Starting phenix.real_space_refine on Sat Aug 8 02:31:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t00_40930/08_2026/8t00_40930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t00_40930/08_2026/8t00_40930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t00_40930/08_2026/8t00_40930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t00_40930/08_2026/8t00_40930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t00_40930/08_2026/8t00_40930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t00_40930/08_2026/8t00_40930.map" } resolution = 4.69 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= 0.003 sd= 0.035 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 52 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 15676 2.51 5 N 4433 2.21 5 O 4946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s 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: 25215 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1721 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 10397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1318, 10397 Classifications: {'peptide': 1318} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1262} Chain breaks: 2 Chain: "J" Number of atoms: 10355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1332, 10355 Classifications: {'peptide': 1332} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1276} Chain breaks: 3 Chain: "A" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "B" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14240 SG CYS J 70 83.663 117.649 94.118 1.00404.65 S ATOM 14254 SG CYS J 72 84.745 119.695 95.029 1.00421.27 S ATOM 14362 SG CYS J 85 82.976 121.324 93.571 1.00434.43 S ATOM 14386 SG CYS J 88 85.591 117.947 92.786 1.00433.81 S ATOM 20067 SG CYS J 814 53.644 72.213 58.499 1.00288.66 S ATOM 20632 SG CYS J 888 57.468 72.803 60.588 1.00270.53 S ATOM 20683 SG CYS J 895 54.797 71.847 61.201 1.00276.54 S ATOM 20704 SG CYS J 898 55.038 70.795 60.693 1.00253.58 S Time building chain proxies: 4.83, per 1000 atoms: 0.19 Number of scatterers: 25215 At special positions: 0 Unit cell: (166.78, 132.348, 162.476, 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 52 15.00 Mg 1 11.99 O 4946 8.00 N 4433 7.00 C 15676 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: 2.18 Conformation dependent library (CDL) restraints added in 890.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1402 " pdb="ZN ZN J1402 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1402 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1402 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1402 " - pdb=" SG CYS J 72 " pdb=" ZN J1403 " pdb="ZN ZN J1403 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1403 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1403 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1403 " - pdb=" SG CYS J 898 " Number of angles added : 12 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 49 sheets defined 38.8% alpha, 15.7% beta 26 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.509A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) 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 154 through 159 removed outlier: 3.891A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 233 removed outlier: 3.762A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.654A 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 154 through 158 Processing helix chain 'H' and resid 212 through 230 removed outlier: 3.686A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 10 removed outlier: 4.188A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.736A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.961A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 246 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 294 removed outlier: 3.786A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.821A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 353 removed outlier: 3.743A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 removed outlier: 3.636A pdb=" N ARG I 371 " --> pdb=" O TYR I 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.849A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.750A pdb=" N MET I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.976A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 544 through 549 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 607 through 614 removed outlier: 3.671A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) Processing helix chain 'I' and resid 656 through 661 Processing helix chain 'I' and resid 662 through 667 removed outlier: 3.892A pdb=" N LEU I 667 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 removed outlier: 3.698A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 703 through 712 removed outlier: 4.436A pdb=" N ALA I 707 " --> pdb=" O GLY I 703 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 removed outlier: 3.504A pdb=" N GLU I 825 " --> pdb=" O ARG I 821 " (cutoff:3.500A) Processing helix chain 'I' and resid 858 through 864 removed outlier: 3.896A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 986 through 992 Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.839A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.037A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 4.077A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1293 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1321 through 1333 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 removed outlier: 3.502A pdb=" N PHE J 62 " --> pdb=" O CYS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 95 through 101 removed outlier: 3.598A pdb=" N ARG J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.809A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 264 through 286 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 417 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 458 removed outlier: 3.723A pdb=" N CYS J 454 " --> pdb=" O HIS J 450 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 581 removed outlier: 3.864A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 648 through 670 removed outlier: 3.553A pdb=" N GLU J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.787A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 729 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.539A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 915 through 925 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 3.815A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.570A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.420A 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 1324 Processing helix chain 'J' and resid 1328 through 1339 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1360 through 1373 removed outlier: 3.680A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.509A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.527A pdb=" N GLY G 149 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 104 removed outlier: 6.491A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.560A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 18 removed outlier: 5.573A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LYS H 25 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET H 205 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR H 27 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE H 203 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 101 removed outlier: 6.753A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (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 104 through 105 Processing sheet with id=AB1, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.365A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.751A 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: 6.671A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.388A 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 removed outlier: 3.534A pdb=" N PHE I 136 " --> pdb=" O ARG I 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 453 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'I' and resid 180 through 181 removed outlier: 3.615A pdb=" N ARG I 180 " --> pdb=" O ASP I 396 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 284 through 285 removed outlier: 4.616A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.777A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.558A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.542A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.446A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'I' and resid 716 through 717 removed outlier: 3.564A pdb=" N ALA I 784 " --> pdb=" O ALA I 716 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.575A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.960A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 1066 through 1067 Processing sheet with id=AD2, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.722A pdb=" N GLY I 846 " --> pdb=" O THR I 843 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU I1047 " --> pdb=" O THR I 935 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR I 935 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE I1049 " --> pdb=" O VAL I 933 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL I 933 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS I1051 " --> pdb=" O VAL I 931 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL I 931 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR I1053 " --> pdb=" O ILE I 929 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD4, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD5, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD6, first strand: chain 'I' and resid 1268 through 1269 removed outlier: 3.576A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 20 through 21 Processing sheet with id=AD8, first strand: chain 'J' and resid 34 through 37 removed outlier: 5.391A pdb=" N SER J 34 " --> pdb=" O MET J 102 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS J 104 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLY J 36 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU J 106 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.733A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 145 through 147 removed outlier: 4.210A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 366 through 369 removed outlier: 6.699A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE3, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE4, first strand: chain 'J' and resid 809 through 811 removed outlier: 6.145A pdb=" N VAL J 894 " --> pdb=" O VAL J 809 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE6, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.043A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 842 through 843 removed outlier: 3.662A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 991 through 996 removed outlier: 4.081A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF1, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 3.660A pdb=" N ALA J1077 " --> pdb=" O THR J1038 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY J1033 " --> pdb=" O ILE J1115 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 3.769A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER J1058 " --> pdb=" O GLN J1049 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE J1106 " --> pdb=" O ARG J1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.605A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1013 hydrogen bonds defined for protein. 2829 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8303 1.34 - 1.46: 3571 1.46 - 1.58: 13542 1.58 - 1.69: 100 1.69 - 1.81: 182 Bond restraints: 25698 Sorted by residual: bond pdb=" C1' DT B 122 " pdb=" N1 DT B 122 " ideal model delta sigma weight residual 1.468 1.535 -0.067 1.40e-02 5.10e+03 2.28e+01 bond pdb=" C1' DT B 118 " pdb=" N1 DT B 118 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" C1' DT B 103 " pdb=" N1 DT B 103 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.10e+01 bond pdb=" C1' DT B 124 " pdb=" N1 DT B 124 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" C1' DT B 101 " pdb=" N1 DT B 101 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.93e+01 ... (remaining 25693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 33769 1.63 - 3.27: 938 3.27 - 4.90: 194 4.90 - 6.53: 20 6.53 - 8.16: 4 Bond angle restraints: 34925 Sorted by residual: angle pdb=" N GLY I1152 " pdb=" CA GLY I1152 " pdb=" C GLY I1152 " ideal model delta sigma weight residual 111.45 117.55 -6.10 1.23e+00 6.61e-01 2.46e+01 angle pdb=" N3 DT B 123 " pdb=" C4 DT B 123 " pdb=" O4 DT B 123 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT B 127 " pdb=" C4 DT B 127 " pdb=" O4 DT B 127 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT B 99 " pdb=" C4 DT B 99 " pdb=" O4 DT B 99 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT B 104 " pdb=" C4 DT B 104 " pdb=" O4 DT B 104 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 ... (remaining 34920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14084 17.95 - 35.89: 1230 35.89 - 53.84: 275 53.84 - 71.79: 109 71.79 - 89.73: 12 Dihedral angle restraints: 15710 sinusoidal: 6837 harmonic: 8873 Sorted by residual: dihedral pdb=" CA PHE I1164 " pdb=" C PHE I1164 " pdb=" N SER I1165 " pdb=" CA SER I1165 " ideal model delta harmonic sigma weight residual 180.00 120.05 59.95 0 5.00e+00 4.00e-02 1.44e+02 dihedral pdb=" CA ARG J 709 " pdb=" C ARG J 709 " pdb=" N ASP J 710 " pdb=" CA ASP J 710 " ideal model delta harmonic sigma weight residual -180.00 -148.46 -31.54 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual -180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 15707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2756 0.036 - 0.071: 777 0.071 - 0.107: 289 0.107 - 0.143: 136 0.143 - 0.178: 34 Chirality restraints: 3992 Sorted by residual: chirality pdb=" CB ILE I 572 " pdb=" CA ILE I 572 " pdb=" CG1 ILE I 572 " pdb=" CG2 ILE I 572 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" C3' DT B 123 " pdb=" C4' DT B 123 " pdb=" O3' DT B 123 " pdb=" C2' DT B 123 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" C3' DT B 122 " pdb=" C4' DT B 122 " pdb=" O3' DT B 122 " pdb=" C2' DT B 122 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 3989 not shown) Planarity restraints: 4386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I1114 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.37e+00 pdb=" CD GLU I1114 " 0.044 2.00e-02 2.50e+03 pdb=" OE1 GLU I1114 " -0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU I1114 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG J 709 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C ARG J 709 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG J 709 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP J 710 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP J1184 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO J1185 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO J1185 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J1185 " 0.029 5.00e-02 4.00e+02 ... (remaining 4383 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 25 2.19 - 2.87: 9351 2.87 - 3.54: 39940 3.54 - 4.22: 60674 4.22 - 4.90: 100778 Nonbonded interactions: 210768 Sorted by model distance: nonbonded pdb=" OD2 ASP J 462 " pdb="MG MG J1401 " model vdw 1.510 2.170 nonbonded pdb=" OG1 THR I 6 " pdb=" OD2 ASP I 781 " model vdw 1.905 3.040 nonbonded pdb=" OG SER I 421 " pdb=" OD1 ASP I 423 " model vdw 1.988 3.040 nonbonded pdb=" O LEU J 614 " pdb=" OG1 THR J 617 " model vdw 2.002 3.040 nonbonded pdb=" OD1 ASP H 15 " pdb=" OG1 THR H 27 " model vdw 2.007 3.040 ... (remaining 210763 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 6 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 149 or (resid 150 and (name N or \ name CA or name C or name O or name CB )) or resid 151 through 158 or resid 170 \ through 232)) selection = (chain 'H' and (resid 6 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 217 or (resid 21 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 219 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: 1.000 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.620 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 25706 Z= 0.242 Angle : 1.015 79.924 34937 Z= 0.431 Chirality : 0.045 0.178 3992 Planarity : 0.005 0.051 4386 Dihedral : 14.969 89.731 10004 Min Nonbonded Distance : 1.510 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.81 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.15), residues: 3071 helix: 0.69 (0.16), residues: 1036 sheet: -1.27 (0.25), residues: 394 loop : -1.60 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 515 TYR 0.014 0.002 TYR I1149 PHE 0.030 0.001 PHE J 773 TRP 0.012 0.001 TRP I 183 HIS 0.007 0.001 HIS J1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.24 (25698) covalent geometry : angle 0.67631 / 0.41 (34925) hydrogen bonds : bond 0.16656 / 11.75 ( 1057) hydrogen bonds : angle 6.90847 / 4.85 ( 2933) metal coordination : bond 0.06779 / 3.73 ( 8) metal coordination : angle 40.80901 / 24.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1016 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 48 LEU cc_start: 0.9331 (mt) cc_final: 0.9087 (mt) REVERT: G 66 HIS cc_start: 0.8630 (p90) cc_final: 0.8406 (p-80) REVERT: G 84 ASN cc_start: 0.8876 (m-40) cc_final: 0.8644 (t0) REVERT: H 37 HIS cc_start: 0.9398 (m90) cc_final: 0.8625 (m90) REVERT: H 45 ARG cc_start: 0.8953 (mtp85) cc_final: 0.8643 (mtp85) REVERT: H 46 ILE cc_start: 0.9710 (tp) cc_final: 0.9419 (tp) REVERT: H 83 LEU cc_start: 0.9607 (mm) cc_final: 0.9272 (mm) REVERT: H 84 ASN cc_start: 0.9674 (m110) cc_final: 0.9259 (t0) REVERT: H 141 SER cc_start: 0.9404 (t) cc_final: 0.9046 (m) REVERT: H 142 MET cc_start: 0.9542 (ptm) cc_final: 0.8958 (ttp) REVERT: H 185 TYR cc_start: 0.7972 (p90) cc_final: 0.7472 (p90) REVERT: H 187 VAL cc_start: 0.8826 (m) cc_final: 0.8547 (t) REVERT: I 9 LYS cc_start: 0.9475 (mttm) cc_final: 0.9076 (mttm) REVERT: I 27 LEU cc_start: 0.9497 (mt) cc_final: 0.8955 (mt) REVERT: I 32 LEU cc_start: 0.9576 (mt) cc_final: 0.9147 (pp) REVERT: I 53 PHE cc_start: 0.8828 (m-80) cc_final: 0.8384 (m-10) REVERT: I 57 PHE cc_start: 0.8920 (m-80) cc_final: 0.8503 (m-80) REVERT: I 69 GLN cc_start: 0.9624 (pt0) cc_final: 0.9273 (pm20) REVERT: I 92 TYR cc_start: 0.9254 (t80) cc_final: 0.8767 (t80) REVERT: I 124 MET cc_start: 0.9181 (tpp) cc_final: 0.8722 (tpp) REVERT: I 144 VAL cc_start: 0.9363 (t) cc_final: 0.9139 (p) REVERT: I 158 ASP cc_start: 0.9004 (t0) cc_final: 0.8693 (t0) REVERT: I 160 ASP cc_start: 0.8712 (m-30) cc_final: 0.8129 (m-30) REVERT: I 163 LYS cc_start: 0.8988 (pttt) cc_final: 0.8717 (tptp) REVERT: I 336 LEU cc_start: 0.9005 (mt) cc_final: 0.8467 (mt) REVERT: I 400 VAL cc_start: 0.9483 (t) cc_final: 0.8915 (t) REVERT: I 430 LYS cc_start: 0.9635 (mmtm) cc_final: 0.9305 (mmtt) REVERT: I 434 ASP cc_start: 0.9646 (m-30) cc_final: 0.9385 (t0) REVERT: I 461 GLU cc_start: 0.9190 (tp30) cc_final: 0.8904 (tp30) REVERT: I 464 PHE cc_start: 0.9656 (t80) cc_final: 0.9342 (t80) REVERT: I 465 ARG cc_start: 0.9224 (mtt-85) cc_final: 0.8950 (mtt-85) REVERT: I 548 ARG cc_start: 0.9301 (mtt180) cc_final: 0.9064 (mmm160) REVERT: I 623 LEU cc_start: 0.9349 (pp) cc_final: 0.9017 (mp) REVERT: I 629 PHE cc_start: 0.9006 (m-10) cc_final: 0.8737 (m-10) REVERT: I 633 LEU cc_start: 0.9478 (pt) cc_final: 0.9152 (mm) REVERT: I 642 SER cc_start: 0.9309 (p) cc_final: 0.8841 (t) REVERT: I 681 MET cc_start: 0.9446 (mtp) cc_final: 0.8851 (mtt) REVERT: I 685 MET cc_start: 0.9302 (mtm) cc_final: 0.8435 (mtm) REVERT: I 697 LYS cc_start: 0.9478 (pttp) cc_final: 0.9223 (mmtm) REVERT: I 720 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8125 (mmm-85) REVERT: I 748 ILE cc_start: 0.9267 (pt) cc_final: 0.8936 (pt) REVERT: I 768 MET cc_start: 0.9429 (ppp) cc_final: 0.9021 (mpp) REVERT: I 800 MET cc_start: 0.9420 (mpp) cc_final: 0.9073 (mpp) REVERT: I 810 TYR cc_start: 0.9233 (m-10) cc_final: 0.8730 (m-80) REVERT: I 816 ILE cc_start: 0.9477 (mt) cc_final: 0.8293 (mt) REVERT: I 817 LEU cc_start: 0.8612 (mm) cc_final: 0.8299 (mm) REVERT: I 827 ARG cc_start: 0.9386 (ptm160) cc_final: 0.8910 (ptm160) REVERT: I 833 ILE cc_start: 0.9025 (mt) cc_final: 0.8603 (tp) REVERT: I 882 ILE cc_start: 0.9445 (mp) cc_final: 0.9106 (mp) REVERT: I 928 VAL cc_start: 0.9461 (t) cc_final: 0.9233 (p) REVERT: I 957 LYS cc_start: 0.9766 (mmtm) cc_final: 0.9347 (pptt) REVERT: I 1025 PHE cc_start: 0.9433 (t80) cc_final: 0.9054 (t80) REVERT: I 1029 LEU cc_start: 0.9601 (tt) cc_final: 0.9224 (mt) REVERT: I 1051 LYS cc_start: 0.9464 (mttt) cc_final: 0.9250 (mmtt) REVERT: I 1066 MET cc_start: 0.8548 (pmm) cc_final: 0.7163 (pmm) REVERT: I 1073 LYS cc_start: 0.9248 (mttt) cc_final: 0.8725 (mmmm) REVERT: I 1112 ILE cc_start: 0.9771 (mp) cc_final: 0.9534 (mp) REVERT: I 1122 LYS cc_start: 0.9667 (tptm) cc_final: 0.9048 (tppt) REVERT: I 1126 ASP cc_start: 0.9426 (m-30) cc_final: 0.8403 (m-30) REVERT: I 1194 GLU cc_start: 0.9130 (tp30) cc_final: 0.8902 (tp30) REVERT: I 1233 LEU cc_start: 0.9396 (mp) cc_final: 0.9038 (mp) REVERT: I 1237 HIS cc_start: 0.9001 (m-70) cc_final: 0.8700 (m90) REVERT: I 1270 PHE cc_start: 0.9127 (t80) cc_final: 0.8116 (t80) REVERT: I 1285 TYR cc_start: 0.8995 (m-80) cc_final: 0.8704 (m-80) REVERT: I 1290 MET cc_start: 0.9378 (tmm) cc_final: 0.8884 (tmm) REVERT: I 1319 MET cc_start: 0.8020 (tpt) cc_final: 0.7147 (tpt) REVERT: I 1321 GLU cc_start: 0.8912 (pm20) cc_final: 0.8703 (pm20) REVERT: I 1329 GLU cc_start: 0.9864 (mt-10) cc_final: 0.9470 (mt-10) REVERT: J 30 ILE cc_start: 0.9433 (mt) cc_final: 0.9213 (mt) REVERT: J 127 LEU cc_start: 0.8990 (tp) cc_final: 0.8716 (tp) REVERT: J 128 LEU cc_start: 0.9048 (mt) cc_final: 0.8694 (mt) REVERT: J 220 ARG cc_start: 0.9740 (ttm110) cc_final: 0.9492 (ptp-110) REVERT: J 242 LEU cc_start: 0.9506 (tt) cc_final: 0.9236 (tt) REVERT: J 243 PRO cc_start: 0.9463 (Cg_exo) cc_final: 0.9163 (Cg_endo) REVERT: J 325 LYS cc_start: 0.8381 (pttm) cc_final: 0.8113 (pttp) REVERT: J 361 LEU cc_start: 0.9221 (mt) cc_final: 0.9009 (pp) REVERT: J 437 PHE cc_start: 0.9354 (m-80) cc_final: 0.8677 (m-80) REVERT: J 452 LEU cc_start: 0.9689 (mt) cc_final: 0.9414 (mp) REVERT: J 461 PHE cc_start: 0.7686 (m-80) cc_final: 0.7356 (m-80) REVERT: J 478 LEU cc_start: 0.9633 (tt) cc_final: 0.9425 (mt) REVERT: J 484 MET cc_start: 0.9188 (mtm) cc_final: 0.8967 (mpp) REVERT: J 487 THR cc_start: 0.9715 (p) cc_final: 0.9321 (p) REVERT: J 503 SER cc_start: 0.8802 (m) cc_final: 0.8216 (p) REVERT: J 531 LYS cc_start: 0.9477 (mttt) cc_final: 0.9244 (mmtt) REVERT: J 576 ARG cc_start: 0.6961 (ttm170) cc_final: 0.6359 (ttm170) REVERT: J 596 LEU cc_start: 0.9568 (tt) cc_final: 0.8811 (tp) REVERT: J 603 LYS cc_start: 0.9274 (pttt) cc_final: 0.8806 (ptpp) REVERT: J 606 ASN cc_start: 0.9555 (t0) cc_final: 0.9123 (m110) REVERT: J 625 MET cc_start: 0.9358 (ttp) cc_final: 0.8899 (tmm) REVERT: J 627 THR cc_start: 0.9811 (t) cc_final: 0.9205 (t) REVERT: J 697 MET cc_start: 0.9620 (ppp) cc_final: 0.9175 (ppp) REVERT: J 698 MET cc_start: 0.9764 (tpp) cc_final: 0.9533 (tpp) REVERT: J 764 ARG cc_start: 0.9214 (ttt-90) cc_final: 0.8507 (mmm-85) REVERT: J 772 TYR cc_start: 0.9111 (t80) cc_final: 0.8904 (t80) REVERT: J 864 LEU cc_start: 0.9189 (mm) cc_final: 0.8970 (mm) REVERT: J 892 PHE cc_start: 0.9094 (m-10) cc_final: 0.8826 (m-10) REVERT: J 930 LEU cc_start: 0.8315 (mt) cc_final: 0.7963 (mt) REVERT: J 1231 ARG cc_start: 0.9448 (mtp85) cc_final: 0.9144 (tpt-90) REVERT: J 1238 GLN cc_start: 0.9608 (mm110) cc_final: 0.9062 (tp-100) REVERT: J 1241 TYR cc_start: 0.9479 (m-80) cc_final: 0.9236 (m-80) REVERT: J 1242 ARG cc_start: 0.8969 (ttp80) cc_final: 0.8680 (ptm-80) REVERT: J 1279 GLN cc_start: 0.7270 (tt0) cc_final: 0.6769 (tp40) outliers start: 0 outliers final: 0 residues processed: 1016 average time/residue: 0.1834 time to fit residues: 277.6589 Evaluate side-chains 749 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 749 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 0.0040 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 517 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 673 HIS I 832 HIS I 932 GLN ** I1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1175 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 GLN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 GLN J1259 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.110005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.069709 restraints weight = 88313.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.072899 restraints weight = 55091.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.075198 restraints weight = 38784.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.077101 restraints weight = 29830.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.078467 restraints weight = 24079.669| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25706 Z= 0.166 Angle : 0.848 36.857 34937 Z= 0.395 Chirality : 0.046 0.202 3992 Planarity : 0.007 0.172 4386 Dihedral : 14.389 62.427 3992 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.94 % Rotamer: Outliers : 0.23 % Allowed : 4.91 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.15), residues: 3071 helix: 0.53 (0.15), residues: 1059 sheet: -0.99 (0.26), residues: 364 loop : -1.70 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 610 TYR 0.020 0.002 TYR J 511 PHE 0.031 0.002 PHE J 629 TRP 0.011 0.001 TRP J 409 HIS 0.006 0.001 HIS J 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (25698) covalent geometry : angle 0.74124 / 0.39 (34925) hydrogen bonds : bond 0.05164 / 3.60 ( 1057) hydrogen bonds : angle 5.95460 / 4.16 ( 2933) metal coordination : bond 0.01957 / 0.92 ( 8) metal coordination : angle 22.18607 / 12.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 862 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.9326 (ptt180) cc_final: 0.9065 (mmt180) REVERT: G 35 PHE cc_start: 0.9734 (m-80) cc_final: 0.9519 (m-80) REVERT: G 37 HIS cc_start: 0.9226 (m-70) cc_final: 0.8697 (m-70) REVERT: G 104 LYS cc_start: 0.8371 (tptp) cc_final: 0.8082 (tmtt) REVERT: G 121 VAL cc_start: 0.9797 (t) cc_final: 0.9152 (t) REVERT: G 185 TYR cc_start: 0.8212 (p90) cc_final: 0.6981 (p90) REVERT: G 205 MET cc_start: 0.9625 (ppp) cc_final: 0.9384 (ppp) REVERT: G 227 GLN cc_start: 0.9685 (mt0) cc_final: 0.9479 (mm-40) REVERT: H 35 PHE cc_start: 0.9115 (m-10) cc_final: 0.8895 (m-10) REVERT: H 46 ILE cc_start: 0.9666 (tp) cc_final: 0.9374 (tp) REVERT: H 71 LYS cc_start: 0.9074 (ttmm) cc_final: 0.8836 (tptp) REVERT: H 141 SER cc_start: 0.9658 (t) cc_final: 0.9330 (m) REVERT: H 142 MET cc_start: 0.9590 (ptm) cc_final: 0.9303 (ttp) REVERT: H 185 TYR cc_start: 0.7819 (p90) cc_final: 0.7214 (p90) REVERT: H 193 GLU cc_start: 0.8737 (tp30) cc_final: 0.8166 (tp30) REVERT: H 194 GLN cc_start: 0.9506 (tp40) cc_final: 0.9170 (mm-40) REVERT: H 200 LYS cc_start: 0.9049 (tmtt) cc_final: 0.8756 (tptp) REVERT: I 6 THR cc_start: 0.9320 (p) cc_final: 0.8783 (p) REVERT: I 9 LYS cc_start: 0.9236 (mttm) cc_final: 0.8788 (mttm) REVERT: I 26 TYR cc_start: 0.8547 (t80) cc_final: 0.8063 (t80) REVERT: I 28 LEU cc_start: 0.9641 (mt) cc_final: 0.9365 (mt) REVERT: I 32 LEU cc_start: 0.9572 (mt) cc_final: 0.9291 (mt) REVERT: I 53 PHE cc_start: 0.8466 (m-80) cc_final: 0.8215 (m-10) REVERT: I 57 PHE cc_start: 0.8742 (m-80) cc_final: 0.8515 (m-80) REVERT: I 69 GLN cc_start: 0.9570 (pt0) cc_final: 0.9275 (pm20) REVERT: I 92 TYR cc_start: 0.9359 (t80) cc_final: 0.9006 (t80) REVERT: I 124 MET cc_start: 0.9580 (tpp) cc_final: 0.9138 (tpp) REVERT: I 144 VAL cc_start: 0.9347 (t) cc_final: 0.9142 (p) REVERT: I 179 TYR cc_start: 0.7751 (t80) cc_final: 0.7545 (t80) REVERT: I 239 MET cc_start: 0.9677 (tmm) cc_final: 0.9354 (tmm) REVERT: I 240 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8516 (mp0) REVERT: I 364 VAL cc_start: 0.9157 (t) cc_final: 0.8930 (t) REVERT: I 368 ARG cc_start: 0.9726 (mtm180) cc_final: 0.9340 (mmm-85) REVERT: I 400 VAL cc_start: 0.9390 (t) cc_final: 0.8878 (t) REVERT: I 405 PHE cc_start: 0.9642 (t80) cc_final: 0.9400 (t80) REVERT: I 464 PHE cc_start: 0.9721 (t80) cc_final: 0.9479 (t80) REVERT: I 591 TYR cc_start: 0.9459 (m-80) cc_final: 0.8821 (m-80) REVERT: I 606 LEU cc_start: 0.9268 (mp) cc_final: 0.8626 (mp) REVERT: I 623 LEU cc_start: 0.9215 (pp) cc_final: 0.8849 (mp) REVERT: I 629 PHE cc_start: 0.9425 (m-10) cc_final: 0.9194 (m-10) REVERT: I 633 LEU cc_start: 0.9583 (pt) cc_final: 0.9241 (mm) REVERT: I 642 SER cc_start: 0.8977 (p) cc_final: 0.8705 (t) REVERT: I 681 MET cc_start: 0.9328 (mtp) cc_final: 0.8868 (mtt) REVERT: I 685 MET cc_start: 0.9412 (mtm) cc_final: 0.9047 (mtm) REVERT: I 696 ASP cc_start: 0.9063 (t0) cc_final: 0.8241 (t0) REVERT: I 731 ARG cc_start: 0.9207 (ptp90) cc_final: 0.8826 (mtm-85) REVERT: I 768 MET cc_start: 0.9289 (ppp) cc_final: 0.9031 (mpp) REVERT: I 790 ASP cc_start: 0.9096 (t0) cc_final: 0.8465 (t0) REVERT: I 799 ASN cc_start: 0.9016 (t0) cc_final: 0.8580 (t0) REVERT: I 805 MET cc_start: 0.9336 (ppp) cc_final: 0.9120 (ppp) REVERT: I 816 ILE cc_start: 0.9465 (mt) cc_final: 0.8647 (mt) REVERT: I 833 ILE cc_start: 0.9263 (mt) cc_final: 0.9004 (tp) REVERT: I 877 VAL cc_start: 0.9251 (p) cc_final: 0.8618 (p) REVERT: I 1025 PHE cc_start: 0.9495 (t80) cc_final: 0.9134 (t80) REVERT: I 1066 MET cc_start: 0.8990 (pmm) cc_final: 0.8367 (pmm) REVERT: I 1083 GLU cc_start: 0.8578 (mp0) cc_final: 0.7561 (mp0) REVERT: I 1106 ARG cc_start: 0.9228 (mmm-85) cc_final: 0.8920 (mmm-85) REVERT: I 1107 MET cc_start: 0.9199 (mmm) cc_final: 0.8002 (tpp) REVERT: I 1113 LEU cc_start: 0.9645 (mp) cc_final: 0.9438 (mp) REVERT: I 1122 LYS cc_start: 0.9656 (tptm) cc_final: 0.9111 (tppt) REVERT: I 1126 ASP cc_start: 0.9496 (m-30) cc_final: 0.8720 (m-30) REVERT: I 1214 ASP cc_start: 0.8739 (t0) cc_final: 0.8367 (t0) REVERT: I 1230 MET cc_start: 0.9480 (tpt) cc_final: 0.9278 (tpt) REVERT: I 1234 LYS cc_start: 0.9525 (tppp) cc_final: 0.9239 (tppp) REVERT: I 1237 HIS cc_start: 0.8832 (m-70) cc_final: 0.8442 (m90) REVERT: I 1270 PHE cc_start: 0.9030 (t80) cc_final: 0.8268 (t80) REVERT: I 1290 MET cc_start: 0.9420 (tmm) cc_final: 0.8938 (tmm) REVERT: I 1304 MET cc_start: 0.9636 (tmm) cc_final: 0.9389 (ptp) REVERT: I 1319 MET cc_start: 0.7786 (tpt) cc_final: 0.6882 (tpt) REVERT: I 1321 GLU cc_start: 0.9065 (pm20) cc_final: 0.8832 (pm20) REVERT: I 1329 GLU cc_start: 0.9862 (mt-10) cc_final: 0.9573 (mt-10) REVERT: J 29 MET cc_start: 0.9166 (ttp) cc_final: 0.8900 (ptp) REVERT: J 92 VAL cc_start: -0.3764 (OUTLIER) cc_final: -0.3999 (m) REVERT: J 102 MET cc_start: 0.6896 (tpt) cc_final: 0.6483 (tpt) REVERT: J 159 ILE cc_start: 0.9141 (pt) cc_final: 0.8566 (pt) REVERT: J 242 LEU cc_start: 0.9456 (tt) cc_final: 0.9172 (tt) REVERT: J 243 PRO cc_start: 0.9592 (Cg_exo) cc_final: 0.9325 (Cg_endo) REVERT: J 325 LYS cc_start: 0.8044 (pttm) cc_final: 0.7512 (pttp) REVERT: J 329 ASP cc_start: 0.9628 (m-30) cc_final: 0.9317 (t0) REVERT: J 361 LEU cc_start: 0.9186 (mt) cc_final: 0.8736 (pp) REVERT: J 437 PHE cc_start: 0.9629 (m-80) cc_final: 0.8740 (m-80) REVERT: J 452 LEU cc_start: 0.9637 (mt) cc_final: 0.9315 (mm) REVERT: J 478 LEU cc_start: 0.9642 (tt) cc_final: 0.9438 (mt) REVERT: J 487 THR cc_start: 0.9692 (p) cc_final: 0.9392 (p) REVERT: J 512 TYR cc_start: 0.9418 (t80) cc_final: 0.9184 (t80) REVERT: J 576 ARG cc_start: 0.5753 (ttm170) cc_final: 0.5038 (ttm170) REVERT: J 594 GLN cc_start: 0.9417 (tm-30) cc_final: 0.8941 (tm-30) REVERT: J 596 LEU cc_start: 0.9460 (tt) cc_final: 0.9202 (tp) REVERT: J 603 LYS cc_start: 0.9241 (pttt) cc_final: 0.8848 (ptpp) REVERT: J 627 THR cc_start: 0.9857 (t) cc_final: 0.9422 (t) REVERT: J 697 MET cc_start: 0.9697 (ppp) cc_final: 0.9322 (ppp) REVERT: J 744 ARG cc_start: 0.8832 (ptm160) cc_final: 0.8236 (ptm-80) REVERT: J 764 ARG cc_start: 0.9116 (ttt-90) cc_final: 0.8828 (ttt-90) REVERT: J 822 MET cc_start: 0.8818 (tpt) cc_final: 0.8428 (tpp) REVERT: J 864 LEU cc_start: 0.9357 (mm) cc_final: 0.9148 (mm) REVERT: J 892 PHE cc_start: 0.8925 (m-10) cc_final: 0.8611 (m-10) REVERT: J 1040 MET cc_start: 0.7922 (mmp) cc_final: 0.7343 (mmm) REVERT: J 1194 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7899 (mtt180) REVERT: J 1215 GLU cc_start: 0.9423 (mp0) cc_final: 0.9193 (mm-30) REVERT: J 1231 ARG cc_start: 0.9634 (mtp85) cc_final: 0.9278 (tpt-90) REVERT: J 1238 GLN cc_start: 0.9721 (mm110) cc_final: 0.9450 (tp40) REVERT: J 1260 MET cc_start: 0.9526 (tmm) cc_final: 0.9116 (tmm) REVERT: J 1266 ILE cc_start: 0.8126 (mt) cc_final: 0.7800 (mt) REVERT: J 1279 GLN cc_start: 0.7051 (tt0) cc_final: 0.6762 (tp40) REVERT: J 1290 ARG cc_start: 0.9428 (mtm110) cc_final: 0.9188 (mtm-85) REVERT: J 1307 LEU cc_start: 0.8780 (mm) cc_final: 0.8481 (mm) outliers start: 6 outliers final: 1 residues processed: 865 average time/residue: 0.1964 time to fit residues: 255.0588 Evaluate side-chains 716 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 714 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 146 optimal weight: 0.5980 chunk 176 optimal weight: 9.9990 chunk 276 optimal weight: 30.0000 chunk 295 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 303 optimal weight: 0.5980 chunk 11 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 208 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN I 86 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I 767 GLN ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1175 ASN I1236 ASN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 954 ASN ** J1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.110312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.070441 restraints weight = 88564.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.073676 restraints weight = 54823.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.076122 restraints weight = 38541.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.077937 restraints weight = 29459.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.079332 restraints weight = 23814.314| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25706 Z= 0.160 Angle : 0.763 31.249 34937 Z= 0.378 Chirality : 0.047 0.318 3992 Planarity : 0.007 0.166 4386 Dihedral : 14.491 63.280 3992 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.80 % Favored : 94.17 % Rotamer: Outliers : 0.23 % Allowed : 3.69 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3071 helix: 0.41 (0.15), residues: 1068 sheet: -0.87 (0.26), residues: 382 loop : -1.72 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 97 TYR 0.016 0.001 TYR J 631 PHE 0.029 0.002 PHE J 62 TRP 0.015 0.002 TRP I 997 HIS 0.004 0.001 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (25698) covalent geometry : angle 0.71482 / 0.37 (34925) hydrogen bonds : bond 0.04834 / 3.39 ( 1057) hydrogen bonds : angle 5.74016 / 3.98 ( 2933) metal coordination : bond 0.01611 / 0.72 ( 8) metal coordination : angle 14.48775 / 8.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 815 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 HIS cc_start: 0.9198 (m-70) cc_final: 0.8600 (m-70) REVERT: G 104 LYS cc_start: 0.8247 (tptp) cc_final: 0.7941 (tmtt) REVERT: G 185 TYR cc_start: 0.7810 (p90) cc_final: 0.6931 (p90) REVERT: G 199 ASP cc_start: 0.7566 (m-30) cc_final: 0.7228 (m-30) REVERT: H 29 GLU cc_start: 0.8269 (pm20) cc_final: 0.8039 (pm20) REVERT: H 37 HIS cc_start: 0.9638 (m90) cc_final: 0.9255 (m-70) REVERT: H 46 ILE cc_start: 0.9665 (tp) cc_final: 0.9375 (tp) REVERT: H 71 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8794 (tptp) REVERT: H 141 SER cc_start: 0.9650 (t) cc_final: 0.9332 (m) REVERT: H 142 MET cc_start: 0.9607 (ptm) cc_final: 0.9327 (ptm) REVERT: H 185 TYR cc_start: 0.7685 (p90) cc_final: 0.7134 (p90) REVERT: H 194 GLN cc_start: 0.9470 (tp40) cc_final: 0.9229 (mm-40) REVERT: H 200 LYS cc_start: 0.9197 (tmtt) cc_final: 0.8877 (tptp) REVERT: I 6 THR cc_start: 0.9310 (p) cc_final: 0.8712 (p) REVERT: I 9 LYS cc_start: 0.9082 (mttm) cc_final: 0.8605 (mttm) REVERT: I 17 LYS cc_start: 0.9652 (mptt) cc_final: 0.9165 (mmtm) REVERT: I 26 TYR cc_start: 0.8547 (t80) cc_final: 0.8067 (t80) REVERT: I 32 LEU cc_start: 0.9603 (mt) cc_final: 0.9157 (mt) REVERT: I 53 PHE cc_start: 0.8490 (m-80) cc_final: 0.8046 (m-10) REVERT: I 69 GLN cc_start: 0.9544 (pt0) cc_final: 0.9341 (pm20) REVERT: I 92 TYR cc_start: 0.9388 (t80) cc_final: 0.9022 (t80) REVERT: I 100 LEU cc_start: 0.9762 (mt) cc_final: 0.9381 (pp) REVERT: I 124 MET cc_start: 0.9589 (tpp) cc_final: 0.9164 (tpp) REVERT: I 160 ASP cc_start: 0.8942 (m-30) cc_final: 0.8741 (m-30) REVERT: I 179 TYR cc_start: 0.7833 (t80) cc_final: 0.7579 (t80) REVERT: I 213 LEU cc_start: 0.9368 (mp) cc_final: 0.8715 (mp) REVERT: I 342 ASP cc_start: 0.9073 (m-30) cc_final: 0.8823 (m-30) REVERT: I 396 ASP cc_start: 0.9206 (t0) cc_final: 0.8881 (t0) REVERT: I 397 LEU cc_start: 0.9056 (mt) cc_final: 0.8710 (mt) REVERT: I 405 PHE cc_start: 0.9631 (t80) cc_final: 0.9355 (t80) REVERT: I 461 GLU cc_start: 0.9359 (tp30) cc_final: 0.8601 (tp30) REVERT: I 464 PHE cc_start: 0.9794 (t80) cc_final: 0.9225 (t80) REVERT: I 477 GLU cc_start: 0.9591 (OUTLIER) cc_final: 0.9388 (mp0) REVERT: I 548 ARG cc_start: 0.9300 (mtt180) cc_final: 0.8564 (mtt180) REVERT: I 606 LEU cc_start: 0.9280 (mp) cc_final: 0.9049 (mp) REVERT: I 633 LEU cc_start: 0.9582 (pt) cc_final: 0.9237 (mm) REVERT: I 642 SER cc_start: 0.8915 (p) cc_final: 0.8616 (t) REVERT: I 668 ILE cc_start: 0.9578 (mm) cc_final: 0.9295 (mm) REVERT: I 671 LEU cc_start: 0.9802 (tp) cc_final: 0.9556 (tp) REVERT: I 672 GLU cc_start: 0.9396 (pm20) cc_final: 0.9030 (pm20) REVERT: I 681 MET cc_start: 0.9251 (mtp) cc_final: 0.8702 (mtt) REVERT: I 685 MET cc_start: 0.9365 (mtm) cc_final: 0.8352 (mtm) REVERT: I 737 ASN cc_start: 0.9399 (m-40) cc_final: 0.9125 (m-40) REVERT: I 748 ILE cc_start: 0.8967 (pt) cc_final: 0.8738 (pt) REVERT: I 805 MET cc_start: 0.9298 (ppp) cc_final: 0.9056 (ppp) REVERT: I 816 ILE cc_start: 0.9537 (mt) cc_final: 0.9303 (mt) REVERT: I 831 ILE cc_start: 0.8716 (mm) cc_final: 0.8292 (mm) REVERT: I 930 ASP cc_start: 0.9780 (t70) cc_final: 0.9357 (t70) REVERT: I 1053 TYR cc_start: 0.8303 (m-80) cc_final: 0.7980 (m-80) REVERT: I 1061 GLN cc_start: 0.9470 (tt0) cc_final: 0.8997 (tm-30) REVERT: I 1095 ASP cc_start: 0.9683 (m-30) cc_final: 0.9440 (m-30) REVERT: I 1106 ARG cc_start: 0.9452 (mmm-85) cc_final: 0.9140 (mmt180) REVERT: I 1107 MET cc_start: 0.9199 (mmm) cc_final: 0.8117 (tpt) REVERT: I 1113 LEU cc_start: 0.9672 (mp) cc_final: 0.9454 (mp) REVERT: I 1122 LYS cc_start: 0.9674 (tptm) cc_final: 0.9194 (tppt) REVERT: I 1126 ASP cc_start: 0.9492 (m-30) cc_final: 0.8735 (m-30) REVERT: I 1187 PHE cc_start: 0.8999 (m-10) cc_final: 0.8534 (m-10) REVERT: I 1230 MET cc_start: 0.9396 (tpt) cc_final: 0.9190 (tpt) REVERT: I 1234 LYS cc_start: 0.9446 (tppp) cc_final: 0.9129 (tppp) REVERT: I 1237 HIS cc_start: 0.8702 (m-70) cc_final: 0.8220 (m90) REVERT: I 1265 PHE cc_start: 0.9181 (t80) cc_final: 0.8939 (t80) REVERT: I 1270 PHE cc_start: 0.9204 (t80) cc_final: 0.8372 (t80) REVERT: I 1273 MET cc_start: 0.7972 (ptt) cc_final: 0.7552 (ptt) REVERT: I 1290 MET cc_start: 0.9474 (tmm) cc_final: 0.8978 (tmm) REVERT: I 1304 MET cc_start: 0.9646 (tmm) cc_final: 0.9225 (ptp) REVERT: I 1319 MET cc_start: 0.7358 (tpt) cc_final: 0.6650 (tpt) REVERT: I 1321 GLU cc_start: 0.8900 (pm20) cc_final: 0.8651 (pm20) REVERT: I 1329 GLU cc_start: 0.9870 (mt-10) cc_final: 0.9573 (mt-10) REVERT: J 30 ILE cc_start: 0.9646 (mt) cc_final: 0.8767 (mt) REVERT: J 102 MET cc_start: 0.6839 (tpt) cc_final: 0.6555 (tpt) REVERT: J 236 TRP cc_start: 0.9360 (m-10) cc_final: 0.9017 (m-10) REVERT: J 242 LEU cc_start: 0.9462 (tt) cc_final: 0.9175 (tt) REVERT: J 243 PRO cc_start: 0.9636 (Cg_exo) cc_final: 0.9366 (Cg_endo) REVERT: J 325 LYS cc_start: 0.8020 (pttm) cc_final: 0.7716 (pttp) REVERT: J 361 LEU cc_start: 0.9062 (mt) cc_final: 0.8607 (pp) REVERT: J 437 PHE cc_start: 0.9609 (m-80) cc_final: 0.8697 (m-80) REVERT: J 445 LYS cc_start: 0.8639 (mmpt) cc_final: 0.8314 (mmtm) REVERT: J 452 LEU cc_start: 0.9597 (mt) cc_final: 0.9377 (mm) REVERT: J 454 CYS cc_start: 0.9380 (m) cc_final: 0.9132 (m) REVERT: J 487 THR cc_start: 0.9637 (p) cc_final: 0.9380 (p) REVERT: J 535 ARG cc_start: 0.9299 (tmt170) cc_final: 0.9093 (ptm160) REVERT: J 596 LEU cc_start: 0.9367 (tt) cc_final: 0.9091 (tp) REVERT: J 599 LYS cc_start: 0.9264 (pttm) cc_final: 0.8919 (ptmt) REVERT: J 603 LYS cc_start: 0.9298 (pttt) cc_final: 0.8916 (ptpp) REVERT: J 627 THR cc_start: 0.9859 (OUTLIER) cc_final: 0.9446 (t) REVERT: J 631 TYR cc_start: 0.9580 (m-80) cc_final: 0.9134 (m-80) REVERT: J 697 MET cc_start: 0.9631 (ppp) cc_final: 0.9320 (ppp) REVERT: J 746 LEU cc_start: 0.7499 (mp) cc_final: 0.6904 (mp) REVERT: J 764 ARG cc_start: 0.9122 (ttt-90) cc_final: 0.8901 (ttt-90) REVERT: J 798 ARG cc_start: 0.9357 (ptp-170) cc_final: 0.9094 (ptt-90) REVERT: J 864 LEU cc_start: 0.9347 (mm) cc_final: 0.9127 (mm) REVERT: J 891 ASP cc_start: 0.8485 (m-30) cc_final: 0.7207 (m-30) REVERT: J 892 PHE cc_start: 0.8966 (m-10) cc_final: 0.8639 (m-10) REVERT: J 932 MET cc_start: 0.5336 (tpp) cc_final: 0.5096 (tpp) REVERT: J 1040 MET cc_start: 0.7974 (mmp) cc_final: 0.7463 (mmm) REVERT: J 1194 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7865 (mtt180) REVERT: J 1215 GLU cc_start: 0.9454 (mp0) cc_final: 0.9232 (mm-30) REVERT: J 1238 GLN cc_start: 0.9728 (mm110) cc_final: 0.9242 (tp40) REVERT: J 1242 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8513 (ptp-170) REVERT: J 1249 ASN cc_start: 0.9553 (t0) cc_final: 0.9143 (t0) REVERT: J 1254 GLU cc_start: 0.9588 (mt-10) cc_final: 0.9387 (mt-10) REVERT: J 1260 MET cc_start: 0.9505 (tmm) cc_final: 0.9059 (tmm) REVERT: J 1266 ILE cc_start: 0.8153 (mt) cc_final: 0.7804 (mt) REVERT: J 1279 GLN cc_start: 0.6966 (tt0) cc_final: 0.6676 (tp40) REVERT: J 1286 LYS cc_start: 0.9727 (pttt) cc_final: 0.9065 (pttt) REVERT: J 1290 ARG cc_start: 0.9434 (mtm110) cc_final: 0.9041 (ptm160) REVERT: J 1307 LEU cc_start: 0.8751 (mm) cc_final: 0.8461 (mm) outliers start: 6 outliers final: 1 residues processed: 818 average time/residue: 0.1629 time to fit residues: 204.2051 Evaluate side-chains 692 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 689 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 202 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 117 optimal weight: 0.0020 chunk 122 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 196 optimal weight: 0.0870 chunk 262 optimal weight: 7.9990 overall best weight: 1.1570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 463 GLN I 526 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1175 ASN ** I1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 GLN J 907 HIS J 954 ASN ** J1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.110714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070928 restraints weight = 87836.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.074194 restraints weight = 54422.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.076630 restraints weight = 38302.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.078503 restraints weight = 29192.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.079852 restraints weight = 23570.071| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25706 Z= 0.150 Angle : 0.714 20.841 34937 Z= 0.363 Chirality : 0.046 0.207 3992 Planarity : 0.006 0.140 4386 Dihedral : 14.524 62.161 3992 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.89 % Favored : 94.07 % Rotamer: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3071 helix: 0.25 (0.15), residues: 1069 sheet: -0.85 (0.26), residues: 367 loop : -1.75 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 97 TYR 0.025 0.002 TYR I 810 PHE 0.023 0.002 PHE J 62 TRP 0.010 0.002 TRP I 997 HIS 0.004 0.001 HIS I1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (25698) covalent geometry : angle 0.69326 / 0.36 (34925) hydrogen bonds : bond 0.04608 / 3.19 ( 1057) hydrogen bonds : angle 5.60244 / 3.87 ( 2933) metal coordination : bond 0.01399 / 0.65 ( 8) metal coordination : angle 9.14550 / 5.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 812 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.9741 (m-80) cc_final: 0.9520 (m-10) REVERT: G 37 HIS cc_start: 0.9183 (m-70) cc_final: 0.8611 (m-70) REVERT: G 84 ASN cc_start: 0.8616 (t0) cc_final: 0.8313 (t0) REVERT: G 104 LYS cc_start: 0.8226 (tptp) cc_final: 0.7927 (tmtt) REVERT: G 130 ILE cc_start: 0.9649 (mp) cc_final: 0.9391 (mp) REVERT: G 185 TYR cc_start: 0.7724 (p90) cc_final: 0.6912 (p90) REVERT: G 227 GLN cc_start: 0.9847 (mt0) cc_final: 0.9583 (mt0) REVERT: G 231 PHE cc_start: 0.9875 (m-80) cc_final: 0.9673 (m-80) REVERT: H 29 GLU cc_start: 0.8312 (pm20) cc_final: 0.8108 (pm20) REVERT: H 37 HIS cc_start: 0.9647 (m90) cc_final: 0.9366 (m90) REVERT: H 141 SER cc_start: 0.9662 (t) cc_final: 0.9385 (m) REVERT: H 142 MET cc_start: 0.9591 (ptm) cc_final: 0.9324 (ptm) REVERT: H 147 GLN cc_start: 0.8792 (mp10) cc_final: 0.8371 (mp10) REVERT: H 185 TYR cc_start: 0.7795 (p90) cc_final: 0.7289 (p90) REVERT: H 200 LYS cc_start: 0.9207 (tmtt) cc_final: 0.8896 (tmtt) REVERT: H 215 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7939 (tm-30) REVERT: I 6 THR cc_start: 0.9325 (p) cc_final: 0.8917 (p) REVERT: I 9 LYS cc_start: 0.9091 (mttm) cc_final: 0.8648 (mttm) REVERT: I 32 LEU cc_start: 0.9488 (mt) cc_final: 0.9087 (pp) REVERT: I 39 ILE cc_start: 0.9301 (pt) cc_final: 0.8671 (pt) REVERT: I 53 PHE cc_start: 0.8732 (m-80) cc_final: 0.8030 (m-10) REVERT: I 69 GLN cc_start: 0.9592 (pt0) cc_final: 0.9341 (pm20) REVERT: I 74 ARG cc_start: 0.9546 (tmt170) cc_final: 0.9327 (ptm-80) REVERT: I 92 TYR cc_start: 0.9371 (t80) cc_final: 0.9011 (t80) REVERT: I 100 LEU cc_start: 0.9736 (mt) cc_final: 0.9373 (pp) REVERT: I 124 MET cc_start: 0.9600 (tpp) cc_final: 0.9077 (tpp) REVERT: I 213 LEU cc_start: 0.9138 (mp) cc_final: 0.8917 (mp) REVERT: I 342 ASP cc_start: 0.9061 (m-30) cc_final: 0.8780 (m-30) REVERT: I 396 ASP cc_start: 0.9165 (t70) cc_final: 0.8941 (t0) REVERT: I 397 LEU cc_start: 0.9011 (mt) cc_final: 0.8742 (mt) REVERT: I 405 PHE cc_start: 0.9623 (t80) cc_final: 0.9271 (t80) REVERT: I 419 ILE cc_start: 0.9273 (pt) cc_final: 0.9020 (pt) REVERT: I 452 ARG cc_start: 0.9103 (mmm-85) cc_final: 0.8348 (mmm-85) REVERT: I 461 GLU cc_start: 0.9485 (tp30) cc_final: 0.9204 (tp30) REVERT: I 464 PHE cc_start: 0.9808 (t80) cc_final: 0.9380 (t80) REVERT: I 548 ARG cc_start: 0.9312 (mtt180) cc_final: 0.8564 (mtt180) REVERT: I 606 LEU cc_start: 0.9268 (mp) cc_final: 0.9029 (mp) REVERT: I 633 LEU cc_start: 0.9590 (pt) cc_final: 0.9295 (mm) REVERT: I 642 SER cc_start: 0.8926 (p) cc_final: 0.8670 (t) REVERT: I 671 LEU cc_start: 0.9804 (tp) cc_final: 0.9557 (tp) REVERT: I 672 GLU cc_start: 0.9449 (pm20) cc_final: 0.9017 (pm20) REVERT: I 681 MET cc_start: 0.9042 (mtp) cc_final: 0.8606 (mtt) REVERT: I 685 MET cc_start: 0.9289 (mtm) cc_final: 0.8442 (mtm) REVERT: I 687 ARG cc_start: 0.8529 (ptt180) cc_final: 0.8240 (ptp-170) REVERT: I 697 LYS cc_start: 0.8422 (mmmt) cc_final: 0.7380 (mmtm) REVERT: I 748 ILE cc_start: 0.8777 (pt) cc_final: 0.8566 (pt) REVERT: I 749 ASP cc_start: 0.9146 (t0) cc_final: 0.8810 (p0) REVERT: I 768 MET cc_start: 0.9263 (ppp) cc_final: 0.9046 (mpp) REVERT: I 789 THR cc_start: 0.9470 (m) cc_final: 0.9111 (p) REVERT: I 790 ASP cc_start: 0.9316 (t0) cc_final: 0.8994 (p0) REVERT: I 799 ASN cc_start: 0.9192 (t0) cc_final: 0.8441 (t0) REVERT: I 805 MET cc_start: 0.9334 (ppp) cc_final: 0.9083 (ppp) REVERT: I 816 ILE cc_start: 0.9450 (mt) cc_final: 0.9152 (mt) REVERT: I 817 LEU cc_start: 0.8020 (mm) cc_final: 0.7303 (mm) REVERT: I 818 VAL cc_start: 0.9541 (p) cc_final: 0.9334 (p) REVERT: I 831 ILE cc_start: 0.8755 (mm) cc_final: 0.8236 (mm) REVERT: I 930 ASP cc_start: 0.9785 (t70) cc_final: 0.9332 (t70) REVERT: I 957 LYS cc_start: 0.9550 (pptt) cc_final: 0.9287 (pttm) REVERT: I 1053 TYR cc_start: 0.8276 (m-80) cc_final: 0.7977 (m-80) REVERT: I 1056 VAL cc_start: 0.8506 (m) cc_final: 0.8025 (m) REVERT: I 1061 GLN cc_start: 0.9429 (tt0) cc_final: 0.8817 (tm-30) REVERT: I 1066 MET cc_start: 0.9015 (pmm) cc_final: 0.8736 (pmm) REVERT: I 1070 HIS cc_start: 0.7334 (m-70) cc_final: 0.6507 (m170) REVERT: I 1080 ASN cc_start: 0.8832 (m-40) cc_final: 0.8386 (t0) REVERT: I 1106 ARG cc_start: 0.9433 (mmm-85) cc_final: 0.9134 (mmt180) REVERT: I 1107 MET cc_start: 0.9159 (mmm) cc_final: 0.8141 (tpt) REVERT: I 1113 LEU cc_start: 0.9614 (mp) cc_final: 0.9410 (mp) REVERT: I 1122 LYS cc_start: 0.9704 (tptm) cc_final: 0.9042 (tppt) REVERT: I 1126 ASP cc_start: 0.9475 (m-30) cc_final: 0.8687 (m-30) REVERT: I 1223 ARG cc_start: 0.9298 (tpm170) cc_final: 0.9074 (tpm170) REVERT: I 1234 LYS cc_start: 0.9466 (tppp) cc_final: 0.9219 (tppp) REVERT: I 1237 HIS cc_start: 0.8611 (m-70) cc_final: 0.8201 (m90) REVERT: I 1264 GLN cc_start: 0.9461 (tp-100) cc_final: 0.9186 (tm-30) REVERT: I 1265 PHE cc_start: 0.9147 (t80) cc_final: 0.8861 (t80) REVERT: I 1270 PHE cc_start: 0.9218 (t80) cc_final: 0.8482 (t80) REVERT: I 1290 MET cc_start: 0.9477 (tmm) cc_final: 0.8974 (tmm) REVERT: I 1304 MET cc_start: 0.9647 (tmm) cc_final: 0.9219 (ptp) REVERT: I 1319 MET cc_start: 0.7555 (tpt) cc_final: 0.6797 (tpt) REVERT: I 1321 GLU cc_start: 0.8940 (pm20) cc_final: 0.8699 (pm20) REVERT: I 1329 GLU cc_start: 0.9869 (mt-10) cc_final: 0.9605 (mt-10) REVERT: J 30 ILE cc_start: 0.9277 (mt) cc_final: 0.8845 (mt) REVERT: J 102 MET cc_start: 0.6826 (tpt) cc_final: 0.6463 (tpt) REVERT: J 207 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9134 (mm-30) REVERT: J 236 TRP cc_start: 0.9406 (m-10) cc_final: 0.9172 (m-10) REVERT: J 242 LEU cc_start: 0.9447 (tt) cc_final: 0.9141 (tt) REVERT: J 243 PRO cc_start: 0.9641 (Cg_exo) cc_final: 0.9375 (Cg_endo) REVERT: J 335 GLN cc_start: 0.8989 (pp30) cc_final: 0.8672 (pp30) REVERT: J 361 LEU cc_start: 0.9107 (mt) cc_final: 0.8553 (pp) REVERT: J 423 LEU cc_start: 0.9835 (mp) cc_final: 0.9553 (mp) REVERT: J 437 PHE cc_start: 0.9597 (m-80) cc_final: 0.8580 (m-80) REVERT: J 445 LYS cc_start: 0.8636 (mmpt) cc_final: 0.8260 (mmtm) REVERT: J 454 CYS cc_start: 0.9320 (m) cc_final: 0.9043 (m) REVERT: J 487 THR cc_start: 0.9590 (p) cc_final: 0.9348 (p) REVERT: J 603 LYS cc_start: 0.9301 (pttt) cc_final: 0.8905 (ptpp) REVERT: J 619 ILE cc_start: 0.9652 (mp) cc_final: 0.9439 (pt) REVERT: J 627 THR cc_start: 0.9856 (t) cc_final: 0.9296 (t) REVERT: J 631 TYR cc_start: 0.9513 (m-80) cc_final: 0.9144 (m-80) REVERT: J 644 MET cc_start: 0.9505 (mpp) cc_final: 0.9254 (mpp) REVERT: J 697 MET cc_start: 0.9624 (ppp) cc_final: 0.9337 (ppp) REVERT: J 765 GLU cc_start: 0.9261 (mp0) cc_final: 0.9002 (mp0) REVERT: J 767 LEU cc_start: 0.9181 (mp) cc_final: 0.8716 (tp) REVERT: J 798 ARG cc_start: 0.9332 (ptp-170) cc_final: 0.9112 (ptt-90) REVERT: J 822 MET cc_start: 0.8578 (tpt) cc_final: 0.7871 (tpp) REVERT: J 864 LEU cc_start: 0.9365 (mm) cc_final: 0.9144 (mm) REVERT: J 870 ASP cc_start: 0.8949 (m-30) cc_final: 0.8732 (m-30) REVERT: J 913 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8188 (mm-30) REVERT: J 1040 MET cc_start: 0.8017 (mmp) cc_final: 0.7405 (mmm) REVERT: J 1194 ARG cc_start: 0.8248 (mtt180) cc_final: 0.8003 (mtt180) REVERT: J 1215 GLU cc_start: 0.9485 (mp0) cc_final: 0.9256 (mm-30) REVERT: J 1238 GLN cc_start: 0.9725 (mm110) cc_final: 0.9248 (tp40) REVERT: J 1242 ARG cc_start: 0.8981 (ttp80) cc_final: 0.8499 (ptp-170) REVERT: J 1249 ASN cc_start: 0.9569 (t0) cc_final: 0.9167 (t0) REVERT: J 1260 MET cc_start: 0.9457 (tmm) cc_final: 0.8977 (tmm) REVERT: J 1266 ILE cc_start: 0.8135 (mt) cc_final: 0.7769 (mt) REVERT: J 1279 GLN cc_start: 0.7078 (tt0) cc_final: 0.6807 (tp40) REVERT: J 1307 LEU cc_start: 0.8769 (mm) cc_final: 0.8493 (mm) outliers start: 1 outliers final: 0 residues processed: 812 average time/residue: 0.1597 time to fit residues: 200.2045 Evaluate side-chains 695 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 33 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 309 optimal weight: 50.0000 chunk 305 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 258 optimal weight: 6.9990 chunk 286 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN I 65 ASN I 69 GLN I 148 GLN I 463 GLN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN J 954 ASN J1279 GLN J1367 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.104245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.066270 restraints weight = 94260.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.069186 restraints weight = 59979.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.071370 restraints weight = 42891.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.073066 restraints weight = 33124.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.074237 restraints weight = 26968.348| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 25706 Z= 0.275 Angle : 0.795 11.986 34937 Z= 0.414 Chirality : 0.047 0.269 3992 Planarity : 0.007 0.110 4386 Dihedral : 14.733 63.425 3992 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.03 % Favored : 92.93 % Rotamer: Outliers : 0.08 % Allowed : 3.46 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.14), residues: 3071 helix: -0.04 (0.15), residues: 1090 sheet: -1.13 (0.25), residues: 376 loop : -1.87 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 81 TYR 0.027 0.003 TYR J 68 PHE 0.043 0.003 PHE I 57 TRP 0.016 0.002 TRP J 409 HIS 0.009 0.002 HIS I 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.27 (25698) covalent geometry : angle 0.78564 / 0.41 (34925) hydrogen bonds : bond 0.05172 / 3.58 ( 1057) hydrogen bonds : angle 5.86631 / 4.05 ( 2933) metal coordination : bond 0.01342 / 0.61 ( 8) metal coordination : angle 6.48112 / 3.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 754 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.9738 (m-80) cc_final: 0.9522 (m-80) REVERT: G 84 ASN cc_start: 0.8718 (t0) cc_final: 0.8407 (t0) REVERT: G 130 ILE cc_start: 0.9728 (mp) cc_final: 0.9451 (mp) REVERT: G 199 ASP cc_start: 0.7740 (m-30) cc_final: 0.7482 (m-30) REVERT: G 227 GLN cc_start: 0.9854 (mt0) cc_final: 0.9595 (mt0) REVERT: H 29 GLU cc_start: 0.8455 (pm20) cc_final: 0.8202 (pm20) REVERT: H 41 ASN cc_start: 0.9433 (t0) cc_final: 0.9214 (m-40) REVERT: H 46 ILE cc_start: 0.9708 (tp) cc_final: 0.9424 (tp) REVERT: H 68 TYR cc_start: 0.9521 (m-10) cc_final: 0.9311 (m-10) REVERT: H 141 SER cc_start: 0.9651 (t) cc_final: 0.9374 (m) REVERT: H 142 MET cc_start: 0.9608 (ptm) cc_final: 0.9349 (ptm) REVERT: H 185 TYR cc_start: 0.7643 (p90) cc_final: 0.6858 (p90) REVERT: H 193 GLU cc_start: 0.8450 (tp30) cc_final: 0.8227 (tp30) REVERT: H 200 LYS cc_start: 0.9250 (tmtt) cc_final: 0.8898 (tmtt) REVERT: I 5 TYR cc_start: 0.8979 (t80) cc_final: 0.8703 (t80) REVERT: I 9 LYS cc_start: 0.9125 (mttm) cc_final: 0.8652 (mttm) REVERT: I 32 LEU cc_start: 0.9545 (mt) cc_final: 0.9091 (pp) REVERT: I 39 ILE cc_start: 0.9370 (pt) cc_final: 0.9060 (pt) REVERT: I 69 GLN cc_start: 0.9630 (pt0) cc_final: 0.9390 (pm20) REVERT: I 92 TYR cc_start: 0.9457 (t80) cc_final: 0.8935 (t80) REVERT: I 100 LEU cc_start: 0.9676 (mt) cc_final: 0.9181 (pp) REVERT: I 342 ASP cc_start: 0.9156 (m-30) cc_final: 0.8834 (m-30) REVERT: I 396 ASP cc_start: 0.9110 (t70) cc_final: 0.8857 (t0) REVERT: I 397 LEU cc_start: 0.9066 (mt) cc_final: 0.8793 (mt) REVERT: I 405 PHE cc_start: 0.9691 (t80) cc_final: 0.9374 (t80) REVERT: I 419 ILE cc_start: 0.9283 (pt) cc_final: 0.8964 (pt) REVERT: I 452 ARG cc_start: 0.9448 (ttt90) cc_final: 0.8943 (mmm-85) REVERT: I 464 PHE cc_start: 0.9806 (t80) cc_final: 0.9417 (t80) REVERT: I 606 LEU cc_start: 0.9365 (mp) cc_final: 0.9155 (mp) REVERT: I 671 LEU cc_start: 0.9780 (tp) cc_final: 0.9552 (tp) REVERT: I 672 GLU cc_start: 0.9529 (pm20) cc_final: 0.9023 (pm20) REVERT: I 681 MET cc_start: 0.9134 (mtp) cc_final: 0.8689 (mtt) REVERT: I 685 MET cc_start: 0.9379 (mtm) cc_final: 0.8735 (mtm) REVERT: I 687 ARG cc_start: 0.8709 (ptt180) cc_final: 0.8384 (ptp-170) REVERT: I 688 GLN cc_start: 0.9473 (pp30) cc_final: 0.9201 (pp30) REVERT: I 697 LYS cc_start: 0.8608 (mmmt) cc_final: 0.7432 (mmtt) REVERT: I 720 ARG cc_start: 0.8948 (mmt90) cc_final: 0.8743 (mpt-90) REVERT: I 748 ILE cc_start: 0.8868 (pt) cc_final: 0.8481 (pt) REVERT: I 749 ASP cc_start: 0.9131 (t0) cc_final: 0.8719 (p0) REVERT: I 755 LYS cc_start: 0.9532 (mmtm) cc_final: 0.9315 (mmmt) REVERT: I 790 ASP cc_start: 0.9458 (t0) cc_final: 0.9084 (p0) REVERT: I 816 ILE cc_start: 0.9375 (mt) cc_final: 0.8343 (mt) REVERT: I 817 LEU cc_start: 0.8008 (mm) cc_final: 0.7423 (mm) REVERT: I 831 ILE cc_start: 0.8877 (mm) cc_final: 0.8568 (mm) REVERT: I 882 ILE cc_start: 0.9590 (mp) cc_final: 0.9220 (mp) REVERT: I 930 ASP cc_start: 0.9747 (t70) cc_final: 0.9123 (t70) REVERT: I 957 LYS cc_start: 0.9620 (pptt) cc_final: 0.9292 (mmmt) REVERT: I 1024 GLU cc_start: 0.9715 (tt0) cc_final: 0.9399 (pt0) REVERT: I 1053 TYR cc_start: 0.8182 (m-80) cc_final: 0.7880 (m-80) REVERT: I 1056 VAL cc_start: 0.8512 (m) cc_final: 0.8015 (m) REVERT: I 1061 GLN cc_start: 0.9388 (tt0) cc_final: 0.8898 (tm-30) REVERT: I 1066 MET cc_start: 0.8654 (pmm) cc_final: 0.7812 (pmm) REVERT: I 1080 ASN cc_start: 0.9035 (m-40) cc_final: 0.8484 (t0) REVERT: I 1106 ARG cc_start: 0.9538 (mmm-85) cc_final: 0.9213 (mmt180) REVERT: I 1107 MET cc_start: 0.9145 (mmm) cc_final: 0.7602 (tmm) REVERT: I 1122 LYS cc_start: 0.9599 (tptm) cc_final: 0.9108 (tppt) REVERT: I 1126 ASP cc_start: 0.9462 (m-30) cc_final: 0.8699 (m-30) REVERT: I 1180 MET cc_start: 0.9257 (ttp) cc_final: 0.9036 (ttp) REVERT: I 1187 PHE cc_start: 0.9025 (m-10) cc_final: 0.8559 (m-10) REVERT: I 1234 LYS cc_start: 0.9510 (tppp) cc_final: 0.9186 (tppp) REVERT: I 1237 HIS cc_start: 0.8935 (m-70) cc_final: 0.8581 (m-70) REVERT: I 1264 GLN cc_start: 0.9424 (tp-100) cc_final: 0.9092 (tm-30) REVERT: I 1270 PHE cc_start: 0.9075 (t80) cc_final: 0.8197 (t80) REVERT: I 1273 MET cc_start: 0.8105 (ptt) cc_final: 0.7875 (ptt) REVERT: I 1290 MET cc_start: 0.9528 (tmm) cc_final: 0.9097 (tmm) REVERT: I 1304 MET cc_start: 0.9675 (tmm) cc_final: 0.9281 (ptp) REVERT: I 1319 MET cc_start: 0.7848 (tpt) cc_final: 0.6973 (tpt) REVERT: I 1321 GLU cc_start: 0.9058 (pm20) cc_final: 0.8776 (pm20) REVERT: I 1329 GLU cc_start: 0.9888 (mt-10) cc_final: 0.9621 (mt-10) REVERT: J 29 MET cc_start: 0.8619 (ppp) cc_final: 0.8409 (ppp) REVERT: J 30 ILE cc_start: 0.9349 (mt) cc_final: 0.8872 (mt) REVERT: J 207 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9153 (mm-30) REVERT: J 242 LEU cc_start: 0.9484 (tt) cc_final: 0.9252 (tt) REVERT: J 361 LEU cc_start: 0.9051 (mt) cc_final: 0.8588 (pp) REVERT: J 409 TRP cc_start: 0.8976 (m100) cc_final: 0.8312 (m100) REVERT: J 423 LEU cc_start: 0.9827 (mp) cc_final: 0.9557 (mp) REVERT: J 437 PHE cc_start: 0.9633 (m-80) cc_final: 0.8594 (m-80) REVERT: J 445 LYS cc_start: 0.8864 (mmpt) cc_final: 0.8486 (mmtm) REVERT: J 454 CYS cc_start: 0.9297 (m) cc_final: 0.9058 (m) REVERT: J 478 LEU cc_start: 0.9672 (tt) cc_final: 0.9453 (mt) REVERT: J 603 LYS cc_start: 0.9341 (pttt) cc_final: 0.8930 (ptpp) REVERT: J 627 THR cc_start: 0.9865 (t) cc_final: 0.9322 (t) REVERT: J 631 TYR cc_start: 0.9501 (m-80) cc_final: 0.9162 (m-80) REVERT: J 645 VAL cc_start: 0.8633 (p) cc_final: 0.8230 (m) REVERT: J 697 MET cc_start: 0.9632 (ppp) cc_final: 0.9360 (ppp) REVERT: J 724 MET cc_start: 0.9425 (mtt) cc_final: 0.8879 (mmp) REVERT: J 792 ASN cc_start: 0.9371 (m110) cc_final: 0.9163 (m110) REVERT: J 822 MET cc_start: 0.8404 (tpt) cc_final: 0.7791 (tpp) REVERT: J 864 LEU cc_start: 0.9394 (mm) cc_final: 0.9176 (mm) REVERT: J 1040 MET cc_start: 0.8099 (mmp) cc_final: 0.7378 (mmm) REVERT: J 1194 ARG cc_start: 0.8304 (mtt180) cc_final: 0.8060 (mtt180) REVERT: J 1215 GLU cc_start: 0.9510 (mp0) cc_final: 0.9238 (mm-30) REVERT: J 1242 ARG cc_start: 0.9064 (ttp80) cc_final: 0.8774 (ptp-170) REVERT: J 1260 MET cc_start: 0.9538 (tmm) cc_final: 0.9124 (tmm) REVERT: J 1266 ILE cc_start: 0.8085 (mt) cc_final: 0.7415 (mt) REVERT: J 1334 GLU cc_start: 0.9358 (tm-30) cc_final: 0.9101 (tm-30) outliers start: 2 outliers final: 0 residues processed: 755 average time/residue: 0.1566 time to fit residues: 182.7085 Evaluate side-chains 647 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 647 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 117 optimal weight: 10.0000 chunk 230 optimal weight: 0.9980 chunk 279 optimal weight: 6.9990 chunk 127 optimal weight: 0.2980 chunk 228 optimal weight: 10.0000 chunk 128 optimal weight: 0.0000 chunk 39 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 262 optimal weight: 8.9990 chunk 267 optimal weight: 5.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS H 37 HIS I 20 GLN I 69 GLN I 148 GLN I 165 HIS I 463 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1146 GLN I1175 ASN ** I1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN J 921 GLN J 954 ASN J1235 ASN ** J1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1367 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.109353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.069827 restraints weight = 89039.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.072972 restraints weight = 55488.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.075362 restraints weight = 39473.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.077211 restraints weight = 30190.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.078618 restraints weight = 24387.982| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 25706 Z= 0.154 Angle : 0.738 11.594 34937 Z= 0.377 Chirality : 0.047 0.265 3992 Planarity : 0.006 0.111 4386 Dihedral : 14.683 63.328 3992 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 0.11 % Allowed : 2.02 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.14), residues: 3071 helix: 0.05 (0.15), residues: 1087 sheet: -1.20 (0.26), residues: 366 loop : -1.75 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG J1284 TYR 0.051 0.002 TYR I 756 PHE 0.073 0.003 PHE J1274 TRP 0.036 0.002 TRP I 183 HIS 0.007 0.001 HIS J 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (25698) covalent geometry : angle 0.73028 / 0.38 (34925) hydrogen bonds : bond 0.04548 / 3.18 ( 1057) hydrogen bonds : angle 5.61172 / 3.87 ( 2933) metal coordination : bond 0.00874 / 0.37 ( 8) metal coordination : angle 5.87371 / 3.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 786 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.9581 (m-80) cc_final: 0.9319 (m-80) REVERT: G 45 ARG cc_start: 0.8802 (mmt180) cc_final: 0.8238 (mmt180) REVERT: G 84 ASN cc_start: 0.8607 (t0) cc_final: 0.8297 (t0) REVERT: G 104 LYS cc_start: 0.8243 (tptp) cc_final: 0.7917 (tmtt) REVERT: G 130 ILE cc_start: 0.9609 (mp) cc_final: 0.9320 (mp) REVERT: G 199 ASP cc_start: 0.7765 (m-30) cc_final: 0.7497 (m-30) REVERT: G 205 MET cc_start: 0.9598 (ppp) cc_final: 0.8935 (ppp) REVERT: G 231 PHE cc_start: 0.9859 (m-80) cc_final: 0.9635 (m-80) REVERT: H 16 ILE cc_start: 0.8261 (pt) cc_final: 0.7854 (mp) REVERT: H 29 GLU cc_start: 0.8372 (pm20) cc_final: 0.8157 (pm20) REVERT: H 37 HIS cc_start: 0.9615 (m-70) cc_final: 0.9245 (m90) REVERT: H 46 ILE cc_start: 0.9696 (tp) cc_final: 0.9427 (tp) REVERT: H 68 TYR cc_start: 0.9527 (m-10) cc_final: 0.9304 (m-10) REVERT: H 79 LEU cc_start: 0.9176 (mp) cc_final: 0.8867 (mp) REVERT: H 83 LEU cc_start: 0.9547 (pp) cc_final: 0.9081 (mm) REVERT: H 141 SER cc_start: 0.9676 (t) cc_final: 0.9379 (m) REVERT: H 142 MET cc_start: 0.9586 (ptm) cc_final: 0.9261 (ptm) REVERT: H 194 GLN cc_start: 0.9547 (tp40) cc_final: 0.9337 (tp40) REVERT: H 200 LYS cc_start: 0.9174 (tmtt) cc_final: 0.8809 (tmtt) REVERT: I 5 TYR cc_start: 0.8897 (t80) cc_final: 0.8629 (t80) REVERT: I 6 THR cc_start: 0.9294 (p) cc_final: 0.8802 (p) REVERT: I 9 LYS cc_start: 0.9099 (mttm) cc_final: 0.8623 (mttm) REVERT: I 32 LEU cc_start: 0.9493 (mt) cc_final: 0.9059 (pp) REVERT: I 39 ILE cc_start: 0.9286 (pt) cc_final: 0.8776 (pt) REVERT: I 53 PHE cc_start: 0.8521 (m-80) cc_final: 0.8186 (m-10) REVERT: I 69 GLN cc_start: 0.9576 (pt0) cc_final: 0.9368 (pm20) REVERT: I 100 LEU cc_start: 0.9699 (mt) cc_final: 0.9249 (pp) REVERT: I 277 LEU cc_start: 0.9654 (mt) cc_final: 0.9180 (pp) REVERT: I 291 TYR cc_start: 0.9580 (t80) cc_final: 0.9355 (t80) REVERT: I 342 ASP cc_start: 0.9109 (m-30) cc_final: 0.8817 (m-30) REVERT: I 396 ASP cc_start: 0.9161 (t70) cc_final: 0.8951 (t0) REVERT: I 405 PHE cc_start: 0.9655 (t80) cc_final: 0.9366 (t80) REVERT: I 419 ILE cc_start: 0.9258 (pt) cc_final: 0.8980 (pt) REVERT: I 430 LYS cc_start: 0.9403 (mmtm) cc_final: 0.9141 (mmmt) REVERT: I 464 PHE cc_start: 0.9794 (t80) cc_final: 0.9194 (t80) REVERT: I 548 ARG cc_start: 0.9335 (mtt180) cc_final: 0.8606 (mtt180) REVERT: I 591 TYR cc_start: 0.9437 (m-80) cc_final: 0.8928 (m-80) REVERT: I 606 LEU cc_start: 0.9319 (mp) cc_final: 0.8734 (mp) REVERT: I 633 LEU cc_start: 0.9588 (pt) cc_final: 0.9267 (mm) REVERT: I 659 GLN cc_start: 0.9512 (pp30) cc_final: 0.8510 (pt0) REVERT: I 668 ILE cc_start: 0.9562 (mm) cc_final: 0.9272 (mm) REVERT: I 671 LEU cc_start: 0.9775 (tp) cc_final: 0.9484 (tp) REVERT: I 672 GLU cc_start: 0.9511 (pm20) cc_final: 0.8992 (pm20) REVERT: I 681 MET cc_start: 0.9144 (mtp) cc_final: 0.8694 (mtt) REVERT: I 685 MET cc_start: 0.9254 (mtm) cc_final: 0.8798 (mtm) REVERT: I 697 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7334 (mmtt) REVERT: I 748 ILE cc_start: 0.8767 (pt) cc_final: 0.8393 (pt) REVERT: I 749 ASP cc_start: 0.9107 (t0) cc_final: 0.8731 (p0) REVERT: I 790 ASP cc_start: 0.9423 (t0) cc_final: 0.9066 (p0) REVERT: I 805 MET cc_start: 0.9354 (ppp) cc_final: 0.9062 (ppp) REVERT: I 816 ILE cc_start: 0.9464 (mt) cc_final: 0.8481 (mt) REVERT: I 817 LEU cc_start: 0.8275 (mm) cc_final: 0.7590 (mm) REVERT: I 831 ILE cc_start: 0.8931 (mm) cc_final: 0.8461 (mm) REVERT: I 930 ASP cc_start: 0.9741 (t70) cc_final: 0.9069 (t0) REVERT: I 1053 TYR cc_start: 0.8181 (m-80) cc_final: 0.7906 (m-80) REVERT: I 1056 VAL cc_start: 0.8659 (m) cc_final: 0.8213 (m) REVERT: I 1061 GLN cc_start: 0.9346 (tt0) cc_final: 0.8924 (tm-30) REVERT: I 1066 MET cc_start: 0.8770 (pmm) cc_final: 0.8086 (pmm) REVERT: I 1080 ASN cc_start: 0.8912 (m-40) cc_final: 0.8426 (t0) REVERT: I 1106 ARG cc_start: 0.9486 (mmm-85) cc_final: 0.9158 (mmt180) REVERT: I 1107 MET cc_start: 0.9087 (mmm) cc_final: 0.7871 (tmm) REVERT: I 1122 LYS cc_start: 0.9572 (tptm) cc_final: 0.9083 (tppt) REVERT: I 1126 ASP cc_start: 0.9407 (m-30) cc_final: 0.8635 (m-30) REVERT: I 1180 MET cc_start: 0.9295 (ttp) cc_final: 0.9042 (ttp) REVERT: I 1187 PHE cc_start: 0.8860 (m-10) cc_final: 0.8364 (m-10) REVERT: I 1216 ARG cc_start: 0.9176 (mtp180) cc_final: 0.8732 (mmm-85) REVERT: I 1223 ARG cc_start: 0.9395 (tpm170) cc_final: 0.8997 (tpm170) REVERT: I 1230 MET cc_start: 0.9354 (tpt) cc_final: 0.9102 (tmm) REVERT: I 1234 LYS cc_start: 0.9427 (tppp) cc_final: 0.9148 (tppp) REVERT: I 1237 HIS cc_start: 0.8682 (m-70) cc_final: 0.8280 (m90) REVERT: I 1264 GLN cc_start: 0.9452 (tp-100) cc_final: 0.9143 (tm-30) REVERT: I 1265 PHE cc_start: 0.9154 (t80) cc_final: 0.8831 (t80) REVERT: I 1270 PHE cc_start: 0.9042 (t80) cc_final: 0.8333 (t80) REVERT: I 1290 MET cc_start: 0.9436 (tmm) cc_final: 0.9001 (tmm) REVERT: I 1304 MET cc_start: 0.9663 (tmm) cc_final: 0.9280 (ptp) REVERT: I 1319 MET cc_start: 0.7769 (tpt) cc_final: 0.7015 (tpt) REVERT: I 1321 GLU cc_start: 0.8945 (pm20) cc_final: 0.8693 (pm20) REVERT: I 1329 GLU cc_start: 0.9885 (mt-10) cc_final: 0.9579 (mt-10) REVERT: J 30 ILE cc_start: 0.9362 (mt) cc_final: 0.8989 (mt) REVERT: J 102 MET cc_start: 0.6734 (tpt) cc_final: 0.6268 (tpt) REVERT: J 207 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9116 (mm-30) REVERT: J 242 LEU cc_start: 0.9487 (tt) cc_final: 0.9267 (tt) REVERT: J 243 PRO cc_start: 0.9647 (Cg_exo) cc_final: 0.9363 (Cg_endo) REVERT: J 335 GLN cc_start: 0.8949 (pp30) cc_final: 0.8703 (pp30) REVERT: J 361 LEU cc_start: 0.9032 (mt) cc_final: 0.8553 (pp) REVERT: J 405 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8582 (mt-10) REVERT: J 409 TRP cc_start: 0.9008 (m100) cc_final: 0.8286 (m100) REVERT: J 437 PHE cc_start: 0.9613 (m-80) cc_final: 0.9000 (m-80) REVERT: J 445 LYS cc_start: 0.8765 (mmpt) cc_final: 0.8555 (mmtm) REVERT: J 454 CYS cc_start: 0.9278 (m) cc_final: 0.9036 (m) REVERT: J 526 VAL cc_start: 0.9030 (p) cc_final: 0.8693 (p) REVERT: J 603 LYS cc_start: 0.9320 (pttt) cc_final: 0.8931 (ptpp) REVERT: J 627 THR cc_start: 0.9848 (t) cc_final: 0.9161 (t) REVERT: J 631 TYR cc_start: 0.9405 (m-80) cc_final: 0.9122 (m-80) REVERT: J 645 VAL cc_start: 0.8581 (p) cc_final: 0.8211 (m) REVERT: J 697 MET cc_start: 0.9631 (ppp) cc_final: 0.9369 (ppp) REVERT: J 763 PHE cc_start: 0.9260 (m-80) cc_final: 0.8646 (m-80) REVERT: J 764 ARG cc_start: 0.9002 (ttt-90) cc_final: 0.8694 (ttt-90) REVERT: J 798 ARG cc_start: 0.9301 (ptp-170) cc_final: 0.9074 (ptt-90) REVERT: J 822 MET cc_start: 0.8448 (tpt) cc_final: 0.7954 (tpp) REVERT: J 870 ASP cc_start: 0.8928 (m-30) cc_final: 0.8660 (m-30) REVERT: J 1040 MET cc_start: 0.7697 (mmp) cc_final: 0.6976 (mmm) REVERT: J 1145 PHE cc_start: 0.9591 (m-80) cc_final: 0.9378 (m-80) REVERT: J 1194 ARG cc_start: 0.8273 (mtt180) cc_final: 0.8068 (mtt180) REVERT: J 1215 GLU cc_start: 0.9513 (mp0) cc_final: 0.9249 (mm-30) REVERT: J 1238 GLN cc_start: 0.9638 (tp-100) cc_final: 0.9138 (tp40) REVERT: J 1249 ASN cc_start: 0.9422 (t0) cc_final: 0.8948 (t0) REVERT: J 1252 HIS cc_start: 0.9253 (m90) cc_final: 0.9035 (m-70) REVERT: J 1254 GLU cc_start: 0.9590 (mt-10) cc_final: 0.9333 (mt-10) REVERT: J 1260 MET cc_start: 0.9480 (tmm) cc_final: 0.9043 (tmm) REVERT: J 1266 ILE cc_start: 0.8376 (mt) cc_final: 0.8081 (mt) REVERT: J 1334 GLU cc_start: 0.9317 (tm-30) cc_final: 0.9102 (tm-30) outliers start: 3 outliers final: 0 residues processed: 789 average time/residue: 0.1670 time to fit residues: 203.4129 Evaluate side-chains 655 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 207 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 188 optimal weight: 20.0000 chunk 288 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 chunk 133 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN I 148 GLN ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1237 HIS ** I1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN J 921 GLN J 951 GLN J 954 ASN J1367 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.106065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.068190 restraints weight = 92720.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.071171 restraints weight = 58215.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.073423 restraints weight = 41246.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.075122 restraints weight = 31589.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.076421 restraints weight = 25583.679| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25706 Z= 0.223 Angle : 0.762 10.403 34937 Z= 0.398 Chirality : 0.047 0.364 3992 Planarity : 0.006 0.102 4386 Dihedral : 14.720 63.384 3992 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.20 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.14), residues: 3071 helix: -0.02 (0.15), residues: 1096 sheet: -1.45 (0.25), residues: 399 loop : -1.83 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG J 610 TYR 0.039 0.002 TYR I 756 PHE 0.043 0.003 PHE J1274 TRP 0.023 0.003 TRP J 236 HIS 0.008 0.002 HIS I 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.22 (25698) covalent geometry : angle 0.75342 / 0.40 (34925) hydrogen bonds : bond 0.04835 / 3.33 ( 1057) hydrogen bonds : angle 5.73592 / 3.96 ( 2933) metal coordination : bond 0.01736 / 0.63 ( 8) metal coordination : angle 6.24268 / 3.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 737 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.9603 (m-80) cc_final: 0.9380 (m-80) REVERT: G 84 ASN cc_start: 0.8719 (t0) cc_final: 0.8375 (t0) REVERT: G 130 ILE cc_start: 0.9654 (mp) cc_final: 0.9358 (mp) REVERT: G 182 ARG cc_start: 0.8354 (ptt90) cc_final: 0.8098 (ppt90) REVERT: G 199 ASP cc_start: 0.7793 (m-30) cc_final: 0.7531 (m-30) REVERT: G 205 MET cc_start: 0.9555 (ppp) cc_final: 0.8900 (ppp) REVERT: G 227 GLN cc_start: 0.9831 (mt0) cc_final: 0.9552 (mt0) REVERT: H 16 ILE cc_start: 0.8327 (pt) cc_final: 0.7914 (mp) REVERT: H 29 GLU cc_start: 0.8351 (pm20) cc_final: 0.8125 (pm20) REVERT: H 37 HIS cc_start: 0.9667 (m-70) cc_final: 0.9436 (m90) REVERT: H 46 ILE cc_start: 0.9728 (tp) cc_final: 0.9475 (tp) REVERT: H 68 TYR cc_start: 0.9529 (m-10) cc_final: 0.9288 (m-10) REVERT: H 79 LEU cc_start: 0.9234 (mp) cc_final: 0.8930 (mp) REVERT: H 83 LEU cc_start: 0.9575 (pp) cc_final: 0.9110 (mm) REVERT: H 141 SER cc_start: 0.9685 (t) cc_final: 0.9388 (m) REVERT: H 142 MET cc_start: 0.9604 (ptm) cc_final: 0.9314 (ptm) REVERT: H 193 GLU cc_start: 0.8473 (tp30) cc_final: 0.8079 (tp30) REVERT: H 194 GLN cc_start: 0.9558 (tp40) cc_final: 0.9346 (tp40) REVERT: H 200 LYS cc_start: 0.9229 (tmtt) cc_final: 0.8869 (tmtt) REVERT: I 5 TYR cc_start: 0.8946 (t80) cc_final: 0.8607 (t80) REVERT: I 6 THR cc_start: 0.9298 (p) cc_final: 0.8820 (p) REVERT: I 9 LYS cc_start: 0.9085 (mttm) cc_final: 0.8620 (mttm) REVERT: I 32 LEU cc_start: 0.9478 (mt) cc_final: 0.8984 (pp) REVERT: I 39 ILE cc_start: 0.9397 (pt) cc_final: 0.8799 (pt) REVERT: I 69 GLN cc_start: 0.9566 (pt0) cc_final: 0.9361 (pm20) REVERT: I 97 ARG cc_start: 0.9593 (mmp80) cc_final: 0.9369 (mmp-170) REVERT: I 100 LEU cc_start: 0.9682 (mt) cc_final: 0.9206 (pp) REVERT: I 277 LEU cc_start: 0.9668 (mt) cc_final: 0.9186 (pp) REVERT: I 291 TYR cc_start: 0.9593 (t80) cc_final: 0.9370 (t80) REVERT: I 342 ASP cc_start: 0.9133 (m-30) cc_final: 0.8791 (m-30) REVERT: I 396 ASP cc_start: 0.9146 (t70) cc_final: 0.8886 (t0) REVERT: I 405 PHE cc_start: 0.9680 (t80) cc_final: 0.9280 (t80) REVERT: I 419 ILE cc_start: 0.9266 (pt) cc_final: 0.8925 (pt) REVERT: I 430 LYS cc_start: 0.9345 (mmtm) cc_final: 0.9120 (mmmt) REVERT: I 461 GLU cc_start: 0.9298 (tp30) cc_final: 0.9055 (tp30) REVERT: I 606 LEU cc_start: 0.9357 (mp) cc_final: 0.9134 (mp) REVERT: I 668 ILE cc_start: 0.9575 (mm) cc_final: 0.9338 (mm) REVERT: I 671 LEU cc_start: 0.9775 (tp) cc_final: 0.9553 (tp) REVERT: I 672 GLU cc_start: 0.9545 (pm20) cc_final: 0.8852 (pm20) REVERT: I 681 MET cc_start: 0.9146 (mtp) cc_final: 0.8701 (mtt) REVERT: I 685 MET cc_start: 0.9302 (mtm) cc_final: 0.8843 (mtm) REVERT: I 688 GLN cc_start: 0.9457 (pp30) cc_final: 0.9108 (pp30) REVERT: I 748 ILE cc_start: 0.8706 (pt) cc_final: 0.8443 (pt) REVERT: I 749 ASP cc_start: 0.9108 (t0) cc_final: 0.8822 (p0) REVERT: I 790 ASP cc_start: 0.9491 (t0) cc_final: 0.9052 (p0) REVERT: I 805 MET cc_start: 0.9361 (ppp) cc_final: 0.9057 (ppp) REVERT: I 816 ILE cc_start: 0.9400 (mt) cc_final: 0.8452 (mt) REVERT: I 817 LEU cc_start: 0.8187 (mm) cc_final: 0.7664 (mm) REVERT: I 831 ILE cc_start: 0.8980 (mm) cc_final: 0.8487 (mm) REVERT: I 930 ASP cc_start: 0.9701 (t70) cc_final: 0.8977 (t70) REVERT: I 1053 TYR cc_start: 0.8209 (m-80) cc_final: 0.7976 (m-80) REVERT: I 1056 VAL cc_start: 0.8591 (m) cc_final: 0.8153 (m) REVERT: I 1066 MET cc_start: 0.8710 (pmm) cc_final: 0.7964 (pmm) REVERT: I 1080 ASN cc_start: 0.8956 (m-40) cc_final: 0.8480 (t0) REVERT: I 1106 ARG cc_start: 0.9546 (mmm-85) cc_final: 0.9245 (mmt180) REVERT: I 1107 MET cc_start: 0.9058 (mmm) cc_final: 0.7916 (tmm) REVERT: I 1122 LYS cc_start: 0.9603 (tptm) cc_final: 0.9122 (tppt) REVERT: I 1126 ASP cc_start: 0.9430 (m-30) cc_final: 0.8704 (m-30) REVERT: I 1187 PHE cc_start: 0.8959 (m-10) cc_final: 0.8575 (m-10) REVERT: I 1216 ARG cc_start: 0.9087 (mtp180) cc_final: 0.8664 (mmm-85) REVERT: I 1234 LYS cc_start: 0.9519 (tppp) cc_final: 0.9111 (tppp) REVERT: I 1237 HIS cc_start: 0.8654 (m90) cc_final: 0.8395 (m-70) REVERT: I 1264 GLN cc_start: 0.9426 (tp-100) cc_final: 0.9064 (tm-30) REVERT: I 1265 PHE cc_start: 0.9196 (t80) cc_final: 0.8833 (t80) REVERT: I 1270 PHE cc_start: 0.9000 (t80) cc_final: 0.8338 (t80) REVERT: I 1285 TYR cc_start: 0.9154 (m-80) cc_final: 0.8885 (m-80) REVERT: I 1290 MET cc_start: 0.9449 (tmm) cc_final: 0.9067 (tmm) REVERT: I 1304 MET cc_start: 0.9678 (tmm) cc_final: 0.9275 (ptp) REVERT: I 1319 MET cc_start: 0.8208 (tpt) cc_final: 0.7164 (tpt) REVERT: I 1321 GLU cc_start: 0.9031 (pm20) cc_final: 0.8817 (pm20) REVERT: I 1329 GLU cc_start: 0.9895 (mt-10) cc_final: 0.9594 (mt-10) REVERT: J 102 MET cc_start: 0.6931 (tpt) cc_final: 0.4547 (ttt) REVERT: J 207 GLU cc_start: 0.9450 (mm-30) cc_final: 0.9168 (mm-30) REVERT: J 361 LEU cc_start: 0.9071 (mt) cc_final: 0.8624 (pp) REVERT: J 405 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8604 (mt-10) REVERT: J 409 TRP cc_start: 0.9023 (m100) cc_final: 0.8255 (m100) REVERT: J 423 LEU cc_start: 0.9852 (mp) cc_final: 0.9570 (mp) REVERT: J 437 PHE cc_start: 0.9598 (m-80) cc_final: 0.8576 (m-80) REVERT: J 454 CYS cc_start: 0.9389 (m) cc_final: 0.9160 (m) REVERT: J 478 LEU cc_start: 0.9677 (tt) cc_final: 0.9445 (mt) REVERT: J 526 VAL cc_start: 0.8976 (p) cc_final: 0.8690 (p) REVERT: J 603 LYS cc_start: 0.9308 (pttt) cc_final: 0.9043 (ptpp) REVERT: J 627 THR cc_start: 0.9827 (t) cc_final: 0.9230 (t) REVERT: J 631 TYR cc_start: 0.9598 (m-80) cc_final: 0.9228 (m-80) REVERT: J 645 VAL cc_start: 0.8556 (p) cc_final: 0.8163 (m) REVERT: J 686 TRP cc_start: 0.9149 (m100) cc_final: 0.8697 (m100) REVERT: J 697 MET cc_start: 0.9652 (ppp) cc_final: 0.9379 (ppp) REVERT: J 763 PHE cc_start: 0.9311 (m-80) cc_final: 0.8705 (m-80) REVERT: J 792 ASN cc_start: 0.9371 (m110) cc_final: 0.9168 (m110) REVERT: J 822 MET cc_start: 0.8521 (tpt) cc_final: 0.7960 (tpp) REVERT: J 1040 MET cc_start: 0.7740 (mmp) cc_final: 0.7001 (mmm) REVERT: J 1194 ARG cc_start: 0.8335 (mtt180) cc_final: 0.8071 (mtt180) REVERT: J 1215 GLU cc_start: 0.9530 (mp0) cc_final: 0.9241 (mm-30) REVERT: J 1238 GLN cc_start: 0.9621 (tp-100) cc_final: 0.9195 (tp-100) REVERT: J 1239 ASP cc_start: 0.9665 (t0) cc_final: 0.9413 (t0) REVERT: J 1254 GLU cc_start: 0.9598 (mt-10) cc_final: 0.9354 (mt-10) REVERT: J 1260 MET cc_start: 0.9474 (tmm) cc_final: 0.9095 (tmm) REVERT: J 1334 GLU cc_start: 0.9345 (tm-30) cc_final: 0.9030 (tm-30) outliers start: 0 outliers final: 0 residues processed: 737 average time/residue: 0.1634 time to fit residues: 187.1459 Evaluate side-chains 632 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 632 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 99 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN I 148 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1175 ASN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN J 921 GLN J 954 ASN J1235 ASN J1367 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.108249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.069139 restraints weight = 89976.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.072241 restraints weight = 56258.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.074630 restraints weight = 40004.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.076430 restraints weight = 30576.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.077785 restraints weight = 24689.551| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 25706 Z= 0.162 Angle : 0.753 10.715 34937 Z= 0.389 Chirality : 0.047 0.323 3992 Planarity : 0.006 0.141 4386 Dihedral : 14.693 63.210 3992 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.77 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3071 helix: -0.05 (0.15), residues: 1097 sheet: -1.54 (0.26), residues: 383 loop : -1.72 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 368 TYR 0.028 0.002 TYR I 756 PHE 0.051 0.002 PHE J 629 TRP 0.103 0.004 TRP J 236 HIS 0.007 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (25698) covalent geometry : angle 0.74672 / 0.39 (34925) hydrogen bonds : bond 0.04670 / 3.21 ( 1057) hydrogen bonds : angle 5.64715 / 3.91 ( 2933) metal coordination : bond 0.01068 / 0.43 ( 8) metal coordination : angle 5.48955 / 3.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 747 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.9611 (m-80) cc_final: 0.9354 (m-80) REVERT: G 84 ASN cc_start: 0.8658 (t0) cc_final: 0.8346 (t0) REVERT: G 104 LYS cc_start: 0.8283 (tptp) cc_final: 0.7876 (tmtt) REVERT: G 130 ILE cc_start: 0.9574 (mp) cc_final: 0.9269 (mp) REVERT: G 133 LEU cc_start: 0.9302 (mm) cc_final: 0.9079 (mm) REVERT: G 181 GLU cc_start: 0.9487 (tp30) cc_final: 0.8444 (pm20) REVERT: G 182 ARG cc_start: 0.8516 (ptt90) cc_final: 0.8158 (ptt90) REVERT: G 199 ASP cc_start: 0.7762 (m-30) cc_final: 0.7504 (m-30) REVERT: G 227 GLN cc_start: 0.9835 (mt0) cc_final: 0.9540 (mt0) REVERT: G 231 PHE cc_start: 0.9855 (m-80) cc_final: 0.9638 (m-80) REVERT: H 16 ILE cc_start: 0.8316 (pt) cc_final: 0.7916 (mp) REVERT: H 29 GLU cc_start: 0.8314 (pm20) cc_final: 0.8066 (pm20) REVERT: H 37 HIS cc_start: 0.9661 (m-70) cc_final: 0.9373 (m90) REVERT: H 46 ILE cc_start: 0.9718 (tp) cc_final: 0.9477 (tp) REVERT: H 68 TYR cc_start: 0.9522 (m-10) cc_final: 0.9271 (m-10) REVERT: H 79 LEU cc_start: 0.9193 (mp) cc_final: 0.8908 (mp) REVERT: H 83 LEU cc_start: 0.9544 (pp) cc_final: 0.9100 (mm) REVERT: H 141 SER cc_start: 0.9665 (t) cc_final: 0.9348 (m) REVERT: H 142 MET cc_start: 0.9585 (ptm) cc_final: 0.9273 (ptm) REVERT: H 193 GLU cc_start: 0.8620 (tp30) cc_final: 0.8231 (tp30) REVERT: H 194 GLN cc_start: 0.9490 (tp40) cc_final: 0.9274 (tp40) REVERT: H 200 LYS cc_start: 0.9182 (tmtt) cc_final: 0.8805 (tmtt) REVERT: I 5 TYR cc_start: 0.8919 (t80) cc_final: 0.8578 (t80) REVERT: I 9 LYS cc_start: 0.9155 (mttm) cc_final: 0.8722 (mttm) REVERT: I 32 LEU cc_start: 0.9470 (mt) cc_final: 0.8964 (pp) REVERT: I 39 ILE cc_start: 0.9287 (pt) cc_final: 0.8807 (pt) REVERT: I 53 PHE cc_start: 0.8486 (m-80) cc_final: 0.8165 (m-10) REVERT: I 100 LEU cc_start: 0.9716 (mt) cc_final: 0.9303 (pp) REVERT: I 277 LEU cc_start: 0.9653 (mt) cc_final: 0.9178 (pp) REVERT: I 291 TYR cc_start: 0.9584 (t80) cc_final: 0.9352 (t80) REVERT: I 342 ASP cc_start: 0.9106 (m-30) cc_final: 0.8786 (m-30) REVERT: I 405 PHE cc_start: 0.9623 (t80) cc_final: 0.9282 (t80) REVERT: I 430 LYS cc_start: 0.9330 (mmtm) cc_final: 0.9060 (mmtt) REVERT: I 461 GLU cc_start: 0.9300 (tp30) cc_final: 0.8916 (tp30) REVERT: I 464 PHE cc_start: 0.9689 (t80) cc_final: 0.9339 (t80) REVERT: I 591 TYR cc_start: 0.9472 (m-80) cc_final: 0.8914 (m-80) REVERT: I 606 LEU cc_start: 0.9326 (mp) cc_final: 0.8726 (mp) REVERT: I 633 LEU cc_start: 0.9582 (pt) cc_final: 0.9269 (mm) REVERT: I 668 ILE cc_start: 0.9530 (mm) cc_final: 0.9294 (mm) REVERT: I 671 LEU cc_start: 0.9788 (tp) cc_final: 0.9537 (tp) REVERT: I 672 GLU cc_start: 0.9522 (pm20) cc_final: 0.8875 (pm20) REVERT: I 681 MET cc_start: 0.9179 (mtp) cc_final: 0.8709 (mtt) REVERT: I 685 MET cc_start: 0.9267 (mtm) cc_final: 0.8920 (mtm) REVERT: I 688 GLN cc_start: 0.9387 (pp30) cc_final: 0.9142 (pp30) REVERT: I 748 ILE cc_start: 0.8637 (pt) cc_final: 0.8197 (pt) REVERT: I 749 ASP cc_start: 0.9042 (t0) cc_final: 0.8788 (p0) REVERT: I 805 MET cc_start: 0.9346 (ppp) cc_final: 0.9120 (ppp) REVERT: I 816 ILE cc_start: 0.9450 (mt) cc_final: 0.8486 (mt) REVERT: I 817 LEU cc_start: 0.8470 (mm) cc_final: 0.7724 (mm) REVERT: I 818 VAL cc_start: 0.9567 (m) cc_final: 0.8989 (p) REVERT: I 831 ILE cc_start: 0.8897 (mm) cc_final: 0.8452 (mm) REVERT: I 930 ASP cc_start: 0.9703 (t70) cc_final: 0.8922 (t0) REVERT: I 957 LYS cc_start: 0.9565 (pptt) cc_final: 0.9285 (pttm) REVERT: I 1053 TYR cc_start: 0.8208 (m-80) cc_final: 0.7983 (m-80) REVERT: I 1056 VAL cc_start: 0.8681 (m) cc_final: 0.8178 (m) REVERT: I 1066 MET cc_start: 0.8871 (pmm) cc_final: 0.8529 (pmm) REVERT: I 1080 ASN cc_start: 0.8824 (m-40) cc_final: 0.8275 (t0) REVERT: I 1095 ASP cc_start: 0.9688 (m-30) cc_final: 0.9051 (t0) REVERT: I 1106 ARG cc_start: 0.9522 (mmm-85) cc_final: 0.9204 (mmt180) REVERT: I 1107 MET cc_start: 0.9075 (mmm) cc_final: 0.8285 (tpp) REVERT: I 1122 LYS cc_start: 0.9564 (tptm) cc_final: 0.9069 (tppt) REVERT: I 1126 ASP cc_start: 0.9418 (m-30) cc_final: 0.8675 (m-30) REVERT: I 1132 LEU cc_start: 0.9542 (tp) cc_final: 0.9106 (tp) REVERT: I 1177 ARG cc_start: 0.9178 (ptm160) cc_final: 0.8823 (ptm160) REVERT: I 1187 PHE cc_start: 0.8848 (m-10) cc_final: 0.8267 (m-10) REVERT: I 1216 ARG cc_start: 0.9039 (mtp180) cc_final: 0.8601 (mmm-85) REVERT: I 1230 MET cc_start: 0.9233 (tpt) cc_final: 0.8269 (tmm) REVERT: I 1234 LYS cc_start: 0.9473 (tppp) cc_final: 0.9102 (tppp) REVERT: I 1237 HIS cc_start: 0.8544 (m90) cc_final: 0.8275 (m-70) REVERT: I 1264 GLN cc_start: 0.9445 (tp-100) cc_final: 0.9074 (tm-30) REVERT: I 1265 PHE cc_start: 0.9171 (t80) cc_final: 0.8802 (t80) REVERT: I 1270 PHE cc_start: 0.9016 (t80) cc_final: 0.8385 (t80) REVERT: I 1290 MET cc_start: 0.9421 (tmm) cc_final: 0.9046 (tmm) REVERT: I 1304 MET cc_start: 0.9670 (tmm) cc_final: 0.9271 (ptp) REVERT: I 1319 MET cc_start: 0.7622 (tpt) cc_final: 0.6706 (tpt) REVERT: I 1321 GLU cc_start: 0.8882 (pm20) cc_final: 0.8639 (pm20) REVERT: I 1329 GLU cc_start: 0.9885 (mt-10) cc_final: 0.9531 (mt-10) REVERT: J 102 MET cc_start: 0.7053 (tpt) cc_final: 0.4940 (ttt) REVERT: J 140 TYR cc_start: 0.9726 (m-80) cc_final: 0.9521 (m-80) REVERT: J 207 GLU cc_start: 0.9429 (mm-30) cc_final: 0.9170 (mm-30) REVERT: J 325 LYS cc_start: 0.7684 (pttm) cc_final: 0.7091 (pttp) REVERT: J 329 ASP cc_start: 0.9737 (m-30) cc_final: 0.9393 (t0) REVERT: J 332 LYS cc_start: 0.9085 (mmtt) cc_final: 0.8616 (mmtt) REVERT: J 361 LEU cc_start: 0.9030 (mt) cc_final: 0.8502 (pp) REVERT: J 371 LYS cc_start: 0.9466 (mmpt) cc_final: 0.9191 (mmmt) REVERT: J 372 MET cc_start: 0.9389 (mpp) cc_final: 0.9142 (ptp) REVERT: J 409 TRP cc_start: 0.9017 (m100) cc_final: 0.8155 (m100) REVERT: J 437 PHE cc_start: 0.9556 (m-80) cc_final: 0.8982 (m-80) REVERT: J 454 CYS cc_start: 0.9348 (m) cc_final: 0.9093 (m) REVERT: J 603 LYS cc_start: 0.9320 (pttt) cc_final: 0.8946 (ptpp) REVERT: J 627 THR cc_start: 0.9820 (t) cc_final: 0.9213 (t) REVERT: J 631 TYR cc_start: 0.9463 (m-80) cc_final: 0.9082 (m-80) REVERT: J 645 VAL cc_start: 0.8548 (p) cc_final: 0.8138 (m) REVERT: J 686 TRP cc_start: 0.9170 (m100) cc_final: 0.8757 (m100) REVERT: J 697 MET cc_start: 0.9646 (ppp) cc_final: 0.9384 (ppp) REVERT: J 727 ASP cc_start: 0.9177 (t70) cc_final: 0.8882 (m-30) REVERT: J 763 PHE cc_start: 0.9299 (m-80) cc_final: 0.7909 (m-80) REVERT: J 792 ASN cc_start: 0.9341 (m110) cc_final: 0.9119 (m-40) REVERT: J 823 THR cc_start: 0.9563 (p) cc_final: 0.9277 (p) REVERT: J 1040 MET cc_start: 0.7744 (mmp) cc_final: 0.7090 (mmm) REVERT: J 1194 ARG cc_start: 0.8288 (mtt180) cc_final: 0.8043 (mtt180) REVERT: J 1238 GLN cc_start: 0.9618 (tp-100) cc_final: 0.8955 (tp40) REVERT: J 1249 ASN cc_start: 0.9431 (t0) cc_final: 0.8835 (t0) REVERT: J 1250 ASP cc_start: 0.9362 (m-30) cc_final: 0.8968 (p0) REVERT: J 1254 GLU cc_start: 0.9591 (mt-10) cc_final: 0.9112 (mt-10) REVERT: J 1260 MET cc_start: 0.9468 (tmm) cc_final: 0.9065 (tmm) REVERT: J 1307 LEU cc_start: 0.8866 (mm) cc_final: 0.8658 (mm) REVERT: J 1334 GLU cc_start: 0.9389 (tm-30) cc_final: 0.9109 (tm-30) outliers start: 0 outliers final: 0 residues processed: 747 average time/residue: 0.1577 time to fit residues: 185.2323 Evaluate side-chains 645 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 171 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 310 optimal weight: 50.0000 chunk 251 optimal weight: 4.9990 chunk 268 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN ** I 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1175 ASN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN J 921 GLN J 954 ASN ** J1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.106655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.067929 restraints weight = 90429.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.070934 restraints weight = 56937.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.073234 restraints weight = 40523.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.074989 restraints weight = 31063.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.076272 restraints weight = 25192.552| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25706 Z= 0.178 Angle : 0.742 10.469 34937 Z= 0.389 Chirality : 0.047 0.296 3992 Planarity : 0.006 0.112 4386 Dihedral : 14.665 63.154 3992 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.23 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 3071 helix: -0.10 (0.15), residues: 1100 sheet: -1.51 (0.25), residues: 388 loop : -1.74 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG I 368 TYR 0.022 0.002 TYR I1231 PHE 0.043 0.002 PHE J 629 TRP 0.087 0.003 TRP J 236 HIS 0.009 0.001 HIS J 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (25698) covalent geometry : angle 0.73780 / 0.39 (34925) hydrogen bonds : bond 0.04766 / 3.30 ( 1057) hydrogen bonds : angle 5.70442 / 3.95 ( 2933) metal coordination : bond 0.01039 / 0.44 ( 8) metal coordination : angle 4.45716 / 2.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 729 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.9627 (m-80) cc_final: 0.9381 (m-80) REVERT: G 84 ASN cc_start: 0.8682 (t0) cc_final: 0.8367 (t0) REVERT: G 130 ILE cc_start: 0.9589 (mp) cc_final: 0.9275 (mp) REVERT: G 181 GLU cc_start: 0.9347 (tp30) cc_final: 0.8798 (pm20) REVERT: G 182 ARG cc_start: 0.8502 (ptt90) cc_final: 0.8218 (ptt90) REVERT: G 199 ASP cc_start: 0.7708 (m-30) cc_final: 0.7445 (m-30) REVERT: G 205 MET cc_start: 0.9545 (ppp) cc_final: 0.8920 (ppp) REVERT: G 227 GLN cc_start: 0.9861 (mt0) cc_final: 0.9519 (mt0) REVERT: H 16 ILE cc_start: 0.8296 (pt) cc_final: 0.8087 (mp) REVERT: H 29 GLU cc_start: 0.8307 (pm20) cc_final: 0.8036 (pm20) REVERT: H 37 HIS cc_start: 0.9671 (m-70) cc_final: 0.8807 (m90) REVERT: H 46 ILE cc_start: 0.9744 (tp) cc_final: 0.9504 (tp) REVERT: H 68 TYR cc_start: 0.9527 (m-10) cc_final: 0.9262 (m-10) REVERT: H 79 LEU cc_start: 0.9240 (mp) cc_final: 0.8955 (mp) REVERT: H 83 LEU cc_start: 0.9536 (pp) cc_final: 0.9064 (mm) REVERT: H 133 LEU cc_start: 0.8988 (tp) cc_final: 0.8742 (tp) REVERT: H 141 SER cc_start: 0.9662 (t) cc_final: 0.9238 (m) REVERT: H 142 MET cc_start: 0.9599 (ptm) cc_final: 0.9195 (ptm) REVERT: H 193 GLU cc_start: 0.8576 (tp30) cc_final: 0.8179 (tp30) REVERT: H 194 GLN cc_start: 0.9503 (tp40) cc_final: 0.9301 (tp40) REVERT: H 200 LYS cc_start: 0.9179 (tmtt) cc_final: 0.8801 (tmtt) REVERT: I 5 TYR cc_start: 0.8901 (t80) cc_final: 0.8535 (t80) REVERT: I 6 THR cc_start: 0.9315 (p) cc_final: 0.8893 (p) REVERT: I 9 LYS cc_start: 0.9147 (mttm) cc_final: 0.8701 (mttm) REVERT: I 32 LEU cc_start: 0.9503 (mt) cc_final: 0.9037 (pp) REVERT: I 277 LEU cc_start: 0.9663 (mt) cc_final: 0.9189 (pp) REVERT: I 291 TYR cc_start: 0.9571 (t80) cc_final: 0.9351 (t80) REVERT: I 342 ASP cc_start: 0.9124 (m-30) cc_final: 0.8795 (m-30) REVERT: I 405 PHE cc_start: 0.9641 (t80) cc_final: 0.9277 (t80) REVERT: I 430 LYS cc_start: 0.9352 (mmtm) cc_final: 0.9070 (mmtt) REVERT: I 461 GLU cc_start: 0.9209 (tp30) cc_final: 0.8748 (tp30) REVERT: I 464 PHE cc_start: 0.9699 (t80) cc_final: 0.9319 (t80) REVERT: I 548 ARG cc_start: 0.9400 (mtt180) cc_final: 0.8675 (mtt180) REVERT: I 591 TYR cc_start: 0.9534 (m-80) cc_final: 0.8952 (m-80) REVERT: I 606 LEU cc_start: 0.9344 (mp) cc_final: 0.8743 (mp) REVERT: I 636 CYS cc_start: 0.9232 (m) cc_final: 0.9007 (m) REVERT: I 668 ILE cc_start: 0.9477 (mm) cc_final: 0.9191 (mm) REVERT: I 671 LEU cc_start: 0.9785 (tp) cc_final: 0.9534 (tp) REVERT: I 672 GLU cc_start: 0.9534 (pm20) cc_final: 0.8903 (pm20) REVERT: I 681 MET cc_start: 0.9173 (mtp) cc_final: 0.8709 (mtt) REVERT: I 685 MET cc_start: 0.9245 (mtm) cc_final: 0.8934 (mtm) REVERT: I 748 ILE cc_start: 0.8127 (pt) cc_final: 0.7803 (pt) REVERT: I 805 MET cc_start: 0.9330 (ppp) cc_final: 0.9019 (ppp) REVERT: I 816 ILE cc_start: 0.9434 (mt) cc_final: 0.8425 (mt) REVERT: I 817 LEU cc_start: 0.8424 (mm) cc_final: 0.7661 (mm) REVERT: I 818 VAL cc_start: 0.9593 (m) cc_final: 0.9256 (p) REVERT: I 831 ILE cc_start: 0.8912 (mm) cc_final: 0.8491 (mm) REVERT: I 930 ASP cc_start: 0.9687 (t70) cc_final: 0.8907 (t0) REVERT: I 957 LYS cc_start: 0.9573 (pptt) cc_final: 0.9348 (pttm) REVERT: I 1053 TYR cc_start: 0.8226 (m-80) cc_final: 0.8021 (m-80) REVERT: I 1056 VAL cc_start: 0.8726 (m) cc_final: 0.8360 (m) REVERT: I 1066 MET cc_start: 0.8799 (pmm) cc_final: 0.8075 (pmm) REVERT: I 1080 ASN cc_start: 0.8890 (m-40) cc_final: 0.8327 (t0) REVERT: I 1106 ARG cc_start: 0.9540 (mmm-85) cc_final: 0.9218 (mmt180) REVERT: I 1107 MET cc_start: 0.9067 (mmm) cc_final: 0.8307 (tpp) REVERT: I 1119 MET cc_start: 0.8921 (mmp) cc_final: 0.8670 (mmp) REVERT: I 1122 LYS cc_start: 0.9578 (tptm) cc_final: 0.9101 (tppt) REVERT: I 1126 ASP cc_start: 0.9343 (m-30) cc_final: 0.8783 (m-30) REVERT: I 1187 PHE cc_start: 0.8880 (m-10) cc_final: 0.8322 (m-10) REVERT: I 1216 ARG cc_start: 0.9075 (mtp180) cc_final: 0.8313 (mmm-85) REVERT: I 1234 LYS cc_start: 0.9466 (tppp) cc_final: 0.9144 (tppp) REVERT: I 1236 ASN cc_start: 0.7651 (m-40) cc_final: 0.7432 (m-40) REVERT: I 1237 HIS cc_start: 0.8511 (m90) cc_final: 0.8267 (m90) REVERT: I 1264 GLN cc_start: 0.9439 (tp-100) cc_final: 0.9068 (tm-30) REVERT: I 1265 PHE cc_start: 0.9143 (t80) cc_final: 0.8801 (t80) REVERT: I 1270 PHE cc_start: 0.8998 (t80) cc_final: 0.8399 (t80) REVERT: I 1290 MET cc_start: 0.9382 (tmm) cc_final: 0.9007 (tmm) REVERT: I 1304 MET cc_start: 0.9666 (tmm) cc_final: 0.9280 (ptp) REVERT: I 1319 MET cc_start: 0.7841 (tpt) cc_final: 0.6912 (tpt) REVERT: I 1321 GLU cc_start: 0.8935 (pm20) cc_final: 0.8707 (pm20) REVERT: I 1329 GLU cc_start: 0.9887 (mt-10) cc_final: 0.9565 (mt-10) REVERT: J 28 ASP cc_start: 0.9854 (t0) cc_final: 0.9653 (p0) REVERT: J 30 ILE cc_start: 0.9409 (mt) cc_final: 0.9033 (mt) REVERT: J 102 MET cc_start: 0.7129 (tpt) cc_final: 0.6525 (tpt) REVERT: J 207 GLU cc_start: 0.9438 (mm-30) cc_final: 0.9169 (mm-30) REVERT: J 268 LEU cc_start: 0.9434 (mt) cc_final: 0.9206 (mt) REVERT: J 325 LYS cc_start: 0.7743 (pttm) cc_final: 0.7319 (pttp) REVERT: J 329 ASP cc_start: 0.9734 (m-30) cc_final: 0.9327 (t0) REVERT: J 332 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8655 (mmtt) REVERT: J 361 LEU cc_start: 0.9067 (mt) cc_final: 0.8566 (pp) REVERT: J 409 TRP cc_start: 0.8890 (m100) cc_final: 0.8104 (m100) REVERT: J 437 PHE cc_start: 0.9560 (m-80) cc_final: 0.9015 (m-80) REVERT: J 454 CYS cc_start: 0.9347 (m) cc_final: 0.9090 (m) REVERT: J 512 TYR cc_start: 0.9367 (t80) cc_final: 0.8996 (t80) REVERT: J 526 VAL cc_start: 0.9018 (p) cc_final: 0.8711 (p) REVERT: J 603 LYS cc_start: 0.9354 (pttt) cc_final: 0.9108 (ptpp) REVERT: J 627 THR cc_start: 0.9826 (t) cc_final: 0.9179 (t) REVERT: J 631 TYR cc_start: 0.9456 (m-80) cc_final: 0.8977 (m-80) REVERT: J 645 VAL cc_start: 0.8495 (p) cc_final: 0.8088 (m) REVERT: J 686 TRP cc_start: 0.9179 (m100) cc_final: 0.8758 (m100) REVERT: J 697 MET cc_start: 0.9659 (ppp) cc_final: 0.9390 (ppp) REVERT: J 763 PHE cc_start: 0.9317 (m-80) cc_final: 0.7991 (m-80) REVERT: J 792 ASN cc_start: 0.9348 (m110) cc_final: 0.9119 (m-40) REVERT: J 1040 MET cc_start: 0.7768 (mmp) cc_final: 0.7020 (mmm) REVERT: J 1194 ARG cc_start: 0.8252 (mtt180) cc_final: 0.8003 (mtt180) REVERT: J 1215 GLU cc_start: 0.9543 (mp0) cc_final: 0.9263 (mm-30) REVERT: J 1238 GLN cc_start: 0.9597 (tp-100) cc_final: 0.9122 (tp40) REVERT: J 1249 ASN cc_start: 0.9372 (t0) cc_final: 0.8927 (t0) REVERT: J 1252 HIS cc_start: 0.9297 (m90) cc_final: 0.9055 (m90) REVERT: J 1254 GLU cc_start: 0.9567 (mt-10) cc_final: 0.9326 (mt-10) REVERT: J 1260 MET cc_start: 0.9484 (tmm) cc_final: 0.9010 (tmm) REVERT: J 1334 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9138 (tm-30) outliers start: 0 outliers final: 0 residues processed: 729 average time/residue: 0.1805 time to fit residues: 206.8038 Evaluate side-chains 635 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 635 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 273 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 234 optimal weight: 0.6980 chunk 296 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 289 optimal weight: 10.0000 chunk 242 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN I 148 GLN ** I 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN J 921 GLN J 954 ASN ** J1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.108078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.069212 restraints weight = 88919.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.072260 restraints weight = 55875.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.074592 restraints weight = 39870.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.076340 restraints weight = 30517.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.077730 restraints weight = 24746.371| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25706 Z= 0.156 Angle : 0.760 11.623 34937 Z= 0.395 Chirality : 0.047 0.270 3992 Planarity : 0.006 0.113 4386 Dihedral : 14.618 63.154 3992 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.81 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3071 helix: -0.04 (0.15), residues: 1096 sheet: -1.57 (0.25), residues: 397 loop : -1.71 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 744 TYR 0.018 0.002 TYR J 537 PHE 0.045 0.002 PHE J 629 TRP 0.088 0.003 TRP J 236 HIS 0.011 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (25698) covalent geometry : angle 0.75624 / 0.40 (34925) hydrogen bonds : bond 0.04585 / 3.20 ( 1057) hydrogen bonds : angle 5.64418 / 3.90 ( 2933) metal coordination : bond 0.00907 / 0.38 ( 8) metal coordination : angle 4.19344 / 2.33 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 724 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 ASN cc_start: 0.8661 (t0) cc_final: 0.8337 (t0) REVERT: G 104 LYS cc_start: 0.8306 (tptp) cc_final: 0.7899 (tmtt) REVERT: G 130 ILE cc_start: 0.9543 (mp) cc_final: 0.9219 (mp) REVERT: G 133 LEU cc_start: 0.9324 (mm) cc_final: 0.9112 (mm) REVERT: G 148 ARG cc_start: 0.8377 (mtt180) cc_final: 0.8155 (mtt180) REVERT: G 199 ASP cc_start: 0.7661 (m-30) cc_final: 0.7362 (m-30) REVERT: G 205 MET cc_start: 0.9535 (ppp) cc_final: 0.8983 (ppp) REVERT: G 227 GLN cc_start: 0.9833 (mt0) cc_final: 0.9513 (mt0) REVERT: H 16 ILE cc_start: 0.8406 (pt) cc_final: 0.8064 (mp) REVERT: H 29 GLU cc_start: 0.8317 (pm20) cc_final: 0.8054 (pm20) REVERT: H 37 HIS cc_start: 0.9668 (m-70) cc_final: 0.8802 (m90) REVERT: H 46 ILE cc_start: 0.9744 (tp) cc_final: 0.9478 (tp) REVERT: H 68 TYR cc_start: 0.9522 (m-10) cc_final: 0.9250 (m-10) REVERT: H 79 LEU cc_start: 0.9266 (mp) cc_final: 0.8987 (mp) REVERT: H 83 LEU cc_start: 0.9525 (pp) cc_final: 0.9066 (mm) REVERT: H 193 GLU cc_start: 0.8493 (tp30) cc_final: 0.7998 (tp30) REVERT: H 194 GLN cc_start: 0.9457 (tp40) cc_final: 0.9244 (tp40) REVERT: H 200 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8793 (tmtt) REVERT: I 5 TYR cc_start: 0.8860 (t80) cc_final: 0.8496 (t80) REVERT: I 6 THR cc_start: 0.9282 (p) cc_final: 0.8863 (p) REVERT: I 9 LYS cc_start: 0.9157 (mttm) cc_final: 0.8699 (mttm) REVERT: I 32 LEU cc_start: 0.9488 (mt) cc_final: 0.8948 (pp) REVERT: I 39 ILE cc_start: 0.9348 (pt) cc_final: 0.8877 (pt) REVERT: I 160 ASP cc_start: 0.8860 (m-30) cc_final: 0.8650 (m-30) REVERT: I 291 TYR cc_start: 0.9560 (t80) cc_final: 0.9347 (t80) REVERT: I 342 ASP cc_start: 0.9094 (m-30) cc_final: 0.8766 (m-30) REVERT: I 405 PHE cc_start: 0.9615 (t80) cc_final: 0.9276 (t80) REVERT: I 461 GLU cc_start: 0.9305 (tp30) cc_final: 0.8632 (tp30) REVERT: I 464 PHE cc_start: 0.9708 (t80) cc_final: 0.9268 (t80) REVERT: I 519 ASN cc_start: 0.9011 (t0) cc_final: 0.8757 (t0) REVERT: I 548 ARG cc_start: 0.9367 (mtt180) cc_final: 0.8737 (mtt180) REVERT: I 591 TYR cc_start: 0.9499 (m-80) cc_final: 0.8928 (m-80) REVERT: I 606 LEU cc_start: 0.9345 (mp) cc_final: 0.8749 (mp) REVERT: I 633 LEU cc_start: 0.9568 (pt) cc_final: 0.9267 (mm) REVERT: I 636 CYS cc_start: 0.9279 (m) cc_final: 0.8998 (m) REVERT: I 671 LEU cc_start: 0.9771 (tp) cc_final: 0.9511 (tp) REVERT: I 672 GLU cc_start: 0.9551 (pm20) cc_final: 0.9056 (pm20) REVERT: I 681 MET cc_start: 0.9170 (mtp) cc_final: 0.8683 (mtt) REVERT: I 685 MET cc_start: 0.9207 (mtm) cc_final: 0.8852 (mtm) REVERT: I 688 GLN cc_start: 0.9461 (pp30) cc_final: 0.9216 (pp30) REVERT: I 748 ILE cc_start: 0.7950 (pt) cc_final: 0.7675 (pt) REVERT: I 805 MET cc_start: 0.9303 (ppp) cc_final: 0.8955 (ppp) REVERT: I 816 ILE cc_start: 0.9443 (mt) cc_final: 0.8465 (mt) REVERT: I 817 LEU cc_start: 0.8465 (mm) cc_final: 0.7735 (mm) REVERT: I 818 VAL cc_start: 0.9583 (m) cc_final: 0.9019 (p) REVERT: I 831 ILE cc_start: 0.8883 (mm) cc_final: 0.8537 (mm) REVERT: I 930 ASP cc_start: 0.9682 (t70) cc_final: 0.8861 (t0) REVERT: I 957 LYS cc_start: 0.9598 (pptt) cc_final: 0.9390 (pttm) REVERT: I 1056 VAL cc_start: 0.8843 (m) cc_final: 0.8563 (m) REVERT: I 1066 MET cc_start: 0.8817 (pmm) cc_final: 0.8173 (pmm) REVERT: I 1070 HIS cc_start: 0.7594 (m-70) cc_final: 0.7115 (m170) REVERT: I 1080 ASN cc_start: 0.8838 (m-40) cc_final: 0.8300 (t0) REVERT: I 1095 ASP cc_start: 0.9709 (m-30) cc_final: 0.9099 (t0) REVERT: I 1106 ARG cc_start: 0.9520 (mmm-85) cc_final: 0.9316 (mmt180) REVERT: I 1115 THR cc_start: 0.9730 (m) cc_final: 0.9524 (m) REVERT: I 1117 LEU cc_start: 0.9411 (tt) cc_final: 0.9204 (tt) REVERT: I 1119 MET cc_start: 0.8917 (mmp) cc_final: 0.8673 (mmp) REVERT: I 1122 LYS cc_start: 0.9551 (tptm) cc_final: 0.9060 (tppt) REVERT: I 1126 ASP cc_start: 0.9351 (m-30) cc_final: 0.8783 (m-30) REVERT: I 1187 PHE cc_start: 0.8839 (m-10) cc_final: 0.8398 (m-10) REVERT: I 1209 GLN cc_start: 0.9429 (mm110) cc_final: 0.8959 (mm-40) REVERT: I 1216 ARG cc_start: 0.9070 (mtp180) cc_final: 0.8297 (mmm-85) REVERT: I 1223 ARG cc_start: 0.9402 (tpm170) cc_final: 0.8928 (tpm170) REVERT: I 1234 LYS cc_start: 0.9433 (tppp) cc_final: 0.9105 (tppp) REVERT: I 1237 HIS cc_start: 0.8500 (m90) cc_final: 0.8191 (m90) REVERT: I 1264 GLN cc_start: 0.9438 (tp-100) cc_final: 0.9063 (tm-30) REVERT: I 1265 PHE cc_start: 0.9148 (t80) cc_final: 0.8775 (t80) REVERT: I 1270 PHE cc_start: 0.8987 (t80) cc_final: 0.8385 (t80) REVERT: I 1290 MET cc_start: 0.9394 (tmm) cc_final: 0.9059 (tmm) REVERT: I 1304 MET cc_start: 0.9672 (tmm) cc_final: 0.9287 (ptp) REVERT: I 1319 MET cc_start: 0.8005 (tpt) cc_final: 0.6972 (tpt) REVERT: I 1321 GLU cc_start: 0.8922 (pm20) cc_final: 0.8669 (pm20) REVERT: I 1326 LEU cc_start: 0.9528 (mt) cc_final: 0.9133 (pp) REVERT: I 1329 GLU cc_start: 0.9883 (mt-10) cc_final: 0.9570 (mt-10) REVERT: J 28 ASP cc_start: 0.9861 (t0) cc_final: 0.9650 (p0) REVERT: J 30 ILE cc_start: 0.9424 (mt) cc_final: 0.9055 (mt) REVERT: J 91 GLU cc_start: 0.8878 (pp20) cc_final: 0.8608 (tm-30) REVERT: J 102 MET cc_start: 0.7070 (tpt) cc_final: 0.6473 (tpt) REVERT: J 207 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9151 (mm-30) REVERT: J 325 LYS cc_start: 0.7815 (pttm) cc_final: 0.7181 (pttp) REVERT: J 329 ASP cc_start: 0.9732 (m-30) cc_final: 0.9368 (t0) REVERT: J 332 LYS cc_start: 0.9134 (mmtt) cc_final: 0.8674 (mmtt) REVERT: J 361 LEU cc_start: 0.9025 (mt) cc_final: 0.8491 (pp) REVERT: J 372 MET cc_start: 0.9514 (mpp) cc_final: 0.9077 (ptp) REVERT: J 409 TRP cc_start: 0.8814 (m100) cc_final: 0.7990 (m100) REVERT: J 437 PHE cc_start: 0.9538 (m-80) cc_final: 0.8979 (m-80) REVERT: J 454 CYS cc_start: 0.9350 (m) cc_final: 0.9108 (m) REVERT: J 512 TYR cc_start: 0.9364 (t80) cc_final: 0.8999 (t80) REVERT: J 525 MET cc_start: 0.9272 (pmm) cc_final: 0.9069 (pmm) REVERT: J 603 LYS cc_start: 0.9338 (pttt) cc_final: 0.9072 (ptpp) REVERT: J 627 THR cc_start: 0.9807 (t) cc_final: 0.9137 (t) REVERT: J 631 TYR cc_start: 0.9473 (m-80) cc_final: 0.8916 (m-80) REVERT: J 645 VAL cc_start: 0.8448 (p) cc_final: 0.8009 (m) REVERT: J 686 TRP cc_start: 0.9124 (m100) cc_final: 0.8645 (m100) REVERT: J 697 MET cc_start: 0.9658 (ppp) cc_final: 0.9395 (ppp) REVERT: J 727 ASP cc_start: 0.9186 (t70) cc_final: 0.8884 (m-30) REVERT: J 743 MET cc_start: 0.9022 (ptm) cc_final: 0.8471 (ttt) REVERT: J 763 PHE cc_start: 0.9255 (m-80) cc_final: 0.8339 (m-80) REVERT: J 764 ARG cc_start: 0.8964 (ttt-90) cc_final: 0.8392 (mtp180) REVERT: J 792 ASN cc_start: 0.9363 (m110) cc_final: 0.9135 (m-40) REVERT: J 813 ASP cc_start: 0.9068 (p0) cc_final: 0.8625 (t70) REVERT: J 821 MET cc_start: 0.9469 (tpt) cc_final: 0.9239 (tpt) REVERT: J 870 ASP cc_start: 0.9067 (m-30) cc_final: 0.8865 (m-30) REVERT: J 1040 MET cc_start: 0.7749 (mmp) cc_final: 0.6995 (mmm) REVERT: J 1194 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7918 (mtt180) REVERT: J 1238 GLN cc_start: 0.9581 (tp-100) cc_final: 0.9102 (tp40) REVERT: J 1249 ASN cc_start: 0.9373 (t0) cc_final: 0.8948 (t0) REVERT: J 1252 HIS cc_start: 0.9283 (m90) cc_final: 0.9058 (m90) REVERT: J 1254 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9318 (mt-10) REVERT: J 1260 MET cc_start: 0.9506 (tmm) cc_final: 0.9214 (tmm) REVERT: J 1334 GLU cc_start: 0.9426 (tm-30) cc_final: 0.9181 (tm-30) outliers start: 0 outliers final: 0 residues processed: 724 average time/residue: 0.1552 time to fit residues: 178.3810 Evaluate side-chains 642 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 642 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 133 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 181 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 300 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 186 ASN ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN ** I 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN J 921 GLN J 954 ASN J1235 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.105412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.066705 restraints weight = 90940.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.069651 restraints weight = 57245.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.071914 restraints weight = 40882.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073635 restraints weight = 31453.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.074925 restraints weight = 25558.052| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25706 Z= 0.183 Angle : 0.761 11.777 34937 Z= 0.399 Chirality : 0.047 0.315 3992 Planarity : 0.006 0.086 4386 Dihedral : 14.626 63.493 3992 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.20 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.14), residues: 3071 helix: -0.11 (0.15), residues: 1100 sheet: -1.58 (0.25), residues: 393 loop : -1.73 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG I 368 TYR 0.035 0.002 TYR I1231 PHE 0.037 0.002 PHE J 629 TRP 0.068 0.003 TRP J 236 HIS 0.010 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (25698) covalent geometry : angle 0.75773 / 0.40 (34925) hydrogen bonds : bond 0.04757 / 3.32 ( 1057) hydrogen bonds : angle 5.70434 / 3.95 ( 2933) metal coordination : bond 0.01008 / 0.44 ( 8) metal coordination : angle 3.96160 / 2.23 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5056.44 seconds wall clock time: 87 minutes 56.51 seconds (5276.51 seconds total)