Starting phenix.real_space_refine on Sat Aug 8 08:00:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8egb_28113/08_2026/8egb_28113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8egb_28113/08_2026/8egb_28113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8egb_28113/08_2026/8egb_28113.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8egb_28113/08_2026/8egb_28113.cif" model { file = "/net/cci-nas-00/data/ceres_data/8egb_28113/08_2026/8egb_28113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8egb_28113/08_2026/8egb_28113.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8egb_28113/08_2026/8egb_28113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8egb_28113/08_2026/8egb_28113.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 69 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 16356 2.51 5 N 4653 2.21 5 O 5233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26419 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 548 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "B" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 236 Classifications: {'RNAv2': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "G" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1684 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10555 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 10360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10360 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1278} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 79} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 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 15796 SG CYS J 70 111.274 60.694 69.590 1.00 94.03 S ATOM 15810 SG CYS J 72 112.697 57.286 69.070 1.00 98.26 S ATOM 15918 SG CYS J 85 113.603 60.145 66.663 1.00 97.17 S ATOM 15942 SG CYS J 88 110.111 58.865 66.547 1.00 95.31 S ATOM 21618 SG CYS J 814 85.843 121.267 78.728 1.00 66.05 S ATOM 22183 SG CYS J 888 85.083 117.612 77.772 1.00 61.83 S ATOM 22234 SG CYS J 895 85.780 118.577 81.374 1.00 58.10 S ATOM 22255 SG CYS J 898 82.613 119.711 79.946 1.00 57.60 S Time building chain proxies: 5.15, per 1000 atoms: 0.19 Number of scatterers: 26419 At special positions: 0 Unit cell: (143, 159.9, 166.4, 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 105 16.00 P 69 15.00 Mg 1 11.99 O 5233 8.00 N 4653 7.00 C 16356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 939.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5900 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 44 sheets defined 37.7% alpha, 14.9% beta 30 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'G' and resid 230 through 232 No H-bonds generated for 'chain 'G' and resid 230 through 232' Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.750A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 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: 3.526A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.638A pdb=" N PHE I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.543A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.862A 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: 4.146A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 290 through 295 removed outlier: 3.716A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.730A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.831A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 451 removed outlier: 3.958A pdb=" N ARG I 451 " --> pdb=" O LEU I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.670A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.863A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 613 removed outlier: 3.643A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 613' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.865A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 898 through 907 Processing helix chain 'I' and resid 942 through 980 Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.816A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.629A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.538A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 4.165A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 removed outlier: 3.506A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.832A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.629A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU I1333 " --> pdb=" O GLU I1329 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 128 removed outlier: 3.517A pdb=" N LEU J 128 " --> pdb=" O ILE J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 193 through 209 removed outlier: 3.648A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN J 209 " --> pdb=" O LEU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 removed outlier: 3.589A pdb=" N LYS J 222 " --> pdb=" O THR J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 307 Processing helix chain 'J' and resid 326 through 331 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.502A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 417 removed outlier: 3.688A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.692A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 581 Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.641A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.669A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 removed outlier: 3.929A pdb=" N ILE J 653 " --> pdb=" O LYS J 649 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.594A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.537A pdb=" N TYR J 899 " --> pdb=" O CYS J 895 " (cutoff:3.500A) Processing helix chain 'J' and resid 915 through 930 Proline residue: J 926 - end of helix removed outlier: 3.564A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.522A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.395A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1325 removed outlier: 4.047A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1373 removed outlier: 3.523A pdb=" N ARG J1373 " --> pdb=" O ARG J1369 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 removed outlier: 4.438A pdb=" N GLY K 33 " --> pdb=" O GLN K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 84 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 16 removed outlier: 5.138A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.547A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.953A pdb=" N GLY G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.580A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 18 removed outlier: 5.338A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 104 removed outlier: 7.837A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY H 53 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.781A pdb=" N GLY H 108 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU H 133 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.585A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.322A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 147 through 148 removed outlier: 6.353A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.633A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 255 through 256 removed outlier: 3.594A pdb=" N ILE I 255 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL I 263 " --> pdb=" O ILE I 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 301 through 302 removed outlier: 7.254A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.524A pdb=" N THR I 589 " --> pdb=" O LEU I 606 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.558A pdb=" N ILE I 616 " --> pdb=" O ARG I 637 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 3.869A pdb=" N ALA I 784 " --> pdb=" O ALA I 716 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 750 through 751 removed outlier: 6.786A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 3.527A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET I1230 " --> pdb=" O MET I 800 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET I 800 " --> pdb=" O MET I1230 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 3.527A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 841 removed outlier: 6.556A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 887 through 888 removed outlier: 3.737A pdb=" N THR I 888 " --> pdb=" O LYS I 914 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS I 914 " --> pdb=" O THR I 888 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.514A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1269 through 1270 removed outlier: 3.521A pdb=" N LYS J 345 " --> pdb=" O PHE I1270 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 1335 through 1339 removed outlier: 3.515A pdb=" N GLU I1338 " --> pdb=" O LYS J 21 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.071A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.655A pdb=" N VAL J 145 " --> pdb=" O LYS J 179 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE1, first strand: chain 'J' and resid 848 through 849 removed outlier: 7.385A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 949 through 951 removed outlier: 6.961A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.691A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1024 through 1026 Processing sheet with id=AE5, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.573A pdb=" N VAL J1081 " --> pdb=" O PHE J1034 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.708A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1187 through 1189 removed outlier: 3.578A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.623A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) 1014 hydrogen bonds defined for protein. 2850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4461 1.29 - 1.43: 6499 1.43 - 1.56: 15655 1.56 - 1.69: 153 1.69 - 1.83: 188 Bond restraints: 26956 Sorted by residual: bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.827 -0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.822 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.728 -0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.728 -0.196 2.00e-02 2.50e+03 9.59e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.702 -0.160 2.00e-02 2.50e+03 6.41e+01 ... (remaining 26951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 36119 2.18 - 4.35: 555 4.35 - 6.53: 40 6.53 - 8.71: 11 8.71 - 10.88: 2 Bond angle restraints: 36727 Sorted by residual: angle pdb=" C3' DC A 5 " pdb=" O3' DC A 5 " pdb=" P DC A 6 " ideal model delta sigma weight residual 119.70 128.03 -8.33 1.20e+00 6.94e-01 4.81e+01 angle pdb=" CA PRO I 897 " pdb=" N PRO I 897 " pdb=" CD PRO I 897 " ideal model delta sigma weight residual 112.00 103.37 8.63 1.40e+00 5.10e-01 3.80e+01 angle pdb=" O4' DC A 6 " pdb=" C4' DC A 6 " pdb=" C3' DC A 6 " ideal model delta sigma weight residual 106.00 102.59 3.41 6.00e-01 2.78e+00 3.23e+01 angle pdb=" N ASP I 915 " pdb=" CA ASP I 915 " pdb=" C ASP I 915 " ideal model delta sigma weight residual 108.23 117.37 -9.14 1.72e+00 3.38e-01 2.82e+01 angle pdb=" N ALA J 315 " pdb=" CA ALA J 315 " pdb=" C ALA J 315 " ideal model delta sigma weight residual 109.59 102.29 7.30 1.47e+00 4.63e-01 2.47e+01 ... (remaining 36722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 15998 35.86 - 71.72: 335 71.72 - 107.57: 21 107.57 - 143.43: 0 143.43 - 179.29: 2 Dihedral angle restraints: 16356 sinusoidal: 7183 harmonic: 9173 Sorted by residual: dihedral pdb=" C4' G R 7 " pdb=" C3' G R 7 " pdb=" C2' G R 7 " pdb=" C1' G R 7 " ideal model delta sinusoidal sigma weight residual 36.35 -37.01 73.36 1 3.10e+00 1.04e-01 7.13e+02 dihedral pdb=" O4' G R 7 " pdb=" C4' G R 7 " pdb=" C3' G R 7 " pdb=" C2' G R 7 " ideal model delta sinusoidal sigma weight residual -35.15 24.14 -59.29 1 4.00e+00 6.25e-02 2.94e+02 dihedral pdb=" O4' G R 7 " pdb=" C2' G R 7 " pdb=" C1' G R 7 " pdb=" C3' G R 7 " ideal model delta sinusoidal sigma weight residual -94.41 -38.21 -56.19 3 3.80e+00 6.93e-02 1.46e+02 ... (remaining 16353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3886 0.094 - 0.187: 313 0.187 - 0.281: 19 0.281 - 0.374: 3 0.374 - 0.468: 1 Chirality restraints: 4222 Sorted by residual: chirality pdb=" CA PRO I 897 " pdb=" N PRO I 897 " pdb=" C PRO I 897 " pdb=" CB PRO I 897 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.85 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C19 1N7 I1402 " pdb=" C18 1N7 I1402 " pdb=" C2 1N7 I1402 " pdb=" C3 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.53 -2.85 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 4219 not shown) Planarity restraints: 4556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 896 " 0.097 5.00e-02 4.00e+02 1.44e-01 3.30e+01 pdb=" N PRO I 897 " -0.248 5.00e-02 4.00e+02 pdb=" CA PRO I 897 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO I 897 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 892 " -0.026 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C GLU I 892 " 0.088 2.00e-02 2.50e+03 pdb=" O GLU I 892 " -0.033 2.00e-02 2.50e+03 pdb=" N THR I 893 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 515 " -0.384 9.50e-02 1.11e+02 1.73e-01 1.94e+01 pdb=" NE ARG J 515 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG J 515 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG J 515 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG J 515 " -0.007 2.00e-02 2.50e+03 ... (remaining 4553 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 277 2.58 - 3.16: 22696 3.16 - 3.74: 40014 3.74 - 4.32: 54669 4.32 - 4.90: 91498 Nonbonded interactions: 209154 Sorted by model distance: nonbonded pdb=" O LEU J 930 " pdb=" OG1 THR J 931 " model vdw 2.001 3.040 nonbonded pdb=" O GLN I1288 " pdb=" OG1 THR I1292 " model vdw 2.011 3.040 nonbonded pdb=" O3' G R 16 " pdb="MG MG J1501 " model vdw 2.014 2.170 nonbonded pdb=" OE1 GLU I 50 " pdb=" OH TYR I 70 " model vdw 2.027 3.040 nonbonded pdb=" O ASP I 516 " pdb=" OG SER I 522 " model vdw 2.038 3.040 ... (remaining 209149 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 158 or resid 169 through 232)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.730 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.006 0.295 26964 Z= 0.333 Angle : 0.653 10.884 36739 Z= 0.393 Chirality : 0.049 0.468 4222 Planarity : 0.005 0.173 4556 Dihedral : 14.508 179.289 10456 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.72 % Favored : 95.25 % Rotamer: Outliers : 0.11 % Allowed : 0.18 % Favored : 99.70 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 3179 helix: 1.47 (0.16), residues: 1086 sheet: -0.38 (0.28), residues: 364 loop : -1.42 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG J 311 TYR 0.015 0.001 TYR I1281 PHE 0.015 0.001 PHE J 719 TRP 0.023 0.001 TRP J 115 HIS 0.011 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.33 (26956) covalent geometry : angle 0.65074 / 0.39 (36727) hydrogen bonds : bond 0.16859 / 19.04 ( 1087) hydrogen bonds : angle 6.55739 / 6.50 ( 3002) metal coordination : bond 0.00674 / 0.57 ( 8) metal coordination : angle 3.23173 / 6.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 352 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.7933 (m110) cc_final: 0.7373 (m110) REVERT: I 286 GLU cc_start: 0.6824 (mt-10) cc_final: 0.5475 (pm20) REVERT: I 337 PHE cc_start: 0.8182 (t80) cc_final: 0.7973 (t80) REVERT: I 403 MET cc_start: 0.8097 (ttt) cc_final: 0.7896 (ttp) REVERT: I 515 MET cc_start: 0.8131 (ttp) cc_final: 0.7771 (ttt) REVERT: J 869 CYS cc_start: 0.8264 (m) cc_final: 0.7900 (m) REVERT: J 870 ASP cc_start: 0.7505 (m-30) cc_final: 0.7274 (m-30) outliers start: 3 outliers final: 1 residues processed: 355 average time/residue: 0.1493 time to fit residues: 88.4235 Evaluate side-chains 266 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 917 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN H 37 HIS H 66 HIS H 75 GLN H 194 GLN I 69 GLN I 150 HIS I 165 HIS I 620 ASN I 799 ASN J 545 HIS ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1023 HIS J1244 GLN K 61 ASN K 73 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.099741 restraints weight = 43613.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100525 restraints weight = 25001.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100811 restraints weight = 19746.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.101250 restraints weight = 17381.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.101397 restraints weight = 15451.015| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 26964 Z= 0.301 Angle : 0.734 12.609 36739 Z= 0.378 Chirality : 0.049 0.879 4222 Planarity : 0.006 0.143 4556 Dihedral : 13.492 172.759 4250 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.15 % Rotamer: Outliers : 1.33 % Allowed : 7.75 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3179 helix: 1.05 (0.16), residues: 1108 sheet: -0.67 (0.26), residues: 406 loop : -1.47 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 515 TYR 0.021 0.002 TYR J1365 PHE 0.015 0.002 PHE J 620 TRP 0.019 0.002 TRP J 115 HIS 0.022 0.002 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.30 (26956) covalent geometry : angle 0.73084 / 0.38 (36727) hydrogen bonds : bond 0.05101 / 5.51 ( 1087) hydrogen bonds : angle 5.21455 / 5.46 ( 3002) metal coordination : bond 0.01508 / 1.45 ( 8) metal coordination : angle 3.72794 / 6.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8360 (m110) cc_final: 0.7720 (m110) REVERT: I 115 LYS cc_start: 0.6218 (mtmt) cc_final: 0.5440 (mtmm) REVERT: I 286 GLU cc_start: 0.7155 (mt-10) cc_final: 0.5600 (pm20) REVERT: I 370 MET cc_start: 0.7635 (mmm) cc_final: 0.7056 (mmm) REVERT: I 445 ILE cc_start: 0.8206 (mm) cc_final: 0.7956 (pt) REVERT: I 488 MET cc_start: 0.2640 (mmt) cc_final: 0.2390 (mmt) REVERT: I 1170 MET cc_start: 0.8254 (tpt) cc_final: 0.8009 (tpp) REVERT: J 52 GLU cc_start: 0.5923 (mm-30) cc_final: 0.5645 (mm-30) REVERT: J 198 CYS cc_start: 0.8103 (t) cc_final: 0.7699 (t) REVERT: J 311 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7351 (mmt90) REVERT: J 484 MET cc_start: 0.9037 (mtt) cc_final: 0.8679 (mtt) REVERT: J 762 ASN cc_start: 0.8579 (p0) cc_final: 0.7918 (p0) REVERT: J 869 CYS cc_start: 0.8405 (m) cc_final: 0.7935 (m) REVERT: J 870 ASP cc_start: 0.7665 (m-30) cc_final: 0.7343 (m-30) REVERT: J 1349 GLU cc_start: 0.7249 (mt-10) cc_final: 0.7027 (mt-10) REVERT: K 60 ASN cc_start: 0.8072 (p0) cc_final: 0.7848 (p0) outliers start: 36 outliers final: 22 residues processed: 303 average time/residue: 0.1698 time to fit residues: 84.8665 Evaluate side-chains 275 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 273 ILE Chi-restraints excluded: chain J residue 311 ARG Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 72 optimal weight: 3.9990 chunk 291 optimal weight: 10.0000 chunk 308 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 chunk 174 optimal weight: 0.5980 chunk 176 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN I 69 GLN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.140602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.103522 restraints weight = 43007.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105957 restraints weight = 23277.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106604 restraints weight = 15509.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.106988 restraints weight = 13535.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.106887 restraints weight = 12452.788| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 26964 Z= 0.128 Angle : 0.574 10.909 36739 Z= 0.299 Chirality : 0.044 0.322 4222 Planarity : 0.005 0.137 4556 Dihedral : 13.402 173.034 4249 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 1.44 % Allowed : 10.45 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 3179 helix: 1.40 (0.16), residues: 1104 sheet: -0.52 (0.27), residues: 383 loop : -1.37 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 744 TYR 0.019 0.001 TYR J1365 PHE 0.018 0.001 PHE I 405 TRP 0.015 0.002 TRP J1193 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (26956) covalent geometry : angle 0.57279 / 0.30 (36727) hydrogen bonds : bond 0.04107 / 4.44 ( 1087) hydrogen bonds : angle 4.74150 / 4.98 ( 3002) metal coordination : bond 0.00456 / 0.41 ( 8) metal coordination : angle 2.46542 / 3.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 293 time to evaluate : 1.010 Fit side-chains REVERT: H 66 HIS cc_start: 0.6971 (OUTLIER) cc_final: 0.6607 (m-70) REVERT: H 84 ASN cc_start: 0.8252 (m110) cc_final: 0.7523 (m110) REVERT: H 181 GLU cc_start: 0.7572 (tp30) cc_final: 0.7335 (tp30) REVERT: I 119 GLU cc_start: 0.7193 (pm20) cc_final: 0.6846 (pm20) REVERT: I 194 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7938 (tt) REVERT: I 202 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.7732 (ttp-110) REVERT: I 218 GLU cc_start: 0.7851 (pp20) cc_final: 0.7567 (pp20) REVERT: I 286 GLU cc_start: 0.6980 (mt-10) cc_final: 0.5398 (pm20) REVERT: I 369 MET cc_start: 0.7498 (tmm) cc_final: 0.6856 (tmm) REVERT: I 370 MET cc_start: 0.7640 (mmm) cc_final: 0.6689 (mmm) REVERT: I 488 MET cc_start: 0.2402 (mmt) cc_final: 0.2095 (mmt) REVERT: I 962 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: I 1170 MET cc_start: 0.8189 (tpt) cc_final: 0.7961 (tpp) REVERT: I 1304 MET cc_start: 0.8984 (tpp) cc_final: 0.8751 (tpp) REVERT: J 52 GLU cc_start: 0.5705 (mm-30) cc_final: 0.5286 (mm-30) REVERT: J 100 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7844 (tm-30) REVERT: J 130 MET cc_start: 0.8192 (ttp) cc_final: 0.7731 (ttp) REVERT: J 131 PRO cc_start: 0.8239 (Cg_exo) cc_final: 0.8008 (Cg_endo) REVERT: J 198 CYS cc_start: 0.8130 (t) cc_final: 0.7691 (t) REVERT: J 236 TRP cc_start: 0.9074 (m-10) cc_final: 0.8821 (m-10) REVERT: J 298 MET cc_start: 0.7560 (mmp) cc_final: 0.7356 (mmt) REVERT: J 484 MET cc_start: 0.9010 (mtt) cc_final: 0.8584 (mtt) REVERT: J 762 ASN cc_start: 0.8621 (p0) cc_final: 0.8318 (p0) REVERT: J 822 MET cc_start: 0.8431 (tpp) cc_final: 0.8204 (tpp) REVERT: J 869 CYS cc_start: 0.8590 (m) cc_final: 0.8129 (m) REVERT: J 870 ASP cc_start: 0.7297 (m-30) cc_final: 0.7019 (m-30) REVERT: J 1344 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8585 (pp) REVERT: J 1349 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6783 (mt-10) outliers start: 39 outliers final: 16 residues processed: 317 average time/residue: 0.1697 time to fit residues: 88.1594 Evaluate side-chains 272 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 299 optimal weight: 20.0000 chunk 294 optimal weight: 9.9990 chunk 273 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 188 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 295 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102384 restraints weight = 43048.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.102486 restraints weight = 26673.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.103077 restraints weight = 20379.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.103491 restraints weight = 18481.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.103629 restraints weight = 16062.071| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 26964 Z= 0.185 Angle : 0.591 9.606 36739 Z= 0.306 Chirality : 0.044 0.262 4222 Planarity : 0.004 0.132 4556 Dihedral : 13.458 172.277 4249 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.91 % Favored : 95.06 % Rotamer: Outliers : 1.77 % Allowed : 11.74 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 3179 helix: 1.42 (0.16), residues: 1107 sheet: -0.52 (0.27), residues: 372 loop : -1.38 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 744 TYR 0.021 0.001 TYR J1365 PHE 0.015 0.001 PHE I 405 TRP 0.015 0.001 TRP J1193 HIS 0.007 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (26956) covalent geometry : angle 0.58880 / 0.31 (36727) hydrogen bonds : bond 0.04068 / 4.35 ( 1087) hydrogen bonds : angle 4.61308 / 4.89 ( 3002) metal coordination : bond 0.00908 / 0.86 ( 8) metal coordination : angle 2.66790 / 4.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 273 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8325 (m110) cc_final: 0.7660 (m110) REVERT: H 181 GLU cc_start: 0.7687 (tp30) cc_final: 0.7404 (tp30) REVERT: I 115 LYS cc_start: 0.6692 (mtmt) cc_final: 0.5915 (mtmm) REVERT: I 194 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7997 (tt) REVERT: I 218 GLU cc_start: 0.7797 (pp20) cc_final: 0.7503 (pp20) REVERT: I 286 GLU cc_start: 0.7018 (mt-10) cc_final: 0.5415 (pm20) REVERT: I 369 MET cc_start: 0.7535 (tmm) cc_final: 0.7045 (tmm) REVERT: I 370 MET cc_start: 0.7595 (mmm) cc_final: 0.6772 (mmm) REVERT: I 962 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: J 52 GLU cc_start: 0.5713 (mm-30) cc_final: 0.5278 (mm-30) REVERT: J 100 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7778 (tm-30) REVERT: J 130 MET cc_start: 0.8163 (ttp) cc_final: 0.7707 (ttp) REVERT: J 198 CYS cc_start: 0.8149 (t) cc_final: 0.7698 (t) REVERT: J 236 TRP cc_start: 0.9072 (m-10) cc_final: 0.8006 (m-10) REVERT: J 293 ARG cc_start: 0.7694 (mpt90) cc_final: 0.7481 (mtt90) REVERT: J 484 MET cc_start: 0.9107 (mtt) cc_final: 0.8678 (mtt) REVERT: J 656 GLU cc_start: 0.6189 (tp30) cc_final: 0.5918 (tp30) REVERT: J 762 ASN cc_start: 0.8669 (p0) cc_final: 0.8411 (p0) REVERT: J 777 HIS cc_start: 0.8076 (m-70) cc_final: 0.7708 (t-90) REVERT: J 822 MET cc_start: 0.8466 (tpp) cc_final: 0.8212 (tpp) REVERT: J 869 CYS cc_start: 0.8580 (m) cc_final: 0.8112 (m) REVERT: J 870 ASP cc_start: 0.7327 (m-30) cc_final: 0.7050 (m-30) REVERT: J 1344 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8612 (pp) REVERT: J 1349 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6760 (mt-10) outliers start: 48 outliers final: 31 residues processed: 303 average time/residue: 0.1702 time to fit residues: 85.0257 Evaluate side-chains 293 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 199 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 224 optimal weight: 0.3980 chunk 181 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 649 GLN I 799 ASN J 424 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104435 restraints weight = 42730.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.106022 restraints weight = 24399.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106271 restraints weight = 18035.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.106726 restraints weight = 16330.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106853 restraints weight = 14492.844| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 26964 Z= 0.115 Angle : 0.546 10.290 36739 Z= 0.284 Chirality : 0.043 0.267 4222 Planarity : 0.004 0.128 4556 Dihedral : 13.419 171.933 4249 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 1.59 % Allowed : 13.22 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 3179 helix: 1.60 (0.16), residues: 1105 sheet: -0.47 (0.28), residues: 355 loop : -1.34 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 311 TYR 0.018 0.001 TYR J1365 PHE 0.021 0.001 PHE I 337 TRP 0.013 0.001 TRP J 115 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (26956) covalent geometry : angle 0.54437 / 0.28 (36727) hydrogen bonds : bond 0.03678 / 3.94 ( 1087) hydrogen bonds : angle 4.42142 / 4.68 ( 3002) metal coordination : bond 0.00445 / 0.41 ( 8) metal coordination : angle 2.26167 / 3.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 286 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8303 (m110) cc_final: 0.7563 (m110) REVERT: H 181 GLU cc_start: 0.7548 (tp30) cc_final: 0.7234 (tp30) REVERT: I 70 TYR cc_start: 0.8150 (t80) cc_final: 0.7835 (t80) REVERT: I 119 GLU cc_start: 0.7156 (pm20) cc_final: 0.6726 (pm20) REVERT: I 202 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.7746 (ttp-110) REVERT: I 218 GLU cc_start: 0.7752 (pp20) cc_final: 0.7440 (pp20) REVERT: I 286 GLU cc_start: 0.6966 (mt-10) cc_final: 0.5380 (pm20) REVERT: I 427 ASP cc_start: 0.7851 (m-30) cc_final: 0.7430 (m-30) REVERT: I 545 PHE cc_start: 0.7320 (m-80) cc_final: 0.7104 (m-80) REVERT: I 962 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: I 1170 MET cc_start: 0.8192 (tpt) cc_final: 0.7894 (tpp) REVERT: J 52 GLU cc_start: 0.5854 (mm-30) cc_final: 0.5401 (mm-30) REVERT: J 100 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7726 (tm-30) REVERT: J 198 CYS cc_start: 0.8154 (t) cc_final: 0.7677 (t) REVERT: J 236 TRP cc_start: 0.8998 (m-10) cc_final: 0.7925 (m-10) REVERT: J 484 MET cc_start: 0.9060 (mtt) cc_final: 0.8580 (mtt) REVERT: J 747 MET cc_start: 0.6787 (mmt) cc_final: 0.6466 (mmt) REVERT: J 777 HIS cc_start: 0.8139 (m-70) cc_final: 0.7662 (t-90) REVERT: J 822 MET cc_start: 0.8434 (tpp) cc_final: 0.8192 (tpp) REVERT: J 869 CYS cc_start: 0.8584 (m) cc_final: 0.8110 (m) REVERT: J 870 ASP cc_start: 0.7242 (m-30) cc_final: 0.6965 (m-30) REVERT: J 1344 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8576 (pp) REVERT: J 1349 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6809 (mt-10) outliers start: 43 outliers final: 26 residues processed: 312 average time/residue: 0.1677 time to fit residues: 86.6440 Evaluate side-chains 286 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 53 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 255 optimal weight: 0.8980 chunk 307 optimal weight: 8.9990 chunk 322 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 94 optimal weight: 7.9990 chunk 289 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.103552 restraints weight = 42825.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.104052 restraints weight = 26311.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.104553 restraints weight = 20464.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.104998 restraints weight = 17560.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105159 restraints weight = 15333.126| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 26964 Z= 0.154 Angle : 0.566 10.252 36739 Z= 0.292 Chirality : 0.043 0.263 4222 Planarity : 0.004 0.124 4556 Dihedral : 13.445 171.632 4249 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 1.55 % Allowed : 14.51 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 3179 helix: 1.59 (0.16), residues: 1108 sheet: -0.47 (0.28), residues: 362 loop : -1.33 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 26 TYR 0.023 0.001 TYR J1365 PHE 0.013 0.001 PHE I 405 TRP 0.010 0.001 TRP J 686 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (26956) covalent geometry : angle 0.56487 / 0.29 (36727) hydrogen bonds : bond 0.03710 / 3.96 ( 1087) hydrogen bonds : angle 4.38265 / 4.67 ( 3002) metal coordination : bond 0.00680 / 0.64 ( 8) metal coordination : angle 2.26299 / 3.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8323 (m110) cc_final: 0.7690 (m-40) REVERT: H 181 GLU cc_start: 0.7624 (tp30) cc_final: 0.7279 (tp30) REVERT: I 115 LYS cc_start: 0.6495 (mtmt) cc_final: 0.6001 (mtmt) REVERT: I 119 GLU cc_start: 0.7339 (pm20) cc_final: 0.7124 (pm20) REVERT: I 202 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7730 (ttp-110) REVERT: I 286 GLU cc_start: 0.6997 (mt-10) cc_final: 0.5384 (pm20) REVERT: I 370 MET cc_start: 0.7471 (mmm) cc_final: 0.7141 (mmm) REVERT: I 488 MET cc_start: 0.3189 (mmt) cc_final: 0.2837 (mmt) REVERT: I 545 PHE cc_start: 0.7330 (m-80) cc_final: 0.7118 (m-80) REVERT: I 962 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: J 52 GLU cc_start: 0.5905 (mm-30) cc_final: 0.5451 (mm-30) REVERT: J 100 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7744 (tm-30) REVERT: J 130 MET cc_start: 0.7976 (ttp) cc_final: 0.7574 (ttp) REVERT: J 198 CYS cc_start: 0.8146 (t) cc_final: 0.7677 (t) REVERT: J 236 TRP cc_start: 0.9017 (m-10) cc_final: 0.7880 (m-10) REVERT: J 322 ARG cc_start: 0.7791 (mtm110) cc_final: 0.7568 (mtm110) REVERT: J 484 MET cc_start: 0.9107 (mtt) cc_final: 0.8674 (mtt) REVERT: J 656 GLU cc_start: 0.6495 (tp30) cc_final: 0.6244 (tp30) REVERT: J 747 MET cc_start: 0.6889 (mmt) cc_final: 0.6519 (mmt) REVERT: J 777 HIS cc_start: 0.8216 (m-70) cc_final: 0.7718 (t-90) REVERT: J 822 MET cc_start: 0.8415 (tpp) cc_final: 0.8136 (tpp) REVERT: J 869 CYS cc_start: 0.8608 (m) cc_final: 0.8124 (m) REVERT: J 870 ASP cc_start: 0.7292 (m-30) cc_final: 0.7005 (m-30) REVERT: J 1344 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8618 (pp) REVERT: J 1349 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7011 (mt-10) outliers start: 42 outliers final: 33 residues processed: 297 average time/residue: 0.1617 time to fit residues: 80.3842 Evaluate side-chains 289 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 66 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 281 optimal weight: 8.9990 chunk 319 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 284 optimal weight: 0.0570 chunk 261 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 673 HIS K 61 ASN K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104570 restraints weight = 42841.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.104783 restraints weight = 25198.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105376 restraints weight = 20749.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105809 restraints weight = 17434.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106038 restraints weight = 15417.196| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 26964 Z= 0.129 Angle : 0.546 10.615 36739 Z= 0.281 Chirality : 0.042 0.258 4222 Planarity : 0.004 0.120 4556 Dihedral : 13.475 171.329 4249 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 1.77 % Allowed : 15.10 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3179 helix: 1.68 (0.16), residues: 1108 sheet: -0.43 (0.28), residues: 363 loop : -1.29 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 576 TYR 0.022 0.001 TYR J1365 PHE 0.016 0.001 PHE I 337 TRP 0.011 0.001 TRP J 686 HIS 0.007 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (26956) covalent geometry : angle 0.54457 / 0.28 (36727) hydrogen bonds : bond 0.03545 / 3.78 ( 1087) hydrogen bonds : angle 4.28575 / 4.57 ( 3002) metal coordination : bond 0.00557 / 0.52 ( 8) metal coordination : angle 2.10363 / 3.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8283 (m110) cc_final: 0.7625 (m-40) REVERT: H 181 GLU cc_start: 0.7610 (tp30) cc_final: 0.7269 (tp30) REVERT: I 70 TYR cc_start: 0.8067 (t80) cc_final: 0.7758 (t80) REVERT: I 115 LYS cc_start: 0.6125 (mtmt) cc_final: 0.5718 (mtmt) REVERT: I 119 GLU cc_start: 0.7514 (pm20) cc_final: 0.7228 (pm20) REVERT: I 202 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.7733 (ttp-110) REVERT: I 286 GLU cc_start: 0.6890 (mt-10) cc_final: 0.5249 (pm20) REVERT: I 370 MET cc_start: 0.7564 (mmm) cc_final: 0.7025 (mmm) REVERT: I 488 MET cc_start: 0.3193 (mmt) cc_final: 0.2799 (mmt) REVERT: I 545 PHE cc_start: 0.7296 (m-80) cc_final: 0.7070 (m-80) REVERT: I 962 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: I 1083 GLU cc_start: 0.8781 (pm20) cc_final: 0.8561 (pm20) REVERT: J 52 GLU cc_start: 0.6066 (mm-30) cc_final: 0.5836 (mm-30) REVERT: J 100 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7710 (tm-30) REVERT: J 130 MET cc_start: 0.7917 (ttp) cc_final: 0.7533 (ttp) REVERT: J 198 CYS cc_start: 0.8159 (t) cc_final: 0.7682 (t) REVERT: J 236 TRP cc_start: 0.9011 (m-10) cc_final: 0.7871 (m-10) REVERT: J 270 ARG cc_start: 0.8743 (ttm110) cc_final: 0.8292 (ttp80) REVERT: J 412 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8496 (tt) REVERT: J 466 MET cc_start: 0.8263 (mtp) cc_final: 0.7864 (ptp) REVERT: J 484 MET cc_start: 0.9102 (mtt) cc_final: 0.8653 (mtt) REVERT: J 747 MET cc_start: 0.6842 (mmt) cc_final: 0.6583 (mmt) REVERT: J 777 HIS cc_start: 0.8199 (m-70) cc_final: 0.7712 (t-90) REVERT: J 822 MET cc_start: 0.8285 (tpp) cc_final: 0.8077 (tpp) REVERT: J 831 VAL cc_start: 0.5105 (OUTLIER) cc_final: 0.4902 (m) REVERT: J 869 CYS cc_start: 0.8626 (m) cc_final: 0.8132 (m) REVERT: J 870 ASP cc_start: 0.7319 (m-30) cc_final: 0.7008 (m-30) REVERT: J 1344 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8588 (pp) REVERT: J 1349 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6911 (mt-10) REVERT: K 30 MET cc_start: 0.8926 (mtt) cc_final: 0.8678 (mtt) outliers start: 48 outliers final: 33 residues processed: 307 average time/residue: 0.1518 time to fit residues: 77.3056 Evaluate side-chains 296 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 169 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 236 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 ASN J 762 ASN K 61 ASN K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.139698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103756 restraints weight = 43122.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.104724 restraints weight = 26017.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.104834 restraints weight = 21059.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105413 restraints weight = 17644.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105587 restraints weight = 15245.061| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 26964 Z= 0.142 Angle : 0.557 11.555 36739 Z= 0.285 Chirality : 0.042 0.248 4222 Planarity : 0.004 0.116 4556 Dihedral : 13.512 171.248 4249 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.12 % Rotamer: Outliers : 1.92 % Allowed : 15.54 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3179 helix: 1.64 (0.16), residues: 1113 sheet: -0.48 (0.28), residues: 353 loop : -1.27 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 576 TYR 0.022 0.001 TYR J1365 PHE 0.015 0.001 PHE I 337 TRP 0.012 0.001 TRP J 686 HIS 0.007 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (26956) covalent geometry : angle 0.55556 / 0.28 (36727) hydrogen bonds : bond 0.03524 / 3.75 ( 1087) hydrogen bonds : angle 4.27467 / 4.58 ( 3002) metal coordination : bond 0.00624 / 0.58 ( 8) metal coordination : angle 2.09728 / 3.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 267 time to evaluate : 0.826 Fit side-chains REVERT: H 84 ASN cc_start: 0.8292 (m110) cc_final: 0.7641 (m-40) REVERT: H 181 GLU cc_start: 0.7621 (tp30) cc_final: 0.7281 (tp30) REVERT: H 205 MET cc_start: 0.7804 (tpp) cc_final: 0.7553 (tpp) REVERT: I 70 TYR cc_start: 0.7992 (t80) cc_final: 0.7686 (t80) REVERT: I 115 LYS cc_start: 0.6140 (mtmt) cc_final: 0.5732 (mtmt) REVERT: I 119 GLU cc_start: 0.7530 (pm20) cc_final: 0.7204 (pm20) REVERT: I 202 ARG cc_start: 0.8322 (ttp-110) cc_final: 0.7752 (ttp-110) REVERT: I 286 GLU cc_start: 0.7029 (mt-10) cc_final: 0.5185 (pm20) REVERT: I 369 MET cc_start: 0.7671 (tmm) cc_final: 0.7034 (tmm) REVERT: I 370 MET cc_start: 0.7563 (mmm) cc_final: 0.6750 (mmm) REVERT: I 427 ASP cc_start: 0.7868 (m-30) cc_final: 0.7463 (m-30) REVERT: I 488 MET cc_start: 0.3252 (mmt) cc_final: 0.2831 (mmt) REVERT: I 545 PHE cc_start: 0.7321 (m-80) cc_final: 0.7091 (m-80) REVERT: I 962 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: I 1083 GLU cc_start: 0.8785 (pm20) cc_final: 0.8569 (pm20) REVERT: I 1170 MET cc_start: 0.8251 (tpt) cc_final: 0.8024 (tpp) REVERT: J 52 GLU cc_start: 0.6045 (mm-30) cc_final: 0.5794 (mm-30) REVERT: J 100 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7692 (tm-30) REVERT: J 130 MET cc_start: 0.7892 (ttp) cc_final: 0.7522 (ttp) REVERT: J 198 CYS cc_start: 0.8161 (t) cc_final: 0.7683 (t) REVERT: J 236 TRP cc_start: 0.9019 (m-10) cc_final: 0.7872 (m-10) REVERT: J 270 ARG cc_start: 0.8763 (ttm110) cc_final: 0.8315 (ttp80) REVERT: J 412 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8524 (tt) REVERT: J 484 MET cc_start: 0.9137 (mtt) cc_final: 0.8690 (mtt) REVERT: J 747 MET cc_start: 0.6868 (mmt) cc_final: 0.6595 (mmt) REVERT: J 777 HIS cc_start: 0.8235 (m-70) cc_final: 0.7743 (t-90) REVERT: J 869 CYS cc_start: 0.8634 (m) cc_final: 0.8112 (m) REVERT: J 870 ASP cc_start: 0.7295 (m-30) cc_final: 0.6998 (m-30) REVERT: J 1344 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8624 (pp) outliers start: 52 outliers final: 39 residues processed: 301 average time/residue: 0.1350 time to fit residues: 67.4976 Evaluate side-chains 299 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 184 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 31 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 0.0270 chunk 99 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS K 61 ASN K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.103025 restraints weight = 43009.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.103391 restraints weight = 26071.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.104149 restraints weight = 19805.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104416 restraints weight = 17427.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.104686 restraints weight = 15541.151| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 26964 Z= 0.169 Angle : 0.574 11.233 36739 Z= 0.294 Chirality : 0.043 0.239 4222 Planarity : 0.004 0.114 4556 Dihedral : 13.557 171.195 4249 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 1.99 % Allowed : 15.69 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 3179 helix: 1.57 (0.16), residues: 1114 sheet: -0.56 (0.28), residues: 363 loop : -1.27 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 576 TYR 0.024 0.001 TYR J1365 PHE 0.015 0.001 PHE I 337 TRP 0.014 0.001 TRP J 686 HIS 0.007 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (26956) covalent geometry : angle 0.57301 / 0.29 (36727) hydrogen bonds : bond 0.03634 / 3.87 ( 1087) hydrogen bonds : angle 4.29221 / 4.62 ( 3002) metal coordination : bond 0.00782 / 0.74 ( 8) metal coordination : angle 2.17441 / 3.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 267 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8352 (m110) cc_final: 0.7677 (m-40) REVERT: H 181 GLU cc_start: 0.7652 (tp30) cc_final: 0.7316 (tp30) REVERT: I 70 TYR cc_start: 0.8022 (t80) cc_final: 0.7683 (t80) REVERT: I 115 LYS cc_start: 0.6112 (mtmt) cc_final: 0.5700 (mtmt) REVERT: I 119 GLU cc_start: 0.7619 (pm20) cc_final: 0.7274 (pm20) REVERT: I 202 ARG cc_start: 0.8330 (ttp-110) cc_final: 0.7740 (ttp-110) REVERT: I 488 MET cc_start: 0.3279 (mmt) cc_final: 0.2956 (mmt) REVERT: I 562 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8417 (tm-30) REVERT: I 962 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: I 1083 GLU cc_start: 0.8807 (pm20) cc_final: 0.8581 (pm20) REVERT: J 52 GLU cc_start: 0.6073 (mm-30) cc_final: 0.5794 (mm-30) REVERT: J 100 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7692 (tm-30) REVERT: J 130 MET cc_start: 0.7896 (ttp) cc_final: 0.7530 (ttp) REVERT: J 198 CYS cc_start: 0.8161 (t) cc_final: 0.7687 (t) REVERT: J 236 TRP cc_start: 0.9003 (m-10) cc_final: 0.7889 (m-10) REVERT: J 270 ARG cc_start: 0.8747 (ttm110) cc_final: 0.8317 (ttp80) REVERT: J 412 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8506 (tt) REVERT: J 484 MET cc_start: 0.9150 (mtt) cc_final: 0.8778 (mtt) REVERT: J 777 HIS cc_start: 0.8240 (m-70) cc_final: 0.7737 (t-90) REVERT: J 869 CYS cc_start: 0.8622 (m) cc_final: 0.8119 (m) REVERT: J 870 ASP cc_start: 0.7355 (m-30) cc_final: 0.7034 (m-30) REVERT: J 1344 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8564 (pp) REVERT: J 1349 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7105 (mt-10) REVERT: K 30 MET cc_start: 0.8828 (mtt) cc_final: 0.8538 (mtt) outliers start: 54 outliers final: 43 residues processed: 300 average time/residue: 0.1334 time to fit residues: 66.7175 Evaluate side-chains 309 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 581 MET Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 313 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 209 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 249 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS K 61 ASN K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.103272 restraints weight = 42949.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.104332 restraints weight = 25344.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.104855 restraints weight = 18734.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.105153 restraints weight = 16887.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105347 restraints weight = 15022.016| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 26964 Z= 0.146 Angle : 0.566 11.368 36739 Z= 0.289 Chirality : 0.042 0.238 4222 Planarity : 0.004 0.111 4556 Dihedral : 13.557 171.090 4249 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 1.85 % Allowed : 16.17 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 3179 helix: 1.58 (0.16), residues: 1112 sheet: -0.53 (0.28), residues: 361 loop : -1.28 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 371 TYR 0.023 0.001 TYR J1365 PHE 0.014 0.001 PHE I 405 TRP 0.013 0.001 TRP J 686 HIS 0.007 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (26956) covalent geometry : angle 0.56468 / 0.29 (36727) hydrogen bonds : bond 0.03563 / 3.81 ( 1087) hydrogen bonds : angle 4.27560 / 4.62 ( 3002) metal coordination : bond 0.00658 / 0.62 ( 8) metal coordination : angle 2.11473 / 3.54 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8344 (m110) cc_final: 0.7664 (m-40) REVERT: H 181 GLU cc_start: 0.7650 (tp30) cc_final: 0.7325 (tp30) REVERT: I 32 LEU cc_start: 0.8485 (mm) cc_final: 0.8227 (mm) REVERT: I 70 TYR cc_start: 0.8033 (t80) cc_final: 0.7765 (t80) REVERT: I 115 LYS cc_start: 0.6112 (mtmt) cc_final: 0.5713 (mtmt) REVERT: I 562 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8388 (tm-30) REVERT: I 962 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: I 1083 GLU cc_start: 0.8801 (pm20) cc_final: 0.8580 (pm20) REVERT: I 1170 MET cc_start: 0.8242 (tpt) cc_final: 0.8012 (tpp) REVERT: J 52 GLU cc_start: 0.6145 (mm-30) cc_final: 0.5786 (mm-30) REVERT: J 100 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7688 (tm-30) REVERT: J 130 MET cc_start: 0.7878 (ttp) cc_final: 0.7484 (ttp) REVERT: J 198 CYS cc_start: 0.8177 (t) cc_final: 0.7696 (t) REVERT: J 236 TRP cc_start: 0.9002 (m-10) cc_final: 0.7889 (m-10) REVERT: J 270 ARG cc_start: 0.8699 (ttm110) cc_final: 0.8251 (ttp80) REVERT: J 291 ILE cc_start: 0.8231 (mt) cc_final: 0.7953 (tp) REVERT: J 412 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8512 (tt) REVERT: J 484 MET cc_start: 0.9127 (mtt) cc_final: 0.8706 (mtt) REVERT: J 762 ASN cc_start: 0.8998 (p0) cc_final: 0.8710 (p0) REVERT: J 765 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: J 777 HIS cc_start: 0.8263 (m-70) cc_final: 0.7778 (t-90) REVERT: J 869 CYS cc_start: 0.8617 (m) cc_final: 0.8115 (m) REVERT: J 870 ASP cc_start: 0.7320 (m-30) cc_final: 0.7011 (m-30) REVERT: J 1344 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8572 (pp) REVERT: K 30 MET cc_start: 0.8903 (mtt) cc_final: 0.8609 (mtt) REVERT: K 55 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7439 (tm-30) outliers start: 50 outliers final: 41 residues processed: 302 average time/residue: 0.1499 time to fit residues: 74.9703 Evaluate side-chains 314 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 269 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 581 MET Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 304 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 311 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 323 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS I 69 GLN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.137684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101625 restraints weight = 43070.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.102620 restraints weight = 24710.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.102767 restraints weight = 19880.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.103428 restraints weight = 17135.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103542 restraints weight = 14971.818| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 26964 Z= 0.192 Angle : 0.604 11.855 36739 Z= 0.308 Chirality : 0.043 0.229 4222 Planarity : 0.004 0.110 4556 Dihedral : 13.621 170.954 4249 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.24 % Rotamer: Outliers : 1.81 % Allowed : 16.65 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3179 helix: 1.42 (0.16), residues: 1121 sheet: -0.59 (0.28), residues: 361 loop : -1.31 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 368 TYR 0.024 0.001 TYR J1365 PHE 0.016 0.001 PHE I 405 TRP 0.016 0.002 TRP J 686 HIS 0.007 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (26956) covalent geometry : angle 0.60272 / 0.31 (36727) hydrogen bonds : bond 0.03756 / 4.01 ( 1087) hydrogen bonds : angle 4.36156 / 4.72 ( 3002) metal coordination : bond 0.00969 / 0.93 ( 8) metal coordination : angle 2.40459 / 4.15 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3614.14 seconds wall clock time: 63 minutes 40.95 seconds (3820.95 seconds total)