Starting phenix.real_space_refine on Wed Jun 25 21:34:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xui_33470/06_2025/7xui_33470.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xui_33470/06_2025/7xui_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xui_33470/06_2025/7xui_33470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xui_33470/06_2025/7xui_33470.map" model { file = "/net/cci-nas-00/data/ceres_data/7xui_33470/06_2025/7xui_33470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xui_33470/06_2025/7xui_33470.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.98, per 1000 atoms: 0.57 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: 7.87 Conformation dependent library (CDL) restraints added in 3.3 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: 10.53 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: 14.68 Time building geometry restraints manager: 9.10 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: 1.910 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: 1.300 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 81.780 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.920 ------------------------------------------------------------------------------- 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 : 9.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (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 TRP 0.008 0.002 TRP L 315 HIS 0.016 0.002 HIS J 545 PHE 0.022 0.003 PHE I 464 TYR 0.030 0.002 TYR J 140 ARG 0.015 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.15532 ( 1226) hydrogen bonds : angle 6.88654 ( 3395) metal coordination : bond 0.03263 ( 8) metal coordination : angle 7.51852 ( 12) covalent geometry : bond 0.00947 (30284) covalent geometry : angle 0.87947 (41421) *********************** 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 : 3.163 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: 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: 0.8341 (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: 0.9340 (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: 0.4631 time to fit residues: 322.0675 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 : 5.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 1.9990 chunk 269 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 278 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 322 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.159300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.116857 restraints weight = 48385.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113076 restraints weight = 53594.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115135 restraints weight = 50398.323| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 30292 Z= 0.181 Angle : 0.705 12.046 41433 Z= 0.365 Chirality : 0.045 0.221 4798 Planarity : 0.005 0.078 5001 Dihedral : 15.238 121.106 5504 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.32 % Allowed : 9.64 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.14), residues: 3449 helix: 0.06 (0.14), residues: 1312 sheet: -2.03 (0.26), residues: 380 loop : -2.20 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 580 HIS 0.004 0.001 HIS J 545 PHE 0.013 0.002 PHE I1265 TYR 0.016 0.001 TYR J 457 ARG 0.006 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.05333 ( 1226) hydrogen bonds : angle 5.21836 ( 3395) metal coordination : bond 0.01601 ( 8) metal coordination : angle 5.21754 ( 12) covalent geometry : bond 0.00417 (30284) covalent geometry : angle 0.69968 (41421) *********************** 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 485 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 446 time to evaluate : 3.977 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: G 186 ASN cc_start: 0.8515 (t0) cc_final: 0.7976 (t0) REVERT: H 41 ASN cc_start: 0.8968 (t0) cc_final: 0.8461 (t0) REVERT: H 95 LYS cc_start: 0.8527 (pttm) cc_final: 0.8250 (pttm) REVERT: I 183 TRP cc_start: 0.8456 (m-90) cc_final: 0.8199 (m-90) REVERT: I 346 TYR cc_start: 0.6401 (m-80) cc_final: 0.6151 (m-80) REVERT: I 461 GLU cc_start: 0.7006 (tt0) cc_final: 0.6725 (tt0) REVERT: I 516 ASP cc_start: 0.8388 (t0) cc_final: 0.8158 (t0) REVERT: I 600 THR cc_start: 0.8385 (m) cc_final: 0.7845 (p) REVERT: I 681 MET cc_start: 0.7755 (mtt) cc_final: 0.7514 (mtp) REVERT: I 848 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: I 949 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7572 (tp30) REVERT: I 1036 ILE cc_start: 0.9398 (pt) cc_final: 0.9139 (pt) REVERT: I 1119 MET cc_start: 0.8463 (tpt) cc_final: 0.8089 (tpt) REVERT: I 1292 THR cc_start: 0.9529 (m) cc_final: 0.9203 (p) REVERT: I 1325 VAL cc_start: 0.8885 (t) cc_final: 0.7766 (p) REVERT: J 180 MET cc_start: 0.5510 (tmm) cc_final: 0.5115 (tmm) REVERT: J 194 LEU cc_start: 0.8797 (mp) cc_final: 0.8544 (mt) REVERT: J 201 LEU cc_start: 0.9337 (mt) cc_final: 0.9001 (mt) REVERT: J 307 LEU cc_start: 0.8654 (mp) cc_final: 0.8234 (mp) REVERT: J 413 ASP cc_start: 0.8116 (t0) cc_final: 0.7909 (t0) REVERT: J 500 ILE cc_start: 0.9058 (tt) cc_final: 0.8775 (tt) REVERT: K 42 GLU cc_start: 0.6518 (pt0) cc_final: 0.6301 (pt0) REVERT: K 53 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7134 (mt-10) REVERT: K 63 ILE cc_start: 0.8527 (mm) cc_final: 0.8253 (mm) REVERT: L 379 MET cc_start: 0.8264 (tmm) cc_final: 0.7760 (tmm) outliers start: 39 outliers final: 24 residues processed: 459 average time/residue: 0.4918 time to fit residues: 364.2065 Evaluate side-chains 406 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 381 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 848 GLU 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 134 ASP 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 705 THR 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 344 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 92 optimal weight: 0.7980 chunk 304 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 300 optimal weight: 0.8980 chunk 165 optimal weight: 0.3980 chunk 313 optimal weight: 7.9990 chunk 284 optimal weight: 0.0570 chunk 117 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 I 450 ASN I1017 GLN J 158 GLN J 229 GLN J 979 ASN K 31 GLN ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.163915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110151 restraints weight = 48504.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107774 restraints weight = 33597.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109118 restraints weight = 28405.498| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30292 Z= 0.134 Angle : 0.658 13.078 41433 Z= 0.337 Chirality : 0.043 0.228 4798 Planarity : 0.005 0.188 5001 Dihedral : 14.970 118.910 5504 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.37 % Allowed : 12.48 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3449 helix: 0.43 (0.14), residues: 1303 sheet: -1.56 (0.26), residues: 373 loop : -2.00 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP J1193 HIS 0.003 0.001 HIS G 128 PHE 0.012 0.001 PHE I 186 TYR 0.013 0.001 TYR J 679 ARG 0.021 0.000 ARG L 122 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 1226) hydrogen bonds : angle 4.86456 ( 3395) metal coordination : bond 0.01032 ( 8) metal coordination : angle 4.09485 ( 12) covalent geometry : bond 0.00290 (30284) covalent geometry : angle 0.65418 (41421) *********************** 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 506 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 436 time to evaluate : 3.216 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 9 LEU cc_start: 0.8683 (mt) cc_final: 0.7986 (mt) REVERT: G 186 ASN cc_start: 0.8471 (t0) cc_final: 0.7929 (t0) REVERT: H 41 ASN cc_start: 0.8911 (t0) cc_final: 0.8382 (t0) REVERT: H 62 ASP cc_start: 0.8106 (p0) cc_final: 0.7661 (p0) REVERT: H 95 LYS cc_start: 0.8471 (pttm) cc_final: 0.8270 (pttm) REVERT: H 104 LYS cc_start: 0.8075 (tmtt) cc_final: 0.7796 (tmtt) REVERT: H 141 SER cc_start: 0.8814 (t) cc_final: 0.8187 (p) REVERT: H 143 ARG cc_start: 0.8196 (mpp80) cc_final: 0.7942 (mpp80) REVERT: I 343 HIS cc_start: 0.7888 (m90) cc_final: 0.7494 (m90) REVERT: I 461 GLU cc_start: 0.6948 (tt0) cc_final: 0.6709 (tt0) REVERT: I 516 ASP cc_start: 0.8206 (t0) cc_final: 0.7900 (t0) REVERT: I 600 THR cc_start: 0.8410 (m) cc_final: 0.7969 (p) REVERT: I 848 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: I 1292 THR cc_start: 0.9522 (m) cc_final: 0.9195 (p) REVERT: I 1325 VAL cc_start: 0.8995 (t) cc_final: 0.8231 (p) REVERT: J 180 MET cc_start: 0.5611 (tmm) cc_final: 0.5162 (tmm) REVERT: J 194 LEU cc_start: 0.8627 (mp) cc_final: 0.8144 (mt) REVERT: J 201 LEU cc_start: 0.9470 (mt) cc_final: 0.9256 (mt) REVERT: J 414 GLU cc_start: 0.7726 (tt0) cc_final: 0.7489 (tt0) REVERT: J 500 ILE cc_start: 0.8960 (tt) cc_final: 0.8691 (tt) REVERT: K 8 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7482 (p0) REVERT: K 63 ILE cc_start: 0.8411 (mm) cc_final: 0.8202 (mm) REVERT: K 67 ARG cc_start: 0.9022 (mmt90) cc_final: 0.8715 (tpp80) REVERT: K 69 ARG cc_start: 0.8446 (mmm160) cc_final: 0.8180 (mmm160) REVERT: L 379 MET cc_start: 0.8342 (tmm) cc_final: 0.7814 (tmm) outliers start: 70 outliers final: 38 residues processed: 475 average time/residue: 0.4026 time to fit residues: 309.2419 Evaluate side-chains 425 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 385 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 178 SER 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 186 PHE Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 550 VAL 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 848 GLU 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 42 GLU Chi-restraints excluded: chain J residue 134 ASP 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 249 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL 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 J residue 1324 SER Chi-restraints excluded: chain K residue 8 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 167 optimal weight: 0.6980 chunk 286 optimal weight: 40.0000 chunk 317 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 350 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 272 optimal weight: 20.0000 chunk 160 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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** K 29 GLN K 70 GLN ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 342 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.158654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105094 restraints weight = 48847.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.101132 restraints weight = 37613.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102295 restraints weight = 32325.211| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30292 Z= 0.228 Angle : 0.695 13.437 41433 Z= 0.354 Chirality : 0.044 0.327 4798 Planarity : 0.005 0.137 5001 Dihedral : 14.961 117.557 5504 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.71 % Allowed : 15.05 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3449 helix: 0.42 (0.14), residues: 1312 sheet: -1.57 (0.26), residues: 383 loop : -1.97 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP J1193 HIS 0.005 0.001 HIS J 777 PHE 0.014 0.002 PHE I 15 TYR 0.019 0.001 TYR I1018 ARG 0.009 0.000 ARG L 122 Details of bonding type rmsd hydrogen bonds : bond 0.04851 ( 1226) hydrogen bonds : angle 4.82318 ( 3395) metal coordination : bond 0.01594 ( 8) metal coordination : angle 4.00823 ( 12) covalent geometry : bond 0.00531 (30284) covalent geometry : angle 0.69200 (41421) *********************** 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 475 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 395 time to evaluate : 3.230 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: G 186 ASN cc_start: 0.8547 (t0) cc_final: 0.8106 (t0) REVERT: H 41 ASN cc_start: 0.8956 (t0) cc_final: 0.8498 (t0) REVERT: H 95 LYS cc_start: 0.8497 (pttm) cc_final: 0.8270 (pttm) REVERT: I 516 ASP cc_start: 0.8426 (t0) cc_final: 0.8217 (t0) REVERT: I 1325 VAL cc_start: 0.8844 (t) cc_final: 0.8469 (p) REVERT: J 166 LEU cc_start: 0.9365 (pp) cc_final: 0.9094 (pp) REVERT: J 180 MET cc_start: 0.5740 (tmm) cc_final: 0.5351 (tmm) REVERT: J 201 LEU cc_start: 0.9473 (mt) cc_final: 0.9228 (mt) REVERT: J 301 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7678 (mm-30) REVERT: K 8 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7797 (p0) REVERT: K 42 GLU cc_start: 0.6451 (pt0) cc_final: 0.6247 (pt0) REVERT: K 67 ARG cc_start: 0.9002 (mmt90) cc_final: 0.8690 (tpp80) REVERT: K 69 ARG cc_start: 0.8548 (mmm160) cc_final: 0.8160 (mmm160) REVERT: L 278 ASP cc_start: 0.9138 (m-30) cc_final: 0.8642 (m-30) REVERT: L 345 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: L 373 ARG cc_start: 0.8302 (mmp-170) cc_final: 0.7780 (mmp80) REVERT: L 379 MET cc_start: 0.8460 (tmm) cc_final: 0.7991 (tmm) outliers start: 80 outliers final: 52 residues processed: 443 average time/residue: 0.4644 time to fit residues: 334.8167 Evaluate side-chains 428 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 374 time to evaluate : 4.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 178 SER 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 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 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 86 GLU 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 224 LEU 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 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 8 ASP 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 345 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 280 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 165 optimal weight: 0.0970 chunk 197 optimal weight: 20.0000 chunk 242 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 81 optimal weight: 0.0060 chunk 93 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 604 HIS I 658 GLN I 752 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN K 70 GLN ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 342 GLN ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106456 restraints weight = 48396.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104002 restraints weight = 32085.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105133 restraints weight = 26955.789| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30292 Z= 0.174 Angle : 0.662 13.016 41433 Z= 0.336 Chirality : 0.043 0.325 4798 Planarity : 0.005 0.111 5001 Dihedral : 14.884 116.884 5504 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.88 % Allowed : 16.47 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3449 helix: 0.52 (0.14), residues: 1312 sheet: -1.41 (0.26), residues: 388 loop : -1.87 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP J1193 HIS 0.004 0.001 HIS J 777 PHE 0.014 0.001 PHE I 464 TYR 0.019 0.001 TYR J 631 ARG 0.007 0.000 ARG L 122 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 1226) hydrogen bonds : angle 4.69050 ( 3395) metal coordination : bond 0.01242 ( 8) metal coordination : angle 3.75755 ( 12) covalent geometry : bond 0.00401 (30284) covalent geometry : angle 0.65911 (41421) *********************** 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 481 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 396 time to evaluate : 3.433 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: G 186 ASN cc_start: 0.8543 (t0) cc_final: 0.7979 (t0) REVERT: H 41 ASN cc_start: 0.8959 (t0) cc_final: 0.8498 (t0) REVERT: H 95 LYS cc_start: 0.8551 (pttm) cc_final: 0.8331 (pttm) REVERT: H 197 ASP cc_start: 0.6519 (p0) cc_final: 0.6313 (p0) REVERT: I 516 ASP cc_start: 0.8373 (t0) cc_final: 0.8112 (t0) REVERT: I 775 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7716 (tp30) REVERT: I 848 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: I 1016 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7488 (pt0) REVERT: I 1292 THR cc_start: 0.9527 (m) cc_final: 0.9187 (p) REVERT: I 1325 VAL cc_start: 0.8891 (t) cc_final: 0.8617 (p) REVERT: J 180 MET cc_start: 0.5692 (tmm) cc_final: 0.5219 (tmm) REVERT: J 201 LEU cc_start: 0.9493 (mt) cc_final: 0.9224 (mt) REVERT: J 301 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7739 (mm-30) REVERT: J 624 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9105 (tt) REVERT: K 8 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7859 (p0) REVERT: K 63 ILE cc_start: 0.8314 (mm) cc_final: 0.7949 (mm) REVERT: K 64 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8269 (mm) REVERT: K 67 ARG cc_start: 0.8976 (mmt90) cc_final: 0.8707 (tpp80) REVERT: K 69 ARG cc_start: 0.8528 (mmm160) cc_final: 0.8274 (mmm160) REVERT: L 365 MET cc_start: 0.7758 (ppp) cc_final: 0.7480 (ppp) REVERT: L 379 MET cc_start: 0.8435 (tmm) cc_final: 0.8049 (tmm) outliers start: 85 outliers final: 60 residues processed: 446 average time/residue: 0.3998 time to fit residues: 290.3175 Evaluate side-chains 436 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 370 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 33 ARG 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 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 90 VAL 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 456 VAL 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 775 GLU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 848 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 J residue 42 GLU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 139 LEU 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 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 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 J residue 1370 MET 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 64 LEU Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 289 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 156 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 332 optimal weight: 50.0000 chunk 119 optimal weight: 0.9990 chunk 341 optimal weight: 20.0000 chunk 256 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 229 GLN J 424 ASN K 29 GLN ** 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** L 406 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.162859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109133 restraints weight = 48380.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106053 restraints weight = 35726.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107447 restraints weight = 29742.660| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 30292 Z= 0.143 Angle : 0.652 13.291 41433 Z= 0.331 Chirality : 0.042 0.305 4798 Planarity : 0.004 0.092 5001 Dihedral : 14.802 116.215 5504 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.18 % Allowed : 17.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3449 helix: 0.60 (0.14), residues: 1319 sheet: -1.28 (0.26), residues: 396 loop : -1.78 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP J1193 HIS 0.005 0.001 HIS J 80 PHE 0.013 0.001 PHE I 464 TYR 0.019 0.001 TYR J1186 ARG 0.006 0.000 ARG L 122 Details of bonding type rmsd hydrogen bonds : bond 0.04334 ( 1226) hydrogen bonds : angle 4.59076 ( 3395) metal coordination : bond 0.01027 ( 8) metal coordination : angle 3.40839 ( 12) covalent geometry : bond 0.00330 (30284) covalent geometry : angle 0.64990 (41421) *********************** 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 492 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 398 time to evaluate : 3.540 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: H 41 ASN cc_start: 0.8858 (t0) cc_final: 0.8407 (t0) REVERT: I 414 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8603 (tp) REVERT: I 516 ASP cc_start: 0.8270 (t0) cc_final: 0.8057 (t0) REVERT: I 848 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: I 1016 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: I 1035 LYS cc_start: 0.8957 (pttp) cc_final: 0.8743 (pttm) REVERT: I 1292 THR cc_start: 0.9496 (m) cc_final: 0.9230 (p) REVERT: I 1325 VAL cc_start: 0.8903 (t) cc_final: 0.8492 (p) REVERT: J 201 LEU cc_start: 0.9423 (mt) cc_final: 0.9219 (mt) REVERT: J 414 GLU cc_start: 0.7627 (tt0) cc_final: 0.7390 (tt0) REVERT: J 624 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9047 (tt) REVERT: J 1027 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8304 (p) REVERT: K 8 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7846 (p0) REVERT: K 63 ILE cc_start: 0.8388 (mm) cc_final: 0.7984 (mm) REVERT: K 64 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8331 (mm) REVERT: K 69 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7992 (mmm160) REVERT: L 413 MET cc_start: 0.7652 (mmm) cc_final: 0.7347 (mmm) outliers start: 94 outliers final: 63 residues processed: 457 average time/residue: 0.4169 time to fit residues: 310.7399 Evaluate side-chains 448 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 378 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 33 ARG 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 54 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 90 VAL 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 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 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 741 MET Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 848 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 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 135 ILE 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 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 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 J residue 1370 MET 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 64 LEU Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 289 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 308 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 212 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 177 optimal weight: 0.0170 chunk 140 optimal weight: 9.9990 chunk 223 optimal weight: 0.0970 chunk 174 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 951 GLN K 29 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** L 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.165354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110889 restraints weight = 48233.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108833 restraints weight = 31737.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109864 restraints weight = 27123.910| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 30292 Z= 0.120 Angle : 0.654 14.109 41433 Z= 0.329 Chirality : 0.042 0.284 4798 Planarity : 0.004 0.075 5001 Dihedral : 14.685 115.378 5504 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.54 % Allowed : 18.37 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3449 helix: 0.73 (0.15), residues: 1316 sheet: -1.06 (0.26), residues: 394 loop : -1.69 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP J1193 HIS 0.003 0.001 HIS J 104 PHE 0.014 0.001 PHE I 464 TYR 0.016 0.001 TYR J1186 ARG 0.008 0.000 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 1226) hydrogen bonds : angle 4.52176 ( 3395) metal coordination : bond 0.00761 ( 8) metal coordination : angle 3.24993 ( 12) covalent geometry : bond 0.00272 (30284) covalent geometry : angle 0.65182 (41421) *********************** 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 489 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 414 time to evaluate : 3.203 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: symmetry clash REVERT: G 56 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8780 (t) REVERT: G 95 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8519 (mtpp) REVERT: H 41 ASN cc_start: 0.8761 (t0) cc_final: 0.8301 (t0) REVERT: H 199 ASP cc_start: 0.7885 (m-30) cc_final: 0.7588 (m-30) REVERT: I 414 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8533 (tp) REVERT: I 516 ASP cc_start: 0.8168 (t0) cc_final: 0.7923 (t0) REVERT: I 600 THR cc_start: 0.8353 (m) cc_final: 0.7956 (p) REVERT: I 848 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7795 (pm20) REVERT: I 1016 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7518 (pt0) REVERT: I 1085 MET cc_start: 0.8496 (mmt) cc_final: 0.8166 (mmt) REVERT: I 1292 THR cc_start: 0.9488 (m) cc_final: 0.9214 (p) REVERT: J 201 LEU cc_start: 0.9487 (mt) cc_final: 0.9220 (mt) REVERT: J 335 GLN cc_start: 0.8060 (mm110) cc_final: 0.7741 (mm-40) REVERT: J 624 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8976 (tt) REVERT: J 1027 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8493 (p) REVERT: J 1189 MET cc_start: 0.7713 (tmm) cc_final: 0.7373 (tpt) REVERT: K 8 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.6766 (p0) REVERT: K 55 GLU cc_start: 0.7702 (tm-30) cc_final: 0.6941 (tm-30) REVERT: K 69 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8157 (mmm160) outliers start: 75 outliers final: 50 residues processed: 460 average time/residue: 0.4363 time to fit residues: 324.0825 Evaluate side-chains 441 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 385 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 178 SER 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 I residue 30 ILE Chi-restraints excluded: chain I residue 90 VAL 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 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 826 ASP 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 J residue 42 GLU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 140 TYR Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 283 LEU 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 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 1324 SER Chi-restraints excluded: chain K residue 8 ASP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 83 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 294 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 chunk 210 optimal weight: 0.0770 chunk 78 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 chunk 252 optimal weight: 0.2980 chunk 291 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 45 ASN J 365 GLN K 29 GLN ** 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** ** L 406 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 = 0.165311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110872 restraints weight = 48679.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107849 restraints weight = 33973.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109985 restraints weight = 27872.072| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 30292 Z= 0.124 Angle : 0.679 18.283 41433 Z= 0.339 Chirality : 0.042 0.284 4798 Planarity : 0.004 0.066 5001 Dihedral : 14.630 114.485 5504 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.40 % Allowed : 19.08 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3449 helix: 0.74 (0.15), residues: 1317 sheet: -1.02 (0.27), residues: 393 loop : -1.58 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J1193 HIS 0.003 0.000 HIS J 104 PHE 0.017 0.001 PHE I 464 TYR 0.017 0.001 TYR H 177 ARG 0.006 0.000 ARG H 191 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 1226) hydrogen bonds : angle 4.47498 ( 3395) metal coordination : bond 0.00818 ( 8) metal coordination : angle 3.41744 ( 12) covalent geometry : bond 0.00284 (30284) covalent geometry : angle 0.67630 (41421) *********************** 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 469 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 398 time to evaluate : 3.358 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 56 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8817 (t) REVERT: H 125 LYS cc_start: 0.8331 (tppt) cc_final: 0.7666 (tppt) REVERT: H 199 ASP cc_start: 0.7857 (m-30) cc_final: 0.7557 (m-30) REVERT: I 414 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8533 (tp) REVERT: I 516 ASP cc_start: 0.8129 (t0) cc_final: 0.7880 (t0) REVERT: I 600 THR cc_start: 0.8335 (m) cc_final: 0.7958 (p) REVERT: I 848 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: I 1085 MET cc_start: 0.8485 (mmt) cc_final: 0.8128 (mmt) REVERT: I 1292 THR cc_start: 0.9469 (m) cc_final: 0.9225 (p) REVERT: J 201 LEU cc_start: 0.9476 (mt) cc_final: 0.9211 (mt) REVERT: J 301 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7739 (mm-30) REVERT: J 335 GLN cc_start: 0.8073 (mm110) cc_final: 0.7745 (mm-40) REVERT: J 1027 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8541 (p) REVERT: K 8 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7539 (p0) REVERT: K 69 ARG cc_start: 0.8528 (mmm160) cc_final: 0.8160 (mmm160) REVERT: L 254 GLU cc_start: 0.6139 (pp20) cc_final: 0.5870 (pp20) REVERT: L 278 ASP cc_start: 0.9207 (m-30) cc_final: 0.8968 (p0) REVERT: L 322 MET cc_start: 0.6402 (pmm) cc_final: 0.6021 (pmm) outliers start: 71 outliers final: 52 residues processed: 441 average time/residue: 0.4053 time to fit residues: 291.1136 Evaluate side-chains 443 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 386 time to evaluate : 3.276 ------------------------------------------------------------------------------- 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 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 I residue 30 ILE Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 414 ILE 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 550 VAL 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 741 MET Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 848 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 J residue 24 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 283 LEU 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 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 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 L residue 288 MET Chi-restraints excluded: chain L residue 289 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 285 optimal weight: 0.9980 chunk 340 optimal weight: 8.9990 chunk 287 optimal weight: 10.0000 chunk 209 optimal weight: 0.0770 chunk 1 optimal weight: 0.2980 chunk 63 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN K 29 GLN ** 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** L 406 GLN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.165687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111336 restraints weight = 48289.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108452 restraints weight = 31337.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109356 restraints weight = 29169.969| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 30292 Z= 0.129 Angle : 0.707 15.728 41433 Z= 0.353 Chirality : 0.042 0.271 4798 Planarity : 0.004 0.063 5001 Dihedral : 14.602 113.893 5504 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.13 % Allowed : 19.65 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3449 helix: 0.73 (0.15), residues: 1330 sheet: -1.02 (0.27), residues: 409 loop : -1.51 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J1193 HIS 0.003 0.000 HIS J 104 PHE 0.023 0.001 PHE I 464 TYR 0.023 0.001 TYR H 177 ARG 0.006 0.000 ARG H 191 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 1226) hydrogen bonds : angle 4.46973 ( 3395) metal coordination : bond 0.00772 ( 8) metal coordination : angle 3.05851 ( 12) covalent geometry : bond 0.00299 (30284) covalent geometry : angle 0.70540 (41421) *********************** 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 474 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 411 time to evaluate : 3.555 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: G 56 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8843 (t) REVERT: G 80 GLU cc_start: 0.8222 (tp30) cc_final: 0.8001 (tp30) REVERT: H 41 ASN cc_start: 0.8633 (t0) cc_final: 0.8329 (t0) REVERT: H 199 ASP cc_start: 0.7826 (m-30) cc_final: 0.7490 (m-30) REVERT: I 414 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8549 (tp) REVERT: I 516 ASP cc_start: 0.8091 (t0) cc_final: 0.7857 (t0) REVERT: I 600 THR cc_start: 0.8346 (m) cc_final: 0.8012 (p) REVERT: I 848 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7773 (pm20) REVERT: J 86 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: J 165 TYR cc_start: 0.8947 (t80) cc_final: 0.8601 (t80) REVERT: J 186 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8058 (tm-30) REVERT: J 201 LEU cc_start: 0.9506 (mt) cc_final: 0.9239 (mt) REVERT: J 301 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7724 (mm-30) REVERT: J 335 GLN cc_start: 0.8098 (mm110) cc_final: 0.7765 (mm-40) REVERT: J 1027 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8621 (p) REVERT: J 1189 MET cc_start: 0.7766 (tpt) cc_final: 0.7427 (tpp) REVERT: J 1293 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6991 (mm-30) REVERT: K 8 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.6665 (p0) REVERT: K 55 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7134 (tm-30) REVERT: K 63 ILE cc_start: 0.8092 (mm) cc_final: 0.7795 (mm) REVERT: K 69 ARG cc_start: 0.8608 (mmm160) cc_final: 0.8380 (mmm160) REVERT: L 254 GLU cc_start: 0.6154 (pp20) cc_final: 0.5917 (pp20) REVERT: L 278 ASP cc_start: 0.9271 (m-30) cc_final: 0.9025 (p0) REVERT: L 322 MET cc_start: 0.6384 (pmm) cc_final: 0.6171 (pmm) outliers start: 63 outliers final: 53 residues processed: 447 average time/residue: 0.4005 time to fit residues: 292.9853 Evaluate side-chains 443 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 384 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL 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 I residue 30 ILE Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 446 ASP 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 550 VAL 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 741 MET Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 848 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 J residue 24 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 140 TYR Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 283 LEU 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 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 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 L residue 288 MET Chi-restraints excluded: chain L residue 289 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 290 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 chunk 296 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 331 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 299 optimal weight: 0.3980 chunk 323 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN K 29 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.164274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125706 restraints weight = 48704.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121483 restraints weight = 67439.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123124 restraints weight = 61479.819| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 30292 Z= 0.158 Angle : 0.748 22.511 41433 Z= 0.372 Chirality : 0.043 0.290 4798 Planarity : 0.004 0.065 5001 Dihedral : 14.615 113.160 5504 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.00 % Allowed : 20.30 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3449 helix: 0.67 (0.15), residues: 1321 sheet: -1.03 (0.26), residues: 411 loop : -1.52 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J1193 HIS 0.004 0.001 HIS J 450 PHE 0.023 0.001 PHE I 464 TYR 0.024 0.001 TYR H 177 ARG 0.012 0.000 ARG I 368 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 1226) hydrogen bonds : angle 4.54168 ( 3395) metal coordination : bond 0.01048 ( 8) metal coordination : angle 3.02102 ( 12) covalent geometry : bond 0.00371 (30284) covalent geometry : angle 0.74601 (41421) ********************** 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 451 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 392 time to evaluate : 3.139 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 199 ASP cc_start: 0.7550 (m-30) cc_final: 0.7339 (m-30) REVERT: I 516 ASP cc_start: 0.8244 (t0) cc_final: 0.8007 (t0) REVERT: J 335 GLN cc_start: 0.7882 (mm110) cc_final: 0.7599 (mm-40) REVERT: J 1027 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7730 (p) REVERT: J 1189 MET cc_start: 0.7479 (tpt) cc_final: 0.7206 (tpp) REVERT: K 8 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.6579 (p0) REVERT: K 55 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7083 (tm-30) outliers start: 59 outliers final: 52 residues processed: 426 average time/residue: 0.3844 time to fit residues: 268.9998 Evaluate side-chains 432 residues out of total 2964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 378 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL 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 I residue 30 ILE Chi-restraints excluded: chain I residue 90 VAL 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 550 VAL 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 741 MET Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 826 ASP 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 1329 GLU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 214 ARG Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 283 LEU 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 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 1285 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 L residue 288 MET Chi-restraints excluded: chain L residue 289 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 76 optimal weight: 9.9990 chunk 225 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 331 optimal weight: 0.0770 chunk 173 optimal weight: 0.3980 chunk 237 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 345 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1126 GLN K 29 GLN ** 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 = 0.4113 r_free = 0.4113 target = 0.164574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123143 restraints weight = 48449.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119413 restraints weight = 63286.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122110 restraints weight = 57516.530| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3451 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= 0.148 Angle : 0.741 18.522 41433 Z= 0.370 Chirality : 0.043 0.319 4798 Planarity : 0.004 0.066 5001 Dihedral : 14.605 112.662 5504 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.00 % Allowed : 20.26 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3449 helix: 0.65 (0.15), residues: 1319 sheet: -1.00 (0.27), residues: 397 loop : -1.48 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J1193 HIS 0.003 0.001 HIS J 450 PHE 0.024 0.001 PHE I 464 TYR 0.025 0.001 TYR H 177 ARG 0.013 0.000 ARG I 368 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 1226) hydrogen bonds : angle 4.53482 ( 3395) metal coordination : bond 0.00988 ( 8) metal coordination : angle 3.15831 ( 12) covalent geometry : bond 0.00346 (30284) covalent geometry : angle 0.73887 (41421) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10853.16 seconds wall clock time: 190 minutes 8.99 seconds (11408.99 seconds total)