_start: 0.6240 (pmm) cc_final: 0.5845 (pmm) outliers start: 73 outliers final: 63 residues processed: 454 average time/residue: 0.1874 time to fit residues: 138.6232 Evaluate side-chains 446 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 381 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1056 LEU Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 289 LYS Chi-restraints excluded: chain L residue 406 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 321 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 252 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 303 optimal weight: 8.9990 chunk 134 optimal weight: 40.0000 chunk 332 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.163825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.121978 restraints weight = 48495.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119733 restraints weight = 76278.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122096 restraints weight = 60832.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121716 restraints weight = 36212.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.122788 restraints weight = 32846.313| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 30292 Z= 0.144 Angle : 0.711 14.681 41433 Z= 0.356 Chirality : 0.043 0.329 4798 Planarity : 0.004 0.061 5001 Dihedral : 14.668 113.627 5504 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.47 % Allowed : 19.62 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3449 helix: 0.63 (0.15), residues: 1323 sheet: -1.16 (0.26), residues: 405 loop : -1.57 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 69 TYR 0.025 0.001 TYR H 177 PHE 0.017 0.001 PHE I 464 TRP 0.027 0.001 TRP J1193 HIS 0.004 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00339 (30284) covalent geometry : angle 0.70987 (41421) hydrogen bonds : bond 0.04079 ( 1226) hydrogen bonds : angle 4.49760 ( 3395) metal coordination : bond 0.00935 ( 8) metal coordination : angle 2.91538 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6898 Ramachandran restraints generated. 3449 Oldfield, 0 Emsley, 3449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 394 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ASN cc_start: 0.8575 (t0) cc_final: 0.8102 (t0) REVERT: H 172 LEU cc_start: 0.8378 (mt) cc_final: 0.8165 (mm) REVERT: I 516 ASP cc_start: 0.8227 (t0) cc_final: 0.7972 (t0) REVERT: I 600 THR cc_start: 0.8072 (m) cc_final: 0.7868 (p) REVERT: I 1027 LYS cc_start: 0.8335 (ptpp) cc_final: 0.8069 (ptpp) REVERT: I 1030 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7548 (mm-30) REVERT: I 1035 LYS cc_start: 0.8639 (pttp) cc_final: 0.8165 (tttt) REVERT: I 1292 THR cc_start: 0.9446 (m) cc_final: 0.9209 (p) REVERT: J 307 LEU cc_start: 0.8616 (mp) cc_final: 0.8208 (mp) REVERT: J 335 GLN cc_start: 0.7857 (mm110) cc_final: 0.7549 (mm-40) REVERT: J 697 MET cc_start: 0.7951 (tmm) cc_final: 0.7710 (tmm) REVERT: J 725 MET cc_start: 0.8788 (mtp) cc_final: 0.8515 (mtm) REVERT: J 1027 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7698 (p) REVERT: K 56 GLU cc_start: 0.6506 (pp20) cc_final: 0.5686 (pp20) REVERT: K 69 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7581 (mmm-85) REVERT: L 254 GLU cc_start: 0.5775 (pp20) cc_final: 0.5561 (pp20) outliers start: 73 outliers final: 65 residues processed: 441 average time/residue: 0.1821 time to fit residues: 130.6555 Evaluate side-chains 453 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 387 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 479 LEU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1016 GLU Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1056 LEU Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 289 LYS Chi-restraints excluded: chain L residue 406 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 261 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 244 optimal weight: 1.9990 chunk 189 optimal weight: 0.5980 chunk 245 optimal weight: 0.9980 chunk 51 optimal weight: 0.0070 chunk 216 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 282 optimal weight: 5.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN J 365 GLN J 424 ASN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.165274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110417 restraints weight = 48541.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107812 restraints weight = 32881.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108877 restraints weight = 29730.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109001 restraints weight = 25918.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109404 restraints weight = 22053.409| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 30292 Z= 0.129 Angle : 0.715 16.162 41433 Z= 0.357 Chirality : 0.042 0.334 4798 Planarity : 0.004 0.059 5001 Dihedral : 14.620 113.014 5504 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.10 % Allowed : 20.23 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 3449 helix: 0.67 (0.15), residues: 1318 sheet: -1.06 (0.26), residues: 406 loop : -1.51 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 709 TYR 0.023 0.001 TYR G 185 PHE 0.021 0.001 PHE I 464 TRP 0.027 0.001 TRP J1193 HIS 0.003 0.000 HIS J 104 Details of bonding type rmsd covalent geometry : bond 0.00298 (30284) covalent geometry : angle 0.71304 (41421) hydrogen bonds : bond 0.03944 ( 1226) hydrogen bonds : angle 4.49869 ( 3395) metal coordination : bond 0.00728 ( 8) metal coordination : angle 2.79189 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5055.51 seconds wall clock time: 88 minutes 9.23 seconds (5289.23 seconds total)