Starting phenix.real_space_refine on Sun Jul 5 03:58:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t00_40930/07_2026/8t00_40930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t00_40930/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t00_40930/07_2026/8t00_40930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t00_40930/07_2026/8t00_40930.map" model { file = "/net/cci-nas-00/data/ceres_data/8t00_40930/07_2026/8t00_40930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t00_40930/07_2026/8t00_40930.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 5.98, per 1000 atoms: 0.24 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.67 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: 6.97 Time building geometry restraints manager: 3.09 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: 33773 1.63 - 3.27: 934 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 32.390 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.770 ------------------------------------------------------------------------------- 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 : 1.014 79.924 34937 Z= 0.430 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 0.67547 / 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 : 0.809 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: 0.1890 time to fit residues: 286.2479 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 : 0.906 ------------------------------------------------------------------------------- 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 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.110469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.070277 restraints weight = 88354.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.073470 restraints weight = 54978.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.075856 restraints weight = 38752.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.077729 restraints weight = 29611.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.079122 restraints weight = 23890.077| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25706 Z= 0.168 Angle : 0.845 36.961 34937 Z= 0.393 Chirality : 0.046 0.208 3992 Planarity : 0.007 0.175 4386 Dihedral : 14.409 62.673 3992 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 0.19 % Allowed : 4.72 % Favored : 95.09 % 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: -1.19 (0.15), residues: 3071 helix: 0.54 (0.15), residues: 1066 sheet: -1.01 (0.26), residues: 366 loop : -1.69 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 528 TYR 0.019 0.002 TYR J 511 PHE 0.032 0.002 PHE J 629 TRP 0.011 0.001 TRP J 409 HIS 0.006 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (25698) covalent geometry : angle 0.73532 / 0.39 (34925) hydrogen bonds : bond 0.05240 / 3.66 ( 1057) hydrogen bonds : angle 5.96506 / 4.16 ( 2933) metal coordination : bond 0.02085 / 1.01 ( 8) metal coordination : angle 22.50739 / 13.18 ( 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 863 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 858 time to evaluate : 0.689 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: G 12 ARG cc_start: 0.9328 (ptt180) cc_final: 0.9064 (mmt180) REVERT: G 35 PHE cc_start: 0.9733 (m-80) cc_final: 0.9524 (m-80) REVERT: G 37 HIS cc_start: 0.9225 (m-70) cc_final: 0.8699 (m-70) REVERT: G 104 LYS cc_start: 0.8322 (tptp) cc_final: 0.8025 (tmtt) REVERT: G 121 VAL cc_start: 0.9795 (t) cc_final: 0.9148 (t) REVERT: G 185 TYR cc_start: 0.8199 (p90) cc_final: 0.6969 (p90) REVERT: G 205 MET cc_start: 0.9629 (ppp) cc_final: 0.9372 (ppp) REVERT: H 35 PHE cc_start: 0.9131 (m-10) cc_final: 0.8893 (m-10) REVERT: H 46 ILE cc_start: 0.9665 (tp) cc_final: 0.9374 (tp) REVERT: H 95 LYS cc_start: 0.9458 (mppt) cc_final: 0.9258 (ptpp) REVERT: H 141 SER cc_start: 0.9653 (t) cc_final: 0.9372 (m) REVERT: H 142 MET cc_start: 0.9592 (ptm) cc_final: 0.9319 (ttp) REVERT: H 185 TYR cc_start: 0.7811 (p90) cc_final: 0.7209 (p90) REVERT: H 193 GLU cc_start: 0.8736 (tp30) cc_final: 0.8168 (tp30) REVERT: H 194 GLN cc_start: 0.9517 (tp40) cc_final: 0.9179 (mm-40) REVERT: H 200 LYS cc_start: 0.9026 (tmtt) cc_final: 0.8728 (tptp) REVERT: I 6 THR cc_start: 0.9308 (p) cc_final: 0.8786 (p) REVERT: I 9 LYS cc_start: 0.9250 (mttm) cc_final: 0.8799 (mttm) REVERT: I 26 TYR cc_start: 0.8551 (t80) cc_final: 0.8069 (t80) REVERT: I 28 LEU cc_start: 0.9615 (mt) cc_final: 0.9340 (mt) REVERT: I 32 LEU cc_start: 0.9577 (mt) cc_final: 0.9293 (mt) REVERT: I 53 PHE cc_start: 0.8427 (m-80) cc_final: 0.8160 (m-10) REVERT: I 57 PHE cc_start: 0.8760 (m-80) cc_final: 0.8539 (m-80) REVERT: I 69 GLN cc_start: 0.9570 (pt0) cc_final: 0.9275 (pm20) REVERT: I 92 TYR cc_start: 0.9364 (t80) cc_final: 0.9013 (t80) REVERT: I 124 MET cc_start: 0.9576 (tpp) cc_final: 0.9137 (tpp) REVERT: I 144 VAL cc_start: 0.9351 (t) cc_final: 0.9141 (p) REVERT: I 179 TYR cc_start: 0.7740 (t80) cc_final: 0.7515 (t80) REVERT: I 241 LEU cc_start: 0.9116 (tp) cc_final: 0.8883 (tp) REVERT: I 364 VAL cc_start: 0.9157 (t) cc_final: 0.8933 (t) REVERT: I 368 ARG cc_start: 0.9725 (mtm180) cc_final: 0.9342 (mmm-85) REVERT: I 400 VAL cc_start: 0.9375 (t) cc_final: 0.8858 (t) REVERT: I 405 PHE cc_start: 0.9641 (t80) cc_final: 0.9396 (t80) REVERT: I 464 PHE cc_start: 0.9722 (t80) cc_final: 0.9479 (t80) REVERT: I 548 ARG cc_start: 0.9187 (mtt180) cc_final: 0.8485 (mtt180) REVERT: I 591 TYR cc_start: 0.9446 (m-80) cc_final: 0.8789 (m-80) REVERT: I 606 LEU cc_start: 0.9269 (mp) cc_final: 0.8622 (mp) REVERT: I 623 LEU cc_start: 0.9215 (pp) cc_final: 0.8850 (mp) REVERT: I 629 PHE cc_start: 0.9418 (m-10) cc_final: 0.9183 (m-10) REVERT: I 633 LEU cc_start: 0.9583 (pt) cc_final: 0.9241 (mm) REVERT: I 642 SER cc_start: 0.8979 (p) cc_final: 0.8702 (t) REVERT: I 681 MET cc_start: 0.9323 (mtp) cc_final: 0.8763 (mtt) REVERT: I 685 MET cc_start: 0.9413 (mtm) cc_final: 0.8444 (mtm) REVERT: I 696 ASP cc_start: 0.9067 (t0) cc_final: 0.8627 (t0) REVERT: I 731 ARG cc_start: 0.9206 (ptp90) cc_final: 0.8825 (mtm-85) REVERT: I 768 MET cc_start: 0.9293 (ppp) cc_final: 0.9032 (mpp) REVERT: I 790 ASP cc_start: 0.9167 (t0) cc_final: 0.8548 (t0) REVERT: I 805 MET cc_start: 0.9348 (ppp) cc_final: 0.9135 (ppp) REVERT: I 816 ILE cc_start: 0.9459 (mt) cc_final: 0.8629 (mt) REVERT: I 833 ILE cc_start: 0.9262 (mt) cc_final: 0.9000 (tp) REVERT: I 877 VAL cc_start: 0.9252 (p) cc_final: 0.8609 (p) REVERT: I 1025 PHE cc_start: 0.9494 (t80) cc_final: 0.9135 (t80) REVERT: I 1066 MET cc_start: 0.8977 (pmm) cc_final: 0.8331 (pmm) REVERT: I 1083 GLU cc_start: 0.8640 (mp0) cc_final: 0.7650 (mp0) REVERT: I 1106 ARG cc_start: 0.9229 (mmm-85) cc_final: 0.8910 (mmm-85) REVERT: I 1107 MET cc_start: 0.9201 (mmm) cc_final: 0.8000 (tpp) REVERT: I 1113 LEU cc_start: 0.9651 (mp) cc_final: 0.9451 (mp) REVERT: I 1122 LYS cc_start: 0.9657 (tptm) cc_final: 0.9117 (tppt) REVERT: I 1126 ASP cc_start: 0.9498 (m-30) cc_final: 0.8723 (m-30) REVERT: I 1214 ASP cc_start: 0.8742 (t0) cc_final: 0.8374 (t0) REVERT: I 1234 LYS cc_start: 0.9529 (tppp) cc_final: 0.9235 (tppp) REVERT: I 1237 HIS cc_start: 0.8730 (m-70) cc_final: 0.8340 (m90) REVERT: I 1270 PHE cc_start: 0.9021 (t80) cc_final: 0.8240 (t80) REVERT: I 1290 MET cc_start: 0.9416 (tmm) cc_final: 0.8937 (tmm) REVERT: I 1304 MET cc_start: 0.9636 (tmm) cc_final: 0.9392 (ptp) REVERT: I 1319 MET cc_start: 0.7780 (tpt) cc_final: 0.6873 (tpt) REVERT: I 1321 GLU cc_start: 0.9068 (pm20) cc_final: 0.8835 (pm20) REVERT: I 1329 GLU cc_start: 0.9863 (mt-10) cc_final: 0.9574 (mt-10) REVERT: J 29 MET cc_start: 0.9200 (ttp) cc_final: 0.8939 (ptp) REVERT: J 102 MET cc_start: 0.6979 (tpt) cc_final: 0.6589 (tpt) REVERT: J 159 ILE cc_start: 0.9146 (pt) cc_final: 0.8574 (pt) REVERT: J 242 LEU cc_start: 0.9459 (tt) cc_final: 0.9175 (tt) REVERT: J 243 PRO cc_start: 0.9588 (Cg_exo) cc_final: 0.9322 (Cg_endo) REVERT: J 325 LYS cc_start: 0.8046 (pttm) cc_final: 0.7516 (pttp) REVERT: J 329 ASP cc_start: 0.9626 (m-30) cc_final: 0.9313 (t0) REVERT: J 361 LEU cc_start: 0.9175 (mt) cc_final: 0.8697 (pp) REVERT: J 371 LYS cc_start: 0.9599 (mmmt) cc_final: 0.9360 (mmmt) REVERT: J 437 PHE cc_start: 0.9636 (m-80) cc_final: 0.8754 (m-80) REVERT: J 445 LYS cc_start: 0.8740 (mmpt) cc_final: 0.8300 (tppt) REVERT: J 452 LEU cc_start: 0.9621 (mt) cc_final: 0.9293 (mm) REVERT: J 478 LEU cc_start: 0.9644 (tt) cc_final: 0.9440 (mt) REVERT: J 487 THR cc_start: 0.9694 (p) cc_final: 0.9392 (p) REVERT: J 512 TYR cc_start: 0.9410 (t80) cc_final: 0.9188 (t80) REVERT: J 576 ARG cc_start: 0.5757 (ttm170) cc_final: 0.5391 (ttm170) REVERT: J 594 GLN cc_start: 0.9411 (tm-30) cc_final: 0.8955 (tm-30) REVERT: J 596 LEU cc_start: 0.9455 (tt) cc_final: 0.9179 (tp) REVERT: J 603 LYS cc_start: 0.9241 (pttt) cc_final: 0.8857 (ptpp) REVERT: J 625 MET cc_start: 0.9485 (ttp) cc_final: 0.9274 (ttm) REVERT: J 627 THR cc_start: 0.9859 (t) cc_final: 0.9406 (t) REVERT: J 697 MET cc_start: 0.9701 (ppp) cc_final: 0.9347 (ppp) REVERT: J 764 ARG cc_start: 0.9118 (ttt-90) cc_final: 0.8831 (ttt-90) REVERT: J 822 MET cc_start: 0.8814 (tpt) cc_final: 0.8561 (tpp) REVERT: J 864 LEU cc_start: 0.9359 (mm) cc_final: 0.9152 (mm) REVERT: J 870 ASP cc_start: 0.8880 (m-30) cc_final: 0.8553 (m-30) REVERT: J 892 PHE cc_start: 0.8909 (m-10) cc_final: 0.8601 (m-10) REVERT: J 1040 MET cc_start: 0.7906 (mmp) cc_final: 0.7354 (mmm) REVERT: J 1194 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7880 (mtt180) REVERT: J 1215 GLU cc_start: 0.9423 (mp0) cc_final: 0.9187 (mm-30) REVERT: J 1231 ARG cc_start: 0.9623 (mtp85) cc_final: 0.9282 (tpt-90) REVERT: J 1238 GLN cc_start: 0.9720 (mm110) cc_final: 0.9449 (tp40) REVERT: J 1260 MET cc_start: 0.9536 (tmm) cc_final: 0.9135 (tmm) REVERT: J 1266 ILE cc_start: 0.8131 (mt) cc_final: 0.7799 (mt) REVERT: J 1279 GLN cc_start: 0.7048 (tt0) cc_final: 0.6760 (tp40) REVERT: J 1290 ARG cc_start: 0.9425 (mtm110) cc_final: 0.9191 (mtm-85) REVERT: J 1307 LEU cc_start: 0.8773 (mm) cc_final: 0.8474 (mm) outliers start: 5 outliers final: 1 residues processed: 860 average time/residue: 0.1823 time to fit residues: 235.9121 Evaluate side-chains 704 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 703 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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: 5.9990 chunk 176 optimal weight: 9.9990 chunk 276 optimal weight: 30.0000 chunk 295 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 303 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 208 optimal weight: 0.0670 overall best weight: 2.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN I 86 GLN I 526 HIS ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I 767 GLN ** I1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I1236 ASN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN J 700 ASN J 954 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.108421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.069204 restraints weight = 89891.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.072356 restraints weight = 55880.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.074759 restraints weight = 39369.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.076583 restraints weight = 29981.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.077916 restraints weight = 24254.726| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25706 Z= 0.177 Angle : 0.766 31.684 34937 Z= 0.382 Chirality : 0.047 0.271 3992 Planarity : 0.006 0.167 4386 Dihedral : 14.542 63.687 3992 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.22 % Favored : 93.75 % Rotamer: Outliers : 0.19 % Allowed : 3.77 % Favored : 96.04 % 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: -1.30 (0.14), residues: 3071 helix: 0.38 (0.15), residues: 1065 sheet: -0.96 (0.26), residues: 378 loop : -1.72 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 97 TYR 0.015 0.002 TYR J 68 PHE 0.028 0.002 PHE J 62 TRP 0.016 0.002 TRP I 997 HIS 0.005 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (25698) covalent geometry : angle 0.71704 / 0.38 (34925) hydrogen bonds : bond 0.04951 / 3.46 ( 1057) hydrogen bonds : angle 5.80782 / 4.03 ( 2933) metal coordination : bond 0.01664 / 0.76 ( 8) metal coordination : angle 14.53997 / 8.40 ( 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 819 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 814 time to evaluate : 0.764 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 37 HIS cc_start: 0.9255 (m-70) cc_final: 0.8668 (m-70) REVERT: G 68 TYR cc_start: 0.8601 (m-10) cc_final: 0.8329 (m-10) REVERT: G 104 LYS cc_start: 0.8211 (tptp) cc_final: 0.7893 (tmtt) REVERT: G 185 TYR cc_start: 0.7850 (p90) cc_final: 0.6976 (p90) REVERT: G 199 ASP cc_start: 0.7588 (m-30) cc_final: 0.7246 (m-30) REVERT: H 29 GLU cc_start: 0.8300 (pm20) cc_final: 0.8063 (pm20) REVERT: H 37 HIS cc_start: 0.9638 (m90) cc_final: 0.9240 (m90) REVERT: H 41 ASN cc_start: 0.9165 (t0) cc_final: 0.8933 (t0) REVERT: H 46 ILE cc_start: 0.9682 (tp) cc_final: 0.9401 (tp) REVERT: H 95 LYS cc_start: 0.9485 (mppt) cc_final: 0.9274 (ptpp) REVERT: H 141 SER cc_start: 0.9643 (t) cc_final: 0.9365 (m) REVERT: H 142 MET cc_start: 0.9602 (ptm) cc_final: 0.9335 (ptm) REVERT: H 185 TYR cc_start: 0.7799 (p90) cc_final: 0.7235 (p90) REVERT: H 194 GLN cc_start: 0.9487 (tp40) cc_final: 0.9242 (mm-40) REVERT: H 200 LYS cc_start: 0.9236 (tmtt) cc_final: 0.8877 (tmtt) REVERT: I 6 THR cc_start: 0.9370 (p) cc_final: 0.8759 (p) REVERT: I 9 LYS cc_start: 0.9125 (mttm) cc_final: 0.8650 (mttm) REVERT: I 26 TYR cc_start: 0.8608 (t80) cc_final: 0.8178 (t80) REVERT: I 32 LEU cc_start: 0.9612 (mt) cc_final: 0.9260 (mt) REVERT: I 53 PHE cc_start: 0.8460 (m-80) cc_final: 0.7998 (m-10) REVERT: I 92 TYR cc_start: 0.9402 (t80) cc_final: 0.8988 (t80) REVERT: I 100 LEU cc_start: 0.9719 (mt) cc_final: 0.9239 (pp) REVERT: I 124 MET cc_start: 0.9588 (tpp) cc_final: 0.9140 (tpp) REVERT: I 160 ASP cc_start: 0.8942 (m-30) cc_final: 0.8738 (m-30) REVERT: I 179 TYR cc_start: 0.7888 (t80) cc_final: 0.7683 (t80) REVERT: I 213 LEU cc_start: 0.9397 (mp) cc_final: 0.8710 (mp) REVERT: I 215 TYR cc_start: 0.8536 (m-10) cc_final: 0.8260 (m-80) REVERT: I 240 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8619 (mp0) REVERT: I 342 ASP cc_start: 0.9091 (m-30) cc_final: 0.8829 (m-30) REVERT: I 396 ASP cc_start: 0.9209 (t0) cc_final: 0.8882 (t0) REVERT: I 397 LEU cc_start: 0.9069 (mt) cc_final: 0.8772 (mt) REVERT: I 400 VAL cc_start: 0.9352 (t) cc_final: 0.8859 (t) REVERT: I 405 PHE cc_start: 0.9637 (t80) cc_final: 0.9364 (t80) REVERT: I 461 GLU cc_start: 0.9398 (tp30) cc_final: 0.9094 (tp30) REVERT: I 464 PHE cc_start: 0.9801 (t80) cc_final: 0.9350 (t80) REVERT: I 548 ARG cc_start: 0.9243 (mtt180) cc_final: 0.8571 (mtt180) REVERT: I 606 LEU cc_start: 0.9315 (mp) cc_final: 0.9092 (mp) REVERT: I 633 LEU cc_start: 0.9575 (pt) cc_final: 0.9224 (mm) REVERT: I 642 SER cc_start: 0.8925 (p) cc_final: 0.8635 (t) REVERT: I 672 GLU cc_start: 0.9408 (pm20) cc_final: 0.9091 (pm20) REVERT: I 681 MET cc_start: 0.9217 (mtp) cc_final: 0.8919 (mtt) REVERT: I 685 MET cc_start: 0.9462 (mtm) cc_final: 0.9028 (mtm) REVERT: I 737 ASN cc_start: 0.9397 (m-40) cc_final: 0.9119 (m-40) REVERT: I 799 ASN cc_start: 0.8964 (t0) cc_final: 0.8614 (t0) REVERT: I 800 MET cc_start: 0.9442 (mpp) cc_final: 0.8843 (mpp) REVERT: I 805 MET cc_start: 0.9231 (ppp) cc_final: 0.8999 (ppp) REVERT: I 816 ILE cc_start: 0.9523 (mt) cc_final: 0.9111 (mt) REVERT: I 827 ARG cc_start: 0.9285 (ptm160) cc_final: 0.8738 (ptm160) REVERT: I 882 ILE cc_start: 0.9518 (mp) cc_final: 0.9123 (mp) REVERT: I 930 ASP cc_start: 0.9774 (t70) cc_final: 0.9332 (t70) REVERT: I 1053 TYR cc_start: 0.8308 (m-80) cc_final: 0.7965 (m-80) REVERT: I 1061 GLN cc_start: 0.9487 (tt0) cc_final: 0.9051 (tm-30) REVERT: I 1095 ASP cc_start: 0.9663 (m-30) cc_final: 0.9451 (m-30) REVERT: I 1106 ARG cc_start: 0.9452 (mmm-85) cc_final: 0.9146 (mmt180) REVERT: I 1107 MET cc_start: 0.9182 (mmm) cc_final: 0.8063 (tpp) REVERT: I 1113 LEU cc_start: 0.9651 (mp) cc_final: 0.9437 (mp) REVERT: I 1122 LYS cc_start: 0.9677 (tptm) cc_final: 0.9193 (tppt) REVERT: I 1126 ASP cc_start: 0.9499 (m-30) cc_final: 0.8743 (m-30) REVERT: I 1187 PHE cc_start: 0.9074 (m-10) cc_final: 0.8636 (m-10) REVERT: I 1217 THR cc_start: 0.9262 (p) cc_final: 0.8897 (t) REVERT: I 1219 GLU cc_start: 0.9408 (pp20) cc_final: 0.8341 (pm20) REVERT: I 1234 LYS cc_start: 0.9466 (tppp) cc_final: 0.9093 (tppp) REVERT: I 1237 HIS cc_start: 0.8881 (m-70) cc_final: 0.8424 (m90) REVERT: I 1270 PHE cc_start: 0.9127 (t80) cc_final: 0.8270 (t80) REVERT: I 1273 MET cc_start: 0.7973 (ptt) cc_final: 0.7548 (ptt) REVERT: I 1290 MET cc_start: 0.9500 (tmm) cc_final: 0.9014 (tmm) REVERT: I 1304 MET cc_start: 0.9650 (tmm) cc_final: 0.9218 (ptp) REVERT: I 1319 MET cc_start: 0.7483 (tpt) cc_final: 0.6743 (tpt) REVERT: I 1321 GLU cc_start: 0.8959 (pm20) cc_final: 0.8710 (pm20) REVERT: I 1329 GLU cc_start: 0.9872 (mt-10) cc_final: 0.9602 (mt-10) REVERT: J 30 ILE cc_start: 0.9606 (mt) cc_final: 0.8695 (mt) REVERT: J 102 MET cc_start: 0.6809 (tpt) cc_final: 0.6571 (tpt) REVERT: J 192 MET cc_start: 0.8520 (ptp) cc_final: 0.8319 (ptp) REVERT: J 207 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9211 (mm-30) REVERT: J 236 TRP cc_start: 0.9394 (m-10) cc_final: 0.9037 (m-10) REVERT: J 242 LEU cc_start: 0.9474 (tt) cc_final: 0.9185 (tt) REVERT: J 243 PRO cc_start: 0.9606 (Cg_exo) cc_final: 0.9329 (Cg_endo) REVERT: J 361 LEU cc_start: 0.9118 (mt) cc_final: 0.8602 (pp) REVERT: J 423 LEU cc_start: 0.9805 (mp) cc_final: 0.9574 (mp) REVERT: J 437 PHE cc_start: 0.9601 (m-80) cc_final: 0.8696 (m-80) REVERT: J 445 LYS cc_start: 0.8733 (mmpt) cc_final: 0.8371 (mmtm) REVERT: J 452 LEU cc_start: 0.9710 (mt) cc_final: 0.9508 (mm) REVERT: J 454 CYS cc_start: 0.9348 (m) cc_final: 0.9108 (m) REVERT: J 478 LEU cc_start: 0.9665 (tt) cc_final: 0.9448 (mt) REVERT: J 512 TYR cc_start: 0.9391 (t80) cc_final: 0.9176 (t80) REVERT: J 513 MET cc_start: 0.9435 (mmp) cc_final: 0.9220 (mmp) REVERT: J 531 LYS cc_start: 0.9414 (mttt) cc_final: 0.8461 (mmmm) REVERT: J 535 ARG cc_start: 0.9298 (tmt170) cc_final: 0.9096 (ptm160) REVERT: J 594 GLN cc_start: 0.9408 (tm-30) cc_final: 0.9143 (tm-30) REVERT: J 596 LEU cc_start: 0.9342 (tt) cc_final: 0.8893 (tp) REVERT: J 599 LYS cc_start: 0.9284 (pttm) cc_final: 0.8931 (ptmt) REVERT: J 603 LYS cc_start: 0.9314 (pttt) cc_final: 0.8937 (ptpp) REVERT: J 627 THR cc_start: 0.9849 (OUTLIER) cc_final: 0.9370 (t) REVERT: J 631 TYR cc_start: 0.9510 (m-80) cc_final: 0.9108 (m-80) REVERT: J 697 MET cc_start: 0.9634 (ppp) cc_final: 0.9321 (ppp) REVERT: J 746 LEU cc_start: 0.7729 (mp) cc_final: 0.7068 (mp) REVERT: J 777 HIS cc_start: 0.8858 (m-70) cc_final: 0.7706 (m-70) REVERT: J 798 ARG cc_start: 0.9368 (ptp-170) cc_final: 0.9103 (ptt-90) REVERT: J 822 MET cc_start: 0.8635 (mmm) cc_final: 0.8204 (tpt) REVERT: J 864 LEU cc_start: 0.9375 (mm) cc_final: 0.9155 (mm) REVERT: J 870 ASP cc_start: 0.8905 (m-30) cc_final: 0.8668 (m-30) REVERT: J 891 ASP cc_start: 0.8490 (m-30) cc_final: 0.8214 (m-30) REVERT: J 892 PHE cc_start: 0.8968 (m-10) cc_final: 0.8627 (m-10) REVERT: J 1040 MET cc_start: 0.7962 (mmp) cc_final: 0.7416 (mmm) REVERT: J 1194 ARG cc_start: 0.8231 (mtt180) cc_final: 0.7928 (mtt180) REVERT: J 1215 GLU cc_start: 0.9452 (mp0) cc_final: 0.9228 (mm-30) REVERT: J 1231 ARG cc_start: 0.9627 (mtp85) cc_final: 0.9350 (tpt170) REVERT: J 1238 GLN cc_start: 0.9732 (mm110) cc_final: 0.9242 (tp40) REVERT: J 1242 ARG cc_start: 0.8978 (ttp80) cc_final: 0.8531 (ptp-170) REVERT: J 1260 MET cc_start: 0.9495 (tmm) cc_final: 0.8954 (tmm) REVERT: J 1279 GLN cc_start: 0.7531 (tt0) cc_final: 0.7068 (tp40) REVERT: J 1328 THR cc_start: 0.8592 (m) cc_final: 0.8391 (m) REVERT: J 1331 VAL cc_start: 0.9392 (m) cc_final: 0.8997 (p) REVERT: J 1340 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8444 (ttpt) outliers start: 5 outliers final: 1 residues processed: 816 average time/residue: 0.1784 time to fit residues: 222.1915 Evaluate side-chains 687 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 685 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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: 9.9990 chunk 80 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 128 optimal weight: 0.0000 chunk 125 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 227 GLN ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN I 148 GLN I 463 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1146 GLN I1175 ASN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 435 GLN ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN ** J 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 954 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.068614 restraints weight = 90162.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.071731 restraints weight = 55903.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.074082 restraints weight = 39435.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.075880 restraints weight = 30090.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.077252 restraints weight = 24335.521| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25706 Z= 0.175 Angle : 0.723 22.824 34937 Z= 0.369 Chirality : 0.046 0.227 3992 Planarity : 0.006 0.143 4386 Dihedral : 14.637 63.350 3992 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.28 % Favored : 93.68 % Rotamer: Outliers : 0.11 % Allowed : 3.96 % Favored : 95.93 % 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: -1.35 (0.14), residues: 3071 helix: 0.30 (0.15), residues: 1074 sheet: -0.81 (0.27), residues: 340 loop : -1.78 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG J 634 TYR 0.060 0.002 TYR J 631 PHE 0.024 0.002 PHE J 62 TRP 0.013 0.002 TRP J 409 HIS 0.010 0.001 HIS J 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (25698) covalent geometry : angle 0.69834 / 0.37 (34925) hydrogen bonds : bond 0.04742 / 3.30 ( 1057) hydrogen bonds : angle 5.67398 / 3.92 ( 2933) metal coordination : bond 0.01905 / 0.94 ( 8) metal coordination : angle 10.19820 / 5.52 ( 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 793 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 790 time to evaluate : 0.813 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: G 35 PHE cc_start: 0.9740 (m-80) cc_final: 0.9516 (m-80) REVERT: G 84 ASN cc_start: 0.8645 (t0) cc_final: 0.8282 (t0) REVERT: G 104 LYS cc_start: 0.8215 (tptp) cc_final: 0.7891 (tmtt) REVERT: G 130 ILE cc_start: 0.9681 (mp) cc_final: 0.9423 (mp) REVERT: G 199 ASP cc_start: 0.7646 (m-30) cc_final: 0.7408 (m-30) REVERT: H 29 GLU cc_start: 0.8322 (pm20) cc_final: 0.8100 (pm20) REVERT: H 37 HIS cc_start: 0.9663 (m90) cc_final: 0.9391 (m90) REVERT: H 46 ILE cc_start: 0.9699 (tp) cc_final: 0.9452 (tp) REVERT: H 95 LYS cc_start: 0.9471 (mppt) cc_final: 0.9259 (ptpp) REVERT: H 141 SER cc_start: 0.9659 (t) cc_final: 0.9379 (m) REVERT: H 142 MET cc_start: 0.9604 (ptm) cc_final: 0.9351 (ptm) REVERT: H 185 TYR cc_start: 0.7795 (p90) cc_final: 0.7228 (p90) REVERT: H 194 GLN cc_start: 0.9468 (tp40) cc_final: 0.9188 (mm-40) REVERT: H 200 LYS cc_start: 0.9227 (tmtt) cc_final: 0.8873 (tmtt) REVERT: H 215 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8009 (tm-30) REVERT: I 5 TYR cc_start: 0.8928 (t80) cc_final: 0.8721 (t80) REVERT: I 6 THR cc_start: 0.9353 (p) cc_final: 0.8977 (p) REVERT: I 9 LYS cc_start: 0.9126 (mttm) cc_final: 0.8651 (mttm) REVERT: I 32 LEU cc_start: 0.9508 (mt) cc_final: 0.9080 (pp) REVERT: I 39 ILE cc_start: 0.9364 (pt) cc_final: 0.8779 (pt) REVERT: I 53 PHE cc_start: 0.8717 (m-80) cc_final: 0.8040 (m-10) REVERT: I 92 TYR cc_start: 0.9381 (t80) cc_final: 0.9033 (t80) REVERT: I 100 LEU cc_start: 0.9742 (mt) cc_final: 0.9321 (pp) REVERT: I 124 MET cc_start: 0.9611 (tpp) cc_final: 0.9195 (tpp) REVERT: I 179 TYR cc_start: 0.7921 (t80) cc_final: 0.7705 (t80) REVERT: I 213 LEU cc_start: 0.9385 (mp) cc_final: 0.8710 (mp) REVERT: I 215 TYR cc_start: 0.8598 (m-10) cc_final: 0.8318 (m-80) REVERT: I 224 PHE cc_start: 0.9685 (m-80) cc_final: 0.9428 (m-80) REVERT: I 277 LEU cc_start: 0.9678 (mt) cc_final: 0.9241 (pp) REVERT: I 342 ASP cc_start: 0.9072 (m-30) cc_final: 0.8776 (m-30) REVERT: I 396 ASP cc_start: 0.9145 (t70) cc_final: 0.8917 (t0) REVERT: I 397 LEU cc_start: 0.9008 (mt) cc_final: 0.8770 (mt) REVERT: I 405 PHE cc_start: 0.9651 (t80) cc_final: 0.9337 (t80) REVERT: I 419 ILE cc_start: 0.9256 (pt) cc_final: 0.8967 (pt) REVERT: I 452 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8254 (mmm-85) REVERT: I 461 GLU cc_start: 0.9508 (tp30) cc_final: 0.9064 (tp30) REVERT: I 464 PHE cc_start: 0.9803 (t80) cc_final: 0.9329 (t80) REVERT: I 606 LEU cc_start: 0.9310 (mp) cc_final: 0.9088 (mp) REVERT: I 633 LEU cc_start: 0.9571 (pt) cc_final: 0.9249 (mm) REVERT: I 642 SER cc_start: 0.8939 (p) cc_final: 0.8598 (t) REVERT: I 671 LEU cc_start: 0.9796 (tp) cc_final: 0.9549 (tp) REVERT: I 672 GLU cc_start: 0.9458 (pm20) cc_final: 0.8952 (pm20) REVERT: I 681 MET cc_start: 0.9215 (mtp) cc_final: 0.8926 (mtt) REVERT: I 697 LYS cc_start: 0.8623 (mmmt) cc_final: 0.7551 (mmtm) REVERT: I 737 ASN cc_start: 0.9341 (m-40) cc_final: 0.9059 (m-40) REVERT: I 748 ILE cc_start: 0.9010 (pt) cc_final: 0.8768 (pt) REVERT: I 749 ASP cc_start: 0.9185 (t0) cc_final: 0.8744 (p0) REVERT: I 789 THR cc_start: 0.9442 (m) cc_final: 0.9045 (p) REVERT: I 790 ASP cc_start: 0.9385 (t0) cc_final: 0.9081 (p0) REVERT: I 799 ASN cc_start: 0.8998 (t0) cc_final: 0.8562 (t0) REVERT: I 800 MET cc_start: 0.9546 (mpp) cc_final: 0.8899 (mpp) REVERT: I 805 MET cc_start: 0.9313 (ppp) cc_final: 0.8984 (ppp) REVERT: I 827 ARG cc_start: 0.9373 (ptm160) cc_final: 0.8798 (ptm160) REVERT: I 831 ILE cc_start: 0.8981 (mm) cc_final: 0.8445 (mm) REVERT: I 930 ASP cc_start: 0.9772 (t70) cc_final: 0.9288 (t70) REVERT: I 957 LYS cc_start: 0.9558 (pptt) cc_final: 0.9290 (pttm) REVERT: I 1053 TYR cc_start: 0.8263 (m-80) cc_final: 0.8020 (m-80) REVERT: I 1056 VAL cc_start: 0.8601 (m) cc_final: 0.8128 (m) REVERT: I 1061 GLN cc_start: 0.9418 (tt0) cc_final: 0.8818 (tm-30) REVERT: I 1070 HIS cc_start: 0.7684 (m-70) cc_final: 0.6760 (m170) REVERT: I 1080 ASN cc_start: 0.8970 (m-40) cc_final: 0.8569 (m-40) REVERT: I 1106 ARG cc_start: 0.9476 (mmm-85) cc_final: 0.9142 (mmt180) REVERT: I 1107 MET cc_start: 0.9172 (mmm) cc_final: 0.7546 (tmm) REVERT: I 1122 LYS cc_start: 0.9716 (tptm) cc_final: 0.9180 (tppt) REVERT: I 1126 ASP cc_start: 0.9486 (m-30) cc_final: 0.8720 (m-30) REVERT: I 1180 MET cc_start: 0.9270 (ttp) cc_final: 0.9051 (ttp) REVERT: I 1219 GLU cc_start: 0.9357 (pp20) cc_final: 0.8479 (pm20) REVERT: I 1223 ARG cc_start: 0.9217 (tpm170) cc_final: 0.8897 (tpm170) REVERT: I 1234 LYS cc_start: 0.9424 (tppp) cc_final: 0.9082 (tppp) REVERT: I 1237 HIS cc_start: 0.8800 (m-70) cc_final: 0.8350 (m90) REVERT: I 1264 GLN cc_start: 0.9443 (tp-100) cc_final: 0.9127 (tm-30) REVERT: I 1270 PHE cc_start: 0.9108 (t80) cc_final: 0.8285 (t80) REVERT: I 1290 MET cc_start: 0.9504 (tmm) cc_final: 0.9050 (tmm) REVERT: I 1304 MET cc_start: 0.9655 (tmm) cc_final: 0.9247 (ptp) REVERT: I 1319 MET cc_start: 0.7589 (tpt) cc_final: 0.6738 (tpt) REVERT: I 1321 GLU cc_start: 0.8979 (pm20) cc_final: 0.8743 (pm20) REVERT: I 1329 GLU cc_start: 0.9875 (mt-10) cc_final: 0.9579 (mt-10) REVERT: J 30 ILE cc_start: 0.9300 (mt) cc_final: 0.8873 (mt) REVERT: J 102 MET cc_start: 0.7024 (tpt) cc_final: 0.6601 (tpt) REVERT: J 207 GLU cc_start: 0.9425 (mm-30) cc_final: 0.9155 (mm-30) REVERT: J 236 TRP cc_start: 0.9446 (m-10) cc_final: 0.9214 (m-10) REVERT: J 242 LEU cc_start: 0.9475 (tt) cc_final: 0.9230 (tt) REVERT: J 243 PRO cc_start: 0.9706 (Cg_exo) cc_final: 0.9472 (Cg_endo) REVERT: J 325 LYS cc_start: 0.7991 (pttp) cc_final: 0.7632 (pttp) REVERT: J 361 LEU cc_start: 0.9110 (mt) cc_final: 0.8611 (pp) REVERT: J 423 LEU cc_start: 0.9808 (mp) cc_final: 0.9492 (mp) REVERT: J 437 PHE cc_start: 0.9629 (m-80) cc_final: 0.8595 (m-80) REVERT: J 445 LYS cc_start: 0.8802 (mmpt) cc_final: 0.8468 (mmtm) REVERT: J 452 LEU cc_start: 0.9716 (mt) cc_final: 0.9418 (mt) REVERT: J 454 CYS cc_start: 0.9284 (m) cc_final: 0.9020 (m) REVERT: J 512 TYR cc_start: 0.9367 (t80) cc_final: 0.9158 (t80) REVERT: J 603 LYS cc_start: 0.9324 (pttt) cc_final: 0.8929 (ptpp) REVERT: J 627 THR cc_start: 0.9803 (t) cc_final: 0.9398 (t) REVERT: J 629 PHE cc_start: 0.9382 (m-10) cc_final: 0.9157 (m-80) REVERT: J 644 MET cc_start: 0.9567 (mpp) cc_final: 0.9332 (mpp) REVERT: J 645 VAL cc_start: 0.8653 (p) cc_final: 0.8252 (m) REVERT: J 697 MET cc_start: 0.9624 (ppp) cc_final: 0.9343 (ppp) REVERT: J 777 HIS cc_start: 0.8868 (m-70) cc_final: 0.7691 (m-70) REVERT: J 792 ASN cc_start: 0.9390 (m110) cc_final: 0.9185 (m110) REVERT: J 822 MET cc_start: 0.8556 (mmm) cc_final: 0.8253 (tpt) REVERT: J 864 LEU cc_start: 0.9367 (mm) cc_final: 0.9165 (mm) REVERT: J 870 ASP cc_start: 0.8911 (m-30) cc_final: 0.8692 (m-30) REVERT: J 913 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8328 (mm-30) REVERT: J 932 MET cc_start: 0.5655 (tpp) cc_final: 0.5405 (tpp) REVERT: J 1040 MET cc_start: 0.8105 (mmp) cc_final: 0.7558 (mmm) REVERT: J 1145 PHE cc_start: 0.9580 (m-80) cc_final: 0.9374 (m-80) REVERT: J 1215 GLU cc_start: 0.9498 (mp0) cc_final: 0.9261 (mm-30) REVERT: J 1231 ARG cc_start: 0.9653 (mtp85) cc_final: 0.9406 (tpt170) REVERT: J 1242 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8751 (ptp-170) REVERT: J 1249 ASN cc_start: 0.9564 (t0) cc_final: 0.9151 (t0) REVERT: J 1254 GLU cc_start: 0.9616 (mt-10) cc_final: 0.9410 (mt-10) REVERT: J 1260 MET cc_start: 0.9440 (tmm) cc_final: 0.8948 (tmm) REVERT: J 1279 GLN cc_start: 0.7564 (tt0) cc_final: 0.7322 (tp40) REVERT: J 1331 VAL cc_start: 0.9085 (m) cc_final: 0.8829 (p) REVERT: J 1340 LYS cc_start: 0.8767 (ttpp) cc_final: 0.8535 (ttpt) outliers start: 3 outliers final: 1 residues processed: 791 average time/residue: 0.1762 time to fit residues: 215.5841 Evaluate side-chains 683 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 682 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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: 9.9990 chunk 166 optimal weight: 0.0980 chunk 309 optimal weight: 50.0000 chunk 305 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 258 optimal weight: 0.4980 chunk 286 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 227 GLN ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 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** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1175 ASN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN ** J 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 921 GLN 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 = 0.3652 r_free = 0.3652 target = 0.106074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.067912 restraints weight = 91325.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.070858 restraints weight = 57310.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.073096 restraints weight = 40810.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.074820 restraints weight = 31299.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.076058 restraints weight = 25456.341| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25706 Z= 0.218 Angle : 0.738 17.623 34937 Z= 0.382 Chirality : 0.046 0.343 3992 Planarity : 0.006 0.124 4386 Dihedral : 14.722 63.982 3992 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.81 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: -1.50 (0.14), residues: 3071 helix: 0.13 (0.15), residues: 1074 sheet: -1.05 (0.26), residues: 373 loop : -1.80 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG J 634 TYR 0.054 0.002 TYR J 631 PHE 0.025 0.002 PHE I 38 TRP 0.011 0.002 TRP I 183 HIS 0.008 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.22 (25698) covalent geometry : angle 0.72335 / 0.38 (34925) hydrogen bonds : bond 0.04847 / 3.36 ( 1057) hydrogen bonds : angle 5.74198 / 3.98 ( 2933) metal coordination : bond 0.01424 / 0.67 ( 8) metal coordination : angle 7.91955 / 4.15 ( 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 766 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 766 time to evaluate : 0.907 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: G 84 ASN cc_start: 0.8744 (t0) cc_final: 0.8434 (t0) REVERT: G 104 LYS cc_start: 0.8239 (tptp) cc_final: 0.7888 (tmtt) REVERT: G 130 ILE cc_start: 0.9701 (mp) cc_final: 0.9438 (mp) REVERT: G 199 ASP cc_start: 0.7661 (m-30) cc_final: 0.7431 (m-30) REVERT: G 205 MET cc_start: 0.9601 (ppp) cc_final: 0.9276 (ppp) REVERT: G 227 GLN cc_start: 0.9589 (mm-40) cc_final: 0.9328 (mt0) REVERT: H 29 GLU cc_start: 0.8372 (pm20) cc_final: 0.8155 (pm20) REVERT: H 46 ILE cc_start: 0.9715 (tp) cc_final: 0.9477 (tp) REVERT: H 68 TYR cc_start: 0.9517 (m-10) cc_final: 0.9278 (m-10) REVERT: H 79 LEU cc_start: 0.9266 (mp) cc_final: 0.9061 (mp) REVERT: H 95 LYS cc_start: 0.9487 (mppt) cc_final: 0.9181 (ptpp) REVERT: H 141 SER cc_start: 0.9665 (t) cc_final: 0.9419 (m) REVERT: H 142 MET cc_start: 0.9591 (ptm) cc_final: 0.9345 (ptm) REVERT: H 147 GLN cc_start: 0.8869 (mp10) cc_final: 0.8528 (mp10) REVERT: H 185 TYR cc_start: 0.7751 (p90) cc_final: 0.7089 (p90) REVERT: H 193 GLU cc_start: 0.8505 (tp30) cc_final: 0.7889 (tp30) REVERT: H 194 GLN cc_start: 0.9553 (tp40) cc_final: 0.9245 (mm-40) REVERT: H 200 LYS cc_start: 0.9221 (tmtt) cc_final: 0.8872 (tmtt) REVERT: I 5 TYR cc_start: 0.8952 (t80) cc_final: 0.8720 (t80) REVERT: I 9 LYS cc_start: 0.9171 (mttm) cc_final: 0.8739 (mttm) REVERT: I 32 LEU cc_start: 0.9522 (mt) cc_final: 0.9093 (pp) REVERT: I 92 TYR cc_start: 0.9466 (t80) cc_final: 0.9096 (t80) REVERT: I 100 LEU cc_start: 0.9729 (mt) cc_final: 0.9210 (pp) REVERT: I 102 LEU cc_start: 0.9724 (tp) cc_final: 0.9498 (tp) REVERT: I 124 MET cc_start: 0.9606 (tpp) cc_final: 0.9260 (tpp) REVERT: I 151 ARG cc_start: 0.9408 (mmp80) cc_final: 0.9204 (mmp80) REVERT: I 179 TYR cc_start: 0.8035 (t80) cc_final: 0.7825 (t80) REVERT: I 213 LEU cc_start: 0.9398 (mp) cc_final: 0.8726 (mp) REVERT: I 215 TYR cc_start: 0.8675 (m-10) cc_final: 0.8371 (m-80) REVERT: I 224 PHE cc_start: 0.9710 (m-80) cc_final: 0.9429 (m-80) REVERT: I 277 LEU cc_start: 0.9698 (mt) cc_final: 0.9260 (pp) REVERT: I 336 LEU cc_start: 0.8284 (mt) cc_final: 0.8016 (mp) REVERT: I 342 ASP cc_start: 0.9139 (m-30) cc_final: 0.8810 (m-30) REVERT: I 396 ASP cc_start: 0.9157 (t70) cc_final: 0.8940 (t0) REVERT: I 397 LEU cc_start: 0.9056 (mt) cc_final: 0.8798 (mt) REVERT: I 405 PHE cc_start: 0.9668 (t80) cc_final: 0.9351 (t80) REVERT: I 419 ILE cc_start: 0.9234 (pt) cc_final: 0.8921 (pt) REVERT: I 430 LYS cc_start: 0.9515 (mmtm) cc_final: 0.9310 (mmtt) REVERT: I 450 ASN cc_start: 0.8948 (m110) cc_final: 0.8644 (t0) REVERT: I 452 ARG cc_start: 0.9450 (tpt-90) cc_final: 0.9003 (mtp85) REVERT: I 606 LEU cc_start: 0.9346 (mp) cc_final: 0.9121 (mp) REVERT: I 642 SER cc_start: 0.8966 (p) cc_final: 0.8658 (t) REVERT: I 645 PHE cc_start: 0.9054 (m-10) cc_final: 0.8822 (m-10) REVERT: I 671 LEU cc_start: 0.9779 (tp) cc_final: 0.9570 (tp) REVERT: I 672 GLU cc_start: 0.9475 (pm20) cc_final: 0.8926 (pm20) REVERT: I 681 MET cc_start: 0.9250 (mtp) cc_final: 0.8987 (mtt) REVERT: I 685 MET cc_start: 0.9299 (mtp) cc_final: 0.8943 (mtp) REVERT: I 697 LYS cc_start: 0.8628 (mmmt) cc_final: 0.7443 (mmtm) REVERT: I 749 ASP cc_start: 0.9149 (t0) cc_final: 0.8788 (p0) REVERT: I 789 THR cc_start: 0.9484 (m) cc_final: 0.9111 (p) REVERT: I 790 ASP cc_start: 0.9430 (t0) cc_final: 0.9055 (p0) REVERT: I 799 ASN cc_start: 0.9000 (t0) cc_final: 0.8787 (t0) REVERT: I 805 MET cc_start: 0.9342 (ppp) cc_final: 0.9023 (ppp) REVERT: I 817 LEU cc_start: 0.8222 (mm) cc_final: 0.7610 (mm) REVERT: I 831 ILE cc_start: 0.9009 (mm) cc_final: 0.8516 (mm) REVERT: I 930 ASP cc_start: 0.9735 (t70) cc_final: 0.9067 (t70) REVERT: I 957 LYS cc_start: 0.9581 (pptt) cc_final: 0.9259 (mmmt) REVERT: I 1053 TYR cc_start: 0.8257 (m-80) cc_final: 0.7951 (m-80) REVERT: I 1056 VAL cc_start: 0.8602 (m) cc_final: 0.8134 (m) REVERT: I 1061 GLN cc_start: 0.9369 (tt0) cc_final: 0.8855 (tm-30) REVERT: I 1080 ASN cc_start: 0.9019 (m-40) cc_final: 0.8437 (t0) REVERT: I 1106 ARG cc_start: 0.9511 (mmm-85) cc_final: 0.9173 (mmt180) REVERT: I 1107 MET cc_start: 0.9048 (mmm) cc_final: 0.7896 (tmm) REVERT: I 1122 LYS cc_start: 0.9652 (tptm) cc_final: 0.9161 (tppt) REVERT: I 1126 ASP cc_start: 0.9458 (m-30) cc_final: 0.8682 (m-30) REVERT: I 1180 MET cc_start: 0.9284 (ttp) cc_final: 0.9058 (ttp) REVERT: I 1187 PHE cc_start: 0.9035 (m-10) cc_final: 0.8564 (m-10) REVERT: I 1234 LYS cc_start: 0.9442 (tppp) cc_final: 0.8993 (tppp) REVERT: I 1236 ASN cc_start: 0.7752 (m-40) cc_final: 0.7442 (m-40) REVERT: I 1237 HIS cc_start: 0.8852 (m-70) cc_final: 0.8459 (m90) REVERT: I 1264 GLN cc_start: 0.9444 (tp-100) cc_final: 0.9086 (tm-30) REVERT: I 1270 PHE cc_start: 0.9052 (t80) cc_final: 0.8192 (t80) REVERT: I 1273 MET cc_start: 0.8040 (ptt) cc_final: 0.7810 (ptt) REVERT: I 1290 MET cc_start: 0.9497 (tmm) cc_final: 0.9085 (tmm) REVERT: I 1304 MET cc_start: 0.9678 (tmm) cc_final: 0.9292 (ptp) REVERT: I 1319 MET cc_start: 0.7704 (tpt) cc_final: 0.6850 (tpt) REVERT: I 1321 GLU cc_start: 0.9030 (pm20) cc_final: 0.8748 (pm20) REVERT: I 1329 GLU cc_start: 0.9883 (mt-10) cc_final: 0.9608 (mt-10) REVERT: J 30 ILE cc_start: 0.9266 (mt) cc_final: 0.8957 (mt) REVERT: J 102 MET cc_start: 0.7020 (tpt) cc_final: 0.6385 (tpt) REVERT: J 207 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9205 (mm-30) REVERT: J 236 TRP cc_start: 0.9418 (m-10) cc_final: 0.9208 (m-10) REVERT: J 242 LEU cc_start: 0.9518 (tt) cc_final: 0.9302 (tt) REVERT: J 325 LYS cc_start: 0.7564 (pttm) cc_final: 0.7213 (pttp) REVERT: J 329 ASP cc_start: 0.9722 (m-30) cc_final: 0.9485 (t0) REVERT: J 332 LYS cc_start: 0.9290 (mmtt) cc_final: 0.8629 (mmtt) REVERT: J 361 LEU cc_start: 0.9200 (mt) cc_final: 0.8742 (pp) REVERT: J 437 PHE cc_start: 0.9643 (m-80) cc_final: 0.8561 (m-80) REVERT: J 445 LYS cc_start: 0.8782 (mmpt) cc_final: 0.8453 (mmtm) REVERT: J 454 CYS cc_start: 0.9256 (m) cc_final: 0.9019 (m) REVERT: J 512 TYR cc_start: 0.9399 (t80) cc_final: 0.9092 (t80) REVERT: J 603 LYS cc_start: 0.9356 (pttt) cc_final: 0.8999 (ptpp) REVERT: J 625 MET cc_start: 0.9450 (ttm) cc_final: 0.9236 (tpp) REVERT: J 627 THR cc_start: 0.9882 (t) cc_final: 0.9263 (t) REVERT: J 629 PHE cc_start: 0.9430 (m-10) cc_final: 0.8932 (m-80) REVERT: J 645 VAL cc_start: 0.8609 (p) cc_final: 0.8201 (m) REVERT: J 697 MET cc_start: 0.9630 (ppp) cc_final: 0.9362 (ppp) REVERT: J 763 PHE cc_start: 0.9302 (m-80) cc_final: 0.8672 (m-80) REVERT: J 822 MET cc_start: 0.8580 (mmm) cc_final: 0.8225 (tpt) REVERT: J 864 LEU cc_start: 0.9381 (mm) cc_final: 0.9177 (mm) REVERT: J 1040 MET cc_start: 0.8120 (mmp) cc_final: 0.7479 (mmm) REVERT: J 1194 ARG cc_start: 0.8280 (mtt180) cc_final: 0.8022 (mtt180) REVERT: J 1215 GLU cc_start: 0.9510 (mp0) cc_final: 0.9243 (mm-30) REVERT: J 1231 ARG cc_start: 0.9650 (mtp85) cc_final: 0.9377 (tpt170) REVERT: J 1238 GLN cc_start: 0.9644 (tp-100) cc_final: 0.9118 (tp-100) REVERT: J 1260 MET cc_start: 0.9505 (tmm) cc_final: 0.9181 (tmm) REVERT: J 1328 THR cc_start: 0.8857 (m) cc_final: 0.8426 (m) REVERT: J 1334 GLU cc_start: 0.9324 (tm-30) cc_final: 0.9105 (tm-30) REVERT: J 1340 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8580 (ttpt) outliers start: 0 outliers final: 0 residues processed: 766 average time/residue: 0.1750 time to fit residues: 206.7439 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 : 1.034 ------------------------------------------------------------------------------- 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: 6.9990 chunk 230 optimal weight: 0.6980 chunk 279 optimal weight: 6.9990 chunk 127 optimal weight: 0.0470 chunk 228 optimal weight: 7.9990 chunk 128 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 150 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 overall best weight: 1.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS H 37 HIS I 20 GLN I 148 GLN I 165 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1175 ASN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN ** J 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 921 GLN J 954 ASN J1279 GLN J1367 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.108819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.070074 restraints weight = 86736.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.073185 restraints weight = 54091.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.075569 restraints weight = 38260.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.077392 restraints weight = 29218.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.078738 restraints weight = 23610.510| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25706 Z= 0.154 Angle : 0.724 13.183 34937 Z= 0.372 Chirality : 0.046 0.226 3992 Planarity : 0.006 0.114 4386 Dihedral : 14.695 63.713 3992 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.68 % Rotamer: Outliers : 0.11 % Allowed : 2.06 % Favored : 97.83 % 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: -1.49 (0.14), residues: 3071 helix: 0.14 (0.15), residues: 1082 sheet: -1.29 (0.26), residues: 355 loop : -1.73 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 634 TYR 0.047 0.002 TYR J 631 PHE 0.030 0.002 PHE I 812 TRP 0.025 0.002 TRP I 183 HIS 0.006 0.001 HIS J 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (25698) covalent geometry : angle 0.71107 / 0.37 (34925) hydrogen bonds : bond 0.04587 / 3.18 ( 1057) hydrogen bonds : angle 5.63666 / 3.90 ( 2933) metal coordination : bond 0.01189 / 0.50 ( 8) metal coordination : angle 7.40375 / 3.94 ( 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 788 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 785 time to evaluate : 0.958 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 45 ARG cc_start: 0.9063 (mmt180) cc_final: 0.8469 (mmt180) REVERT: G 84 ASN cc_start: 0.8711 (t0) cc_final: 0.8401 (t0) REVERT: G 104 LYS cc_start: 0.8270 (tptp) cc_final: 0.7934 (tmtt) REVERT: G 130 ILE cc_start: 0.9630 (mp) cc_final: 0.9353 (mp) REVERT: G 199 ASP cc_start: 0.7779 (m-30) cc_final: 0.7575 (m-30) REVERT: G 205 MET cc_start: 0.9607 (ppp) cc_final: 0.9340 (ppp) REVERT: G 231 PHE cc_start: 0.9855 (m-80) cc_final: 0.9642 (m-80) REVERT: H 16 ILE cc_start: 0.8304 (pt) cc_final: 0.7899 (mp) REVERT: H 68 TYR cc_start: 0.9523 (m-10) cc_final: 0.9260 (m-10) REVERT: H 79 LEU cc_start: 0.9192 (mp) cc_final: 0.8878 (mp) REVERT: H 83 LEU cc_start: 0.9571 (pp) cc_final: 0.9130 (mm) REVERT: H 95 LYS cc_start: 0.9492 (mppt) cc_final: 0.9181 (ptpp) REVERT: H 141 SER cc_start: 0.9670 (t) cc_final: 0.9350 (m) REVERT: H 142 MET cc_start: 0.9574 (ptm) cc_final: 0.9224 (ptm) REVERT: H 193 GLU cc_start: 0.8696 (tp30) cc_final: 0.8376 (tp30) REVERT: H 200 LYS cc_start: 0.9205 (tmtt) cc_final: 0.8868 (tmtt) REVERT: I 6 THR cc_start: 0.9275 (p) cc_final: 0.8862 (p) REVERT: I 9 LYS cc_start: 0.9106 (mttm) cc_final: 0.8570 (mttm) REVERT: I 32 LEU cc_start: 0.9490 (mt) cc_final: 0.9050 (pp) REVERT: I 39 ILE cc_start: 0.9298 (pt) cc_final: 0.8784 (pt) REVERT: I 53 PHE cc_start: 0.8682 (m-80) cc_final: 0.8001 (m-10) REVERT: I 74 ARG cc_start: 0.9542 (tmt170) cc_final: 0.9340 (ptm-80) REVERT: I 124 MET cc_start: 0.9650 (tpp) cc_final: 0.9410 (tpp) REVERT: I 151 ARG cc_start: 0.9347 (mmp80) cc_final: 0.9064 (mmp80) REVERT: I 213 LEU cc_start: 0.9377 (mp) cc_final: 0.8690 (mp) REVERT: I 215 TYR cc_start: 0.8616 (m-10) cc_final: 0.8324 (m-80) REVERT: I 224 PHE cc_start: 0.9686 (m-80) cc_final: 0.9355 (m-80) REVERT: I 277 LEU cc_start: 0.9689 (mt) cc_final: 0.9241 (pp) REVERT: I 342 ASP cc_start: 0.9083 (m-30) cc_final: 0.8673 (m-30) REVERT: I 405 PHE cc_start: 0.9643 (t80) cc_final: 0.9245 (t80) REVERT: I 419 ILE cc_start: 0.9263 (pt) cc_final: 0.8980 (pt) REVERT: I 430 LYS cc_start: 0.9506 (mmtm) cc_final: 0.9301 (mmtt) REVERT: I 452 ARG cc_start: 0.9418 (tpt-90) cc_final: 0.8850 (tpt90) REVERT: I 461 GLU cc_start: 0.9551 (tp30) cc_final: 0.8859 (tp30) REVERT: I 464 PHE cc_start: 0.9775 (t80) cc_final: 0.9276 (t80) REVERT: I 548 ARG cc_start: 0.9375 (mmt180) cc_final: 0.9011 (mmm160) REVERT: I 606 LEU cc_start: 0.9309 (mp) cc_final: 0.9091 (mp) REVERT: I 633 LEU cc_start: 0.9571 (pt) cc_final: 0.9244 (mm) REVERT: I 642 SER cc_start: 0.8945 (p) cc_final: 0.8637 (t) REVERT: I 668 ILE cc_start: 0.9567 (mm) cc_final: 0.9284 (mm) REVERT: I 671 LEU cc_start: 0.9776 (tp) cc_final: 0.9492 (tp) REVERT: I 672 GLU cc_start: 0.9505 (pm20) cc_final: 0.9024 (pm20) REVERT: I 681 MET cc_start: 0.9242 (mtp) cc_final: 0.8984 (mtt) REVERT: I 685 MET cc_start: 0.9317 (mtp) cc_final: 0.8872 (mtp) REVERT: I 688 GLN cc_start: 0.9459 (pp30) cc_final: 0.9222 (pp30) REVERT: I 697 LYS cc_start: 0.8389 (mmmt) cc_final: 0.7100 (mmtm) REVERT: I 737 ASN cc_start: 0.9336 (m-40) cc_final: 0.9068 (m-40) REVERT: I 749 ASP cc_start: 0.9149 (t0) cc_final: 0.8831 (p0) REVERT: I 768 MET cc_start: 0.9299 (ppp) cc_final: 0.9064 (mpp) REVERT: I 790 ASP cc_start: 0.9416 (t0) cc_final: 0.9016 (p0) REVERT: I 805 MET cc_start: 0.9370 (ppp) cc_final: 0.9114 (ppp) REVERT: I 817 LEU cc_start: 0.8367 (mm) cc_final: 0.7728 (mm) REVERT: I 831 ILE cc_start: 0.8925 (mm) cc_final: 0.8464 (mm) REVERT: I 930 ASP cc_start: 0.9726 (t70) cc_final: 0.9040 (t0) REVERT: I 1053 TYR cc_start: 0.8132 (m-80) cc_final: 0.7908 (m-80) REVERT: I 1056 VAL cc_start: 0.8549 (m) cc_final: 0.8048 (m) REVERT: I 1061 GLN cc_start: 0.9308 (tt0) cc_final: 0.8902 (tm-30) REVERT: I 1080 ASN cc_start: 0.8938 (m-40) cc_final: 0.8403 (t0) REVERT: I 1106 ARG cc_start: 0.9502 (mmm-85) cc_final: 0.9168 (mmt180) REVERT: I 1107 MET cc_start: 0.9085 (mmm) cc_final: 0.7879 (tmm) REVERT: I 1122 LYS cc_start: 0.9636 (tptm) cc_final: 0.9137 (tppt) REVERT: I 1126 ASP cc_start: 0.9354 (m-30) cc_final: 0.8727 (m-30) REVERT: I 1187 PHE cc_start: 0.8902 (m-10) cc_final: 0.8435 (m-10) REVERT: I 1216 ARG cc_start: 0.9170 (mtp180) cc_final: 0.8792 (mmm-85) REVERT: I 1234 LYS cc_start: 0.9409 (tppp) cc_final: 0.8918 (tppp) REVERT: I 1237 HIS cc_start: 0.8778 (m-70) cc_final: 0.8422 (m-70) REVERT: I 1265 PHE cc_start: 0.9156 (t80) cc_final: 0.8878 (t80) REVERT: I 1270 PHE cc_start: 0.8956 (t80) cc_final: 0.8249 (t80) REVERT: I 1290 MET cc_start: 0.9471 (tmm) cc_final: 0.9012 (tmm) REVERT: I 1304 MET cc_start: 0.9679 (tmm) cc_final: 0.9303 (ptp) REVERT: I 1319 MET cc_start: 0.7665 (tpt) cc_final: 0.6890 (tpt) REVERT: I 1321 GLU cc_start: 0.8939 (pm20) cc_final: 0.8693 (pm20) REVERT: I 1326 LEU cc_start: 0.9526 (mt) cc_final: 0.9277 (mt) REVERT: I 1327 LEU cc_start: 0.9541 (mt) cc_final: 0.9261 (mt) REVERT: I 1329 GLU cc_start: 0.9890 (mt-10) cc_final: 0.9690 (mt-10) REVERT: I 1330 ILE cc_start: 0.9847 (mt) cc_final: 0.9506 (mt) REVERT: I 1337 ILE cc_start: 0.9520 (tt) cc_final: 0.8596 (tt) REVERT: J 30 ILE cc_start: 0.9313 (mt) cc_final: 0.8974 (mt) REVERT: J 33 TRP cc_start: 0.8950 (m100) cc_final: 0.8707 (m-10) REVERT: J 56 LEU cc_start: 0.9397 (tt) cc_final: 0.9192 (tt) REVERT: J 102 MET cc_start: 0.6812 (tpt) cc_final: 0.6225 (tpt) REVERT: J 207 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9134 (mm-30) REVERT: J 242 LEU cc_start: 0.9518 (tt) cc_final: 0.9274 (tt) REVERT: J 243 PRO cc_start: 0.9646 (Cg_exo) cc_final: 0.9423 (Cg_endo) REVERT: J 325 LYS cc_start: 0.7648 (pttm) cc_final: 0.7221 (pttm) REVERT: J 329 ASP cc_start: 0.9711 (m-30) cc_final: 0.9438 (t0) REVERT: J 330 MET cc_start: 0.9388 (mpp) cc_final: 0.9093 (mpp) REVERT: J 332 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8805 (mmtt) REVERT: J 361 LEU cc_start: 0.9197 (mt) cc_final: 0.8609 (pp) REVERT: J 365 GLN cc_start: 0.9611 (pt0) cc_final: 0.9316 (pt0) REVERT: J 409 TRP cc_start: 0.9059 (m100) cc_final: 0.8278 (m100) REVERT: J 437 PHE cc_start: 0.9625 (m-80) cc_final: 0.8964 (m-80) REVERT: J 445 LYS cc_start: 0.8639 (mmpt) cc_final: 0.8399 (mmtm) REVERT: J 454 CYS cc_start: 0.9353 (m) cc_final: 0.9117 (m) REVERT: J 484 MET cc_start: 0.8886 (mpp) cc_final: 0.8672 (mpp) REVERT: J 526 VAL cc_start: 0.8987 (p) cc_final: 0.8693 (p) REVERT: J 603 LYS cc_start: 0.9353 (pttt) cc_final: 0.8986 (ptpp) REVERT: J 619 ILE cc_start: 0.9656 (mp) cc_final: 0.9439 (pt) REVERT: J 627 THR cc_start: 0.9877 (t) cc_final: 0.9393 (t) REVERT: J 629 PHE cc_start: 0.9323 (m-10) cc_final: 0.8908 (m-80) REVERT: J 645 VAL cc_start: 0.8575 (p) cc_final: 0.8191 (m) REVERT: J 697 MET cc_start: 0.9646 (ppp) cc_final: 0.9412 (ppp) REVERT: J 743 MET cc_start: 0.9248 (ptm) cc_final: 0.9035 (ptm) REVERT: J 763 PHE cc_start: 0.9293 (m-80) cc_final: 0.8621 (m-80) REVERT: J 764 ARG cc_start: 0.9057 (ttt-90) cc_final: 0.8742 (ttt-90) REVERT: J 792 ASN cc_start: 0.9350 (m110) cc_final: 0.9142 (m-40) REVERT: J 822 MET cc_start: 0.8563 (mmm) cc_final: 0.8272 (tpt) REVERT: J 870 ASP cc_start: 0.8922 (m-30) cc_final: 0.8660 (m-30) REVERT: J 1040 MET cc_start: 0.7713 (mmp) cc_final: 0.6971 (mmm) REVERT: J 1145 PHE cc_start: 0.9610 (m-80) cc_final: 0.9401 (m-80) REVERT: J 1194 ARG cc_start: 0.8265 (mtt180) cc_final: 0.7984 (mtt180) REVERT: J 1215 GLU cc_start: 0.9511 (mp0) cc_final: 0.9236 (mm-30) REVERT: J 1231 ARG cc_start: 0.9656 (mtp85) cc_final: 0.9416 (tpt170) REVERT: J 1238 GLN cc_start: 0.9607 (tp-100) cc_final: 0.9224 (tp40) REVERT: J 1239 ASP cc_start: 0.9662 (t0) cc_final: 0.9398 (t0) REVERT: J 1249 ASN cc_start: 0.9567 (t0) cc_final: 0.9085 (t0) REVERT: J 1254 GLU cc_start: 0.9587 (mt-10) cc_final: 0.9313 (mt-10) REVERT: J 1260 MET cc_start: 0.9467 (tmm) cc_final: 0.9055 (tmm) REVERT: J 1330 ARG cc_start: 0.9577 (ptm-80) cc_final: 0.9340 (ptm-80) REVERT: J 1334 GLU cc_start: 0.9317 (tm-30) cc_final: 0.9007 (tm-30) REVERT: J 1340 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8594 (ttpt) outliers start: 3 outliers final: 2 residues processed: 788 average time/residue: 0.1728 time to fit residues: 208.8393 Evaluate side-chains 665 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 663 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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: 2.9990 chunk 257 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 188 optimal weight: 20.0000 chunk 288 optimal weight: 8.9990 chunk 276 optimal weight: 30.0000 chunk 133 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS I 148 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** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1175 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1237 HIS ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 ASN ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 667 GLN ** J 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN ** J 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 921 GLN J 951 GLN J 954 ASN J1367 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.066126 restraints weight = 92009.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.069068 restraints weight = 57430.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.071275 restraints weight = 40592.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.072951 restraints weight = 31019.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.074236 restraints weight = 25073.853| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 25706 Z= 0.253 Angle : 0.772 11.772 34937 Z= 0.406 Chirality : 0.047 0.312 3992 Planarity : 0.006 0.097 4386 Dihedral : 14.785 64.236 3992 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.36 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -1.65 (0.14), residues: 3071 helix: -0.08 (0.15), residues: 1101 sheet: -1.42 (0.26), residues: 354 loop : -1.76 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 245 TYR 0.033 0.002 TYR I1231 PHE 0.025 0.003 PHE I 38 TRP 0.013 0.002 TRP I 807 HIS 0.008 0.002 HIS I 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.25 (25698) covalent geometry : angle 0.76254 / 0.41 (34925) hydrogen bonds : bond 0.04980 / 3.49 ( 1057) hydrogen bonds : angle 5.89966 / 4.08 ( 2933) metal coordination : bond 0.01376 / 0.62 ( 8) metal coordination : angle 6.43724 / 3.40 ( 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 745 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 745 time to evaluate : 0.914 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 45 ARG cc_start: 0.9184 (mmt180) cc_final: 0.8698 (mmt180) REVERT: G 84 ASN cc_start: 0.8784 (t0) cc_final: 0.8426 (t0) REVERT: G 130 ILE cc_start: 0.9685 (mp) cc_final: 0.9402 (mp) REVERT: G 181 GLU cc_start: 0.9426 (tp30) cc_final: 0.8838 (pm20) REVERT: G 199 ASP cc_start: 0.7686 (m-30) cc_final: 0.7472 (m-30) REVERT: G 227 GLN cc_start: 0.9600 (mm-40) cc_final: 0.9340 (mt0) REVERT: H 16 ILE cc_start: 0.8344 (pt) cc_final: 0.8094 (mp) REVERT: H 46 ILE cc_start: 0.9669 (tp) cc_final: 0.9463 (tp) REVERT: H 68 TYR cc_start: 0.9538 (m-10) cc_final: 0.9233 (m-10) REVERT: H 79 LEU cc_start: 0.9302 (mp) cc_final: 0.8961 (mp) REVERT: H 83 LEU cc_start: 0.9598 (pp) cc_final: 0.9146 (mm) REVERT: H 95 LYS cc_start: 0.9493 (mppt) cc_final: 0.9186 (ptpp) REVERT: H 141 SER cc_start: 0.9676 (t) cc_final: 0.9381 (m) REVERT: H 142 MET cc_start: 0.9597 (ptm) cc_final: 0.9303 (ptm) REVERT: H 185 TYR cc_start: 0.7778 (p90) cc_final: 0.7266 (p90) REVERT: H 200 LYS cc_start: 0.9359 (tmtt) cc_final: 0.9146 (tmtt) REVERT: I 5 TYR cc_start: 0.9063 (t80) cc_final: 0.8779 (t80) REVERT: I 6 THR cc_start: 0.9292 (p) cc_final: 0.8831 (p) REVERT: I 9 LYS cc_start: 0.8909 (mttm) cc_final: 0.8530 (mttm) REVERT: I 32 LEU cc_start: 0.9526 (mt) cc_final: 0.9056 (pp) REVERT: I 124 MET cc_start: 0.9653 (tpp) cc_final: 0.9389 (tpp) REVERT: I 151 ARG cc_start: 0.9365 (mmp80) cc_final: 0.9114 (mmp80) REVERT: I 158 ASP cc_start: 0.9378 (t0) cc_final: 0.8977 (p0) REVERT: I 160 ASP cc_start: 0.8986 (m-30) cc_final: 0.7900 (m-30) REVERT: I 213 LEU cc_start: 0.9417 (mp) cc_final: 0.8753 (mp) REVERT: I 215 TYR cc_start: 0.8732 (m-10) cc_final: 0.8389 (m-80) REVERT: I 291 TYR cc_start: 0.9563 (t80) cc_final: 0.9317 (t80) REVERT: I 342 ASP cc_start: 0.9115 (m-30) cc_final: 0.8750 (m-30) REVERT: I 368 ARG cc_start: 0.9598 (mtm180) cc_final: 0.9288 (mmm-85) REVERT: I 405 PHE cc_start: 0.9664 (t80) cc_final: 0.9336 (t80) REVERT: I 419 ILE cc_start: 0.9324 (pt) cc_final: 0.9075 (pt) REVERT: I 452 ARG cc_start: 0.9519 (tpt-90) cc_final: 0.8838 (tpt90) REVERT: I 461 GLU cc_start: 0.9527 (tp30) cc_final: 0.8844 (tp30) REVERT: I 464 PHE cc_start: 0.9763 (t80) cc_final: 0.9256 (t80) REVERT: I 548 ARG cc_start: 0.9410 (mmt180) cc_final: 0.9055 (mmm160) REVERT: I 606 LEU cc_start: 0.9348 (mp) cc_final: 0.9125 (mp) REVERT: I 633 LEU cc_start: 0.9568 (pt) cc_final: 0.9231 (mm) REVERT: I 642 SER cc_start: 0.8791 (p) cc_final: 0.8469 (t) REVERT: I 668 ILE cc_start: 0.9578 (mm) cc_final: 0.9316 (mm) REVERT: I 671 LEU cc_start: 0.9770 (tp) cc_final: 0.9563 (tp) REVERT: I 672 GLU cc_start: 0.9519 (pm20) cc_final: 0.8889 (pm20) REVERT: I 681 MET cc_start: 0.9306 (mtp) cc_final: 0.8982 (mtt) REVERT: I 685 MET cc_start: 0.9436 (mtp) cc_final: 0.8970 (mtp) REVERT: I 748 ILE cc_start: 0.8871 (pt) cc_final: 0.8545 (pt) REVERT: I 749 ASP cc_start: 0.9184 (t0) cc_final: 0.8867 (p0) REVERT: I 790 ASP cc_start: 0.9489 (t0) cc_final: 0.9008 (p0) REVERT: I 799 ASN cc_start: 0.8622 (t0) cc_final: 0.8347 (m-40) REVERT: I 816 ILE cc_start: 0.9347 (mt) cc_final: 0.8930 (mt) REVERT: I 817 LEU cc_start: 0.8234 (mm) cc_final: 0.7540 (mm) REVERT: I 831 ILE cc_start: 0.9003 (mm) cc_final: 0.8504 (mm) REVERT: I 957 LYS cc_start: 0.9597 (pptt) cc_final: 0.9292 (ptpp) REVERT: I 1056 VAL cc_start: 0.8572 (m) cc_final: 0.8088 (m) REVERT: I 1066 MET cc_start: 0.8919 (pmm) cc_final: 0.8616 (pmm) REVERT: I 1080 ASN cc_start: 0.9074 (m-40) cc_final: 0.8410 (t0) REVERT: I 1106 ARG cc_start: 0.9543 (mmm-85) cc_final: 0.9261 (mmt180) REVERT: I 1107 MET cc_start: 0.9061 (mmm) cc_final: 0.8397 (tpp) REVERT: I 1122 LYS cc_start: 0.9672 (tptm) cc_final: 0.9211 (tppt) REVERT: I 1126 ASP cc_start: 0.9400 (m-30) cc_final: 0.8785 (m-30) REVERT: I 1187 PHE cc_start: 0.9037 (m-10) cc_final: 0.8533 (m-10) REVERT: I 1216 ARG cc_start: 0.9251 (mtp180) cc_final: 0.8879 (mmm-85) REVERT: I 1234 LYS cc_start: 0.9494 (tppp) cc_final: 0.9062 (tppp) REVERT: I 1237 HIS cc_start: 0.8714 (m90) cc_final: 0.8448 (m90) REVERT: I 1264 GLN cc_start: 0.9425 (tp-100) cc_final: 0.9052 (tm-30) REVERT: I 1270 PHE cc_start: 0.8854 (t80) cc_final: 0.8220 (t80) REVERT: I 1290 MET cc_start: 0.9491 (tmm) cc_final: 0.9066 (tmm) REVERT: I 1304 MET cc_start: 0.9678 (tmm) cc_final: 0.9297 (ptp) REVERT: I 1319 MET cc_start: 0.8030 (tpt) cc_final: 0.7097 (tpt) REVERT: I 1321 GLU cc_start: 0.9035 (pm20) cc_final: 0.8761 (pm20) REVERT: I 1329 GLU cc_start: 0.9898 (mt-10) cc_final: 0.9503 (mt-10) REVERT: J 33 TRP cc_start: 0.9007 (m100) cc_final: 0.8761 (m100) REVERT: J 61 ILE cc_start: 0.8901 (tp) cc_final: 0.8690 (pt) REVERT: J 102 MET cc_start: 0.7009 (tpt) cc_final: 0.4534 (ttt) REVERT: J 207 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9154 (mm-30) REVERT: J 222 LYS cc_start: 0.9414 (pttm) cc_final: 0.9107 (pttt) REVERT: J 327 LEU cc_start: 0.9785 (mp) cc_final: 0.9529 (mp) REVERT: J 330 MET cc_start: 0.9386 (mpp) cc_final: 0.9036 (ppp) REVERT: J 331 ILE cc_start: 0.9022 (pt) cc_final: 0.8552 (pt) REVERT: J 361 LEU cc_start: 0.9241 (mt) cc_final: 0.8770 (pp) REVERT: J 372 MET cc_start: 0.9476 (mpp) cc_final: 0.9156 (ptp) REVERT: J 409 TRP cc_start: 0.8987 (m100) cc_final: 0.8232 (m100) REVERT: J 423 LEU cc_start: 0.9882 (mp) cc_final: 0.9632 (mp) REVERT: J 434 ILE cc_start: 0.9536 (tp) cc_final: 0.9282 (tp) REVERT: J 437 PHE cc_start: 0.9611 (m-80) cc_final: 0.8650 (m-80) REVERT: J 454 CYS cc_start: 0.9316 (m) cc_final: 0.9055 (m) REVERT: J 478 LEU cc_start: 0.9669 (tt) cc_final: 0.9434 (mt) REVERT: J 499 ILE cc_start: 0.9446 (tp) cc_final: 0.9239 (mm) REVERT: J 526 VAL cc_start: 0.8948 (p) cc_final: 0.8717 (p) REVERT: J 544 LEU cc_start: 0.9491 (tp) cc_final: 0.9281 (tp) REVERT: J 603 LYS cc_start: 0.9359 (pttt) cc_final: 0.9094 (ptpp) REVERT: J 627 THR cc_start: 0.9867 (t) cc_final: 0.9442 (t) REVERT: J 645 VAL cc_start: 0.8556 (p) cc_final: 0.8241 (m) REVERT: J 697 MET cc_start: 0.9686 (ppp) cc_final: 0.9422 (ppp) REVERT: J 743 MET cc_start: 0.9276 (ptm) cc_final: 0.9042 (ptm) REVERT: J 763 PHE cc_start: 0.9360 (m-80) cc_final: 0.8164 (m-80) REVERT: J 764 ARG cc_start: 0.9133 (ttt-90) cc_final: 0.8897 (ttt-90) REVERT: J 792 ASN cc_start: 0.9382 (m110) cc_final: 0.9162 (m-40) REVERT: J 822 MET cc_start: 0.8608 (mmm) cc_final: 0.8283 (tpt) REVERT: J 823 THR cc_start: 0.9603 (p) cc_final: 0.9400 (p) REVERT: J 870 ASP cc_start: 0.8918 (m-30) cc_final: 0.8678 (m-30) REVERT: J 1040 MET cc_start: 0.7794 (mmp) cc_final: 0.7050 (mmm) REVERT: J 1194 ARG cc_start: 0.8316 (mtt180) cc_final: 0.8049 (mtt180) REVERT: J 1199 PHE cc_start: 0.9590 (m-80) cc_final: 0.9390 (m-80) REVERT: J 1215 GLU cc_start: 0.9534 (mp0) cc_final: 0.9237 (mm-30) REVERT: J 1231 ARG cc_start: 0.9644 (mtp85) cc_final: 0.9361 (tpt170) REVERT: J 1235 ASN cc_start: 0.9805 (m110) cc_final: 0.9590 (m-40) REVERT: J 1254 GLU cc_start: 0.9574 (mt-10) cc_final: 0.9336 (mt-10) REVERT: J 1330 ARG cc_start: 0.9596 (ptm-80) cc_final: 0.9264 (ptm-80) REVERT: J 1334 GLU cc_start: 0.9349 (tm-30) cc_final: 0.8943 (tm-30) outliers start: 0 outliers final: 0 residues processed: 745 average time/residue: 0.1718 time to fit residues: 198.7505 Evaluate side-chains 634 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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: 0.0980 chunk 108 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 232 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 37 HIS I 148 GLN ** I 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 573 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1175 ASN I1236 ASN ** I1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 667 GLN ** J 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN J 910 ASN J 921 GLN J 954 ASN ** J1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1367 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.069985 restraints weight = 87926.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.073167 restraints weight = 54368.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.075513 restraints weight = 38149.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.077331 restraints weight = 29036.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.078698 restraints weight = 23377.759| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 25706 Z= 0.155 Angle : 0.755 11.085 34937 Z= 0.389 Chirality : 0.048 0.290 3992 Planarity : 0.006 0.076 4386 Dihedral : 14.714 63.717 3992 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -1.51 (0.14), residues: 3071 helix: 0.06 (0.15), residues: 1082 sheet: -1.23 (0.27), residues: 347 loop : -1.72 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG J1284 TYR 0.062 0.002 TYR I 756 PHE 0.061 0.003 PHE J1274 TRP 0.022 0.002 TRP I 807 HIS 0.006 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (25698) covalent geometry : angle 0.74816 / 0.39 (34925) hydrogen bonds : bond 0.04590 / 3.21 ( 1057) hydrogen bonds : angle 5.67965 / 3.94 ( 2933) metal coordination : bond 0.00815 / 0.34 ( 8) metal coordination : angle 5.41469 / 2.83 ( 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 764 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 764 time to evaluate : 0.787 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: G 45 ARG cc_start: 0.9118 (mmt180) cc_final: 0.8519 (mmt180) REVERT: G 84 ASN cc_start: 0.8700 (t0) cc_final: 0.8346 (t0) REVERT: G 104 LYS cc_start: 0.8269 (tptp) cc_final: 0.7947 (tmtt) REVERT: G 130 ILE cc_start: 0.9555 (mp) cc_final: 0.9250 (mp) REVERT: G 181 GLU cc_start: 0.9251 (tp30) cc_final: 0.8408 (pm20) REVERT: G 227 GLN cc_start: 0.9594 (mm-40) cc_final: 0.9294 (mt0) REVERT: H 16 ILE cc_start: 0.8375 (pt) cc_final: 0.8030 (mp) REVERT: H 46 ILE cc_start: 0.9627 (tp) cc_final: 0.9412 (tp) REVERT: H 68 TYR cc_start: 0.9523 (m-10) cc_final: 0.9271 (m-10) REVERT: H 79 LEU cc_start: 0.9250 (mp) cc_final: 0.8967 (mp) REVERT: H 83 LEU cc_start: 0.9552 (pp) cc_final: 0.9113 (mm) REVERT: H 95 LYS cc_start: 0.9473 (mppt) cc_final: 0.9250 (pttm) REVERT: H 141 SER cc_start: 0.9645 (t) cc_final: 0.9311 (m) REVERT: H 142 MET cc_start: 0.9567 (ptm) cc_final: 0.9206 (ptm) REVERT: H 193 GLU cc_start: 0.8491 (tp30) cc_final: 0.8071 (tp30) REVERT: I 5 TYR cc_start: 0.8982 (t80) cc_final: 0.8709 (t80) REVERT: I 9 LYS cc_start: 0.8932 (mttm) cc_final: 0.8581 (mttm) REVERT: I 32 LEU cc_start: 0.9482 (mt) cc_final: 0.9020 (pp) REVERT: I 39 ILE cc_start: 0.9365 (pt) cc_final: 0.8888 (pt) REVERT: I 124 MET cc_start: 0.9603 (tpp) cc_final: 0.9378 (tpp) REVERT: I 151 ARG cc_start: 0.9380 (mmp80) cc_final: 0.9116 (mmp80) REVERT: I 160 ASP cc_start: 0.8994 (m-30) cc_final: 0.8763 (m-30) REVERT: I 173 ASN cc_start: 0.8826 (t0) cc_final: 0.8497 (t0) REVERT: I 213 LEU cc_start: 0.9343 (mp) cc_final: 0.8657 (mp) REVERT: I 215 TYR cc_start: 0.8622 (m-10) cc_final: 0.8297 (m-80) REVERT: I 240 GLU cc_start: 0.9055 (tp30) cc_final: 0.8294 (mp0) REVERT: I 241 LEU cc_start: 0.9573 (tp) cc_final: 0.9257 (tp) REVERT: I 277 LEU cc_start: 0.9653 (mt) cc_final: 0.9164 (pp) REVERT: I 291 TYR cc_start: 0.9552 (t80) cc_final: 0.9286 (t80) REVERT: I 342 ASP cc_start: 0.9053 (m-30) cc_final: 0.8655 (m-30) REVERT: I 405 PHE cc_start: 0.9596 (t80) cc_final: 0.9173 (t80) REVERT: I 452 ARG cc_start: 0.9442 (tpt-90) cc_final: 0.8873 (tpt90) REVERT: I 461 GLU cc_start: 0.9582 (tp30) cc_final: 0.8984 (tp30) REVERT: I 464 PHE cc_start: 0.9789 (t80) cc_final: 0.9532 (t80) REVERT: I 503 LYS cc_start: 0.9349 (pttm) cc_final: 0.9122 (pttm) REVERT: I 591 TYR cc_start: 0.9435 (m-80) cc_final: 0.8817 (m-80) REVERT: I 606 LEU cc_start: 0.9308 (mp) cc_final: 0.8718 (mp) REVERT: I 633 LEU cc_start: 0.9582 (pt) cc_final: 0.9276 (mm) REVERT: I 642 SER cc_start: 0.8846 (p) cc_final: 0.8562 (t) REVERT: I 668 ILE cc_start: 0.9551 (mm) cc_final: 0.9276 (mm) REVERT: I 671 LEU cc_start: 0.9756 (tp) cc_final: 0.9477 (tp) REVERT: I 672 GLU cc_start: 0.9488 (pm20) cc_final: 0.8958 (pm20) REVERT: I 681 MET cc_start: 0.9322 (mtp) cc_final: 0.9000 (mtt) REVERT: I 685 MET cc_start: 0.9394 (mtp) cc_final: 0.8965 (mtp) REVERT: I 697 LYS cc_start: 0.8394 (mmmt) cc_final: 0.7397 (mmtt) REVERT: I 706 ARG cc_start: 0.9439 (ttp80) cc_final: 0.9115 (ttp80) REVERT: I 748 ILE cc_start: 0.8725 (pt) cc_final: 0.8387 (pt) REVERT: I 749 ASP cc_start: 0.9107 (t0) cc_final: 0.8836 (p0) REVERT: I 790 ASP cc_start: 0.9462 (t0) cc_final: 0.9130 (p0) REVERT: I 805 MET cc_start: 0.9336 (ppp) cc_final: 0.9050 (ppp) REVERT: I 812 PHE cc_start: 0.8708 (t80) cc_final: 0.8422 (t80) REVERT: I 817 LEU cc_start: 0.8488 (mm) cc_final: 0.7902 (mm) REVERT: I 831 ILE cc_start: 0.8853 (mm) cc_final: 0.8444 (mm) REVERT: I 930 ASP cc_start: 0.9752 (t70) cc_final: 0.9190 (t0) REVERT: I 950 GLU cc_start: 0.9730 (tm-30) cc_final: 0.9476 (mt-10) REVERT: I 1053 TYR cc_start: 0.8263 (m-80) cc_final: 0.8017 (m-80) REVERT: I 1056 VAL cc_start: 0.8679 (m) cc_final: 0.8407 (m) REVERT: I 1080 ASN cc_start: 0.8970 (m-40) cc_final: 0.8290 (t0) REVERT: I 1106 ARG cc_start: 0.9495 (mmm-85) cc_final: 0.9215 (mmt180) REVERT: I 1107 MET cc_start: 0.9058 (mmm) cc_final: 0.8236 (tpp) REVERT: I 1122 LYS cc_start: 0.9624 (tptm) cc_final: 0.9139 (tppt) REVERT: I 1126 ASP cc_start: 0.9340 (m-30) cc_final: 0.8720 (m-30) REVERT: I 1187 PHE cc_start: 0.8885 (m-10) cc_final: 0.8610 (m-10) REVERT: I 1216 ARG cc_start: 0.9196 (mtp180) cc_final: 0.8812 (mmm-85) REVERT: I 1230 MET cc_start: 0.8987 (tpt) cc_final: 0.8596 (tpt) REVERT: I 1234 LYS cc_start: 0.9456 (tppp) cc_final: 0.8968 (tppp) REVERT: I 1237 HIS cc_start: 0.8525 (m90) cc_final: 0.8302 (m90) REVERT: I 1265 PHE cc_start: 0.9175 (t80) cc_final: 0.8857 (t80) REVERT: I 1270 PHE cc_start: 0.9014 (t80) cc_final: 0.8376 (t80) REVERT: I 1290 MET cc_start: 0.9419 (tmm) cc_final: 0.9004 (tmm) REVERT: I 1304 MET cc_start: 0.9675 (tmm) cc_final: 0.9300 (ptp) REVERT: I 1319 MET cc_start: 0.8082 (tpt) cc_final: 0.7231 (tpt) REVERT: I 1321 GLU cc_start: 0.8937 (pm20) cc_final: 0.8731 (pm20) REVERT: I 1329 GLU cc_start: 0.9900 (mt-10) cc_final: 0.9593 (mt-10) REVERT: J 33 TRP cc_start: 0.8969 (m100) cc_final: 0.8748 (m100) REVERT: J 91 GLU cc_start: 0.8721 (pp20) cc_final: 0.8477 (tp30) REVERT: J 102 MET cc_start: 0.7303 (tpt) cc_final: 0.5195 (ttt) REVERT: J 140 TYR cc_start: 0.9725 (m-80) cc_final: 0.9474 (m-80) REVERT: J 207 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9193 (mm-30) REVERT: J 361 LEU cc_start: 0.9143 (mt) cc_final: 0.8675 (pp) REVERT: J 365 GLN cc_start: 0.9658 (pt0) cc_final: 0.9357 (pt0) REVERT: J 405 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8618 (mt-10) REVERT: J 409 TRP cc_start: 0.8967 (m100) cc_final: 0.8252 (m100) REVERT: J 437 PHE cc_start: 0.9582 (m-80) cc_final: 0.8949 (m-80) REVERT: J 454 CYS cc_start: 0.9334 (m) cc_final: 0.8996 (m) REVERT: J 484 MET cc_start: 0.8871 (mpp) cc_final: 0.8649 (mpp) REVERT: J 512 TYR cc_start: 0.9360 (t80) cc_final: 0.9084 (t80) REVERT: J 526 VAL cc_start: 0.8982 (p) cc_final: 0.8611 (p) REVERT: J 544 LEU cc_start: 0.9359 (tp) cc_final: 0.9018 (tp) REVERT: J 594 GLN cc_start: 0.9266 (tm-30) cc_final: 0.8919 (tm-30) REVERT: J 603 LYS cc_start: 0.9350 (pttt) cc_final: 0.9086 (ptpp) REVERT: J 631 TYR cc_start: 0.9562 (m-80) cc_final: 0.9322 (m-80) REVERT: J 634 ARG cc_start: 0.9519 (ptp90) cc_final: 0.9271 (ptp-170) REVERT: J 645 VAL cc_start: 0.8582 (p) cc_final: 0.8180 (m) REVERT: J 697 MET cc_start: 0.9679 (ppp) cc_final: 0.9422 (ppp) REVERT: J 727 ASP cc_start: 0.9167 (t70) cc_final: 0.8877 (m-30) REVERT: J 743 MET cc_start: 0.9062 (ptm) cc_final: 0.8762 (ptm) REVERT: J 763 PHE cc_start: 0.9318 (m-80) cc_final: 0.7882 (m-80) REVERT: J 764 ARG cc_start: 0.9050 (ttt-90) cc_final: 0.8749 (ttt-90) REVERT: J 870 ASP cc_start: 0.8909 (m-30) cc_final: 0.8689 (m-30) REVERT: J 1040 MET cc_start: 0.7767 (mmp) cc_final: 0.7069 (mmm) REVERT: J 1194 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7938 (mtt180) REVERT: J 1231 ARG cc_start: 0.9635 (mtp85) cc_final: 0.9372 (tpt170) REVERT: J 1238 GLN cc_start: 0.9195 (pp30) cc_final: 0.8748 (pp30) REVERT: J 1239 ASP cc_start: 0.9427 (t0) cc_final: 0.9119 (t0) REVERT: J 1242 ARG cc_start: 0.9219 (pmt-80) cc_final: 0.8928 (pmt-80) REVERT: J 1249 ASN cc_start: 0.9346 (t0) cc_final: 0.9042 (t0) REVERT: J 1252 HIS cc_start: 0.9252 (m90) cc_final: 0.9001 (m90) REVERT: J 1254 GLU cc_start: 0.9549 (mt-10) cc_final: 0.9301 (mt-10) REVERT: J 1260 MET cc_start: 0.9479 (tmm) cc_final: 0.9162 (tmm) REVERT: J 1330 ARG cc_start: 0.9549 (ptm-80) cc_final: 0.9218 (ptm-80) REVERT: J 1334 GLU cc_start: 0.9315 (tm-30) cc_final: 0.8928 (tm-30) REVERT: J 1340 LYS cc_start: 0.8902 (ttpp) cc_final: 0.8670 (ttpt) REVERT: J 1373 ARG cc_start: 0.6131 (ptm160) cc_final: 0.5858 (ptm160) outliers start: 0 outliers final: 0 residues processed: 764 average time/residue: 0.1675 time to fit residues: 197.8081 Evaluate side-chains 660 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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: 7.9990 chunk 40 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 310 optimal weight: 50.0000 chunk 251 optimal weight: 8.9990 chunk 268 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS 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** I1175 ASN ** I1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** 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 954 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.105949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.067905 restraints weight = 91362.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.070936 restraints weight = 56777.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.073239 restraints weight = 39994.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074949 restraints weight = 30452.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.076218 restraints weight = 24599.657| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4819 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= 0.189 Angle : 0.744 10.697 34937 Z= 0.388 Chirality : 0.047 0.370 3992 Planarity : 0.006 0.072 4386 Dihedral : 14.693 63.604 3992 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.13 % Favored : 92.84 % 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: -1.57 (0.14), residues: 3071 helix: 0.05 (0.15), residues: 1097 sheet: -1.47 (0.25), residues: 372 loop : -1.73 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 346 TYR 0.047 0.002 TYR I 756 PHE 0.034 0.002 PHE J1274 TRP 0.021 0.002 TRP I 807 HIS 0.010 0.001 HIS J 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (25698) covalent geometry : angle 0.73870 / 0.39 (34925) hydrogen bonds : bond 0.04665 / 3.26 ( 1057) hydrogen bonds : angle 5.74572 / 3.96 ( 2933) metal coordination : bond 0.00968 / 0.43 ( 8) metal coordination : angle 4.87766 / 2.59 ( 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 739 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 739 time to evaluate : 0.717 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 45 ARG cc_start: 0.9239 (mmt180) cc_final: 0.8715 (mmt180) REVERT: G 84 ASN cc_start: 0.8798 (t0) cc_final: 0.8488 (t0) REVERT: G 104 LYS cc_start: 0.8277 (tptp) cc_final: 0.7841 (tmtt) REVERT: G 130 ILE cc_start: 0.9640 (mp) cc_final: 0.9325 (mp) REVERT: G 133 LEU cc_start: 0.9335 (mm) cc_final: 0.9099 (mm) REVERT: G 181 GLU cc_start: 0.9215 (tp30) cc_final: 0.8571 (pm20) REVERT: G 205 MET cc_start: 0.9570 (ppp) cc_final: 0.9076 (ppp) REVERT: G 208 ASN cc_start: 0.9450 (p0) cc_final: 0.9193 (p0) REVERT: G 227 GLN cc_start: 0.9612 (mm-40) cc_final: 0.9340 (mt0) REVERT: H 16 ILE cc_start: 0.8384 (pt) cc_final: 0.8030 (mp) REVERT: H 46 ILE cc_start: 0.9645 (tp) cc_final: 0.9430 (tp) REVERT: H 68 TYR cc_start: 0.9539 (m-10) cc_final: 0.9240 (m-10) REVERT: H 79 LEU cc_start: 0.9275 (mp) cc_final: 0.8975 (mp) REVERT: H 83 LEU cc_start: 0.9567 (pp) cc_final: 0.9128 (mm) REVERT: H 95 LYS cc_start: 0.9488 (mppt) cc_final: 0.9285 (pttm) REVERT: H 102 LEU cc_start: 0.9334 (tp) cc_final: 0.9025 (tt) REVERT: H 133 LEU cc_start: 0.8988 (tp) cc_final: 0.8746 (tp) REVERT: H 141 SER cc_start: 0.9650 (t) cc_final: 0.9387 (m) REVERT: H 193 GLU cc_start: 0.8536 (tp30) cc_final: 0.8202 (tp30) REVERT: I 5 TYR cc_start: 0.9015 (t80) cc_final: 0.8683 (t80) REVERT: I 6 THR cc_start: 0.9230 (p) cc_final: 0.8741 (p) REVERT: I 9 LYS cc_start: 0.8952 (mttm) cc_final: 0.8549 (mttm) REVERT: I 32 LEU cc_start: 0.9486 (mt) cc_final: 0.8955 (pp) REVERT: I 80 PHE cc_start: 0.9198 (m-80) cc_final: 0.8708 (m-10) REVERT: I 124 MET cc_start: 0.9698 (tpp) cc_final: 0.9497 (tpp) REVERT: I 151 ARG cc_start: 0.9417 (mmp80) cc_final: 0.9167 (mmp80) REVERT: I 160 ASP cc_start: 0.8988 (m-30) cc_final: 0.8788 (m-30) REVERT: I 213 LEU cc_start: 0.9379 (mp) cc_final: 0.8734 (mp) REVERT: I 215 TYR cc_start: 0.8728 (m-10) cc_final: 0.8375 (m-80) REVERT: I 235 ASN cc_start: 0.9381 (t0) cc_final: 0.9039 (p0) REVERT: I 277 LEU cc_start: 0.9662 (mt) cc_final: 0.9180 (pp) REVERT: I 291 TYR cc_start: 0.9542 (t80) cc_final: 0.9270 (t80) REVERT: I 342 ASP cc_start: 0.9101 (m-30) cc_final: 0.8734 (m-30) REVERT: I 405 PHE cc_start: 0.9624 (t80) cc_final: 0.9251 (t80) REVERT: I 452 ARG cc_start: 0.9519 (tpt-90) cc_final: 0.8886 (tpt90) REVERT: I 461 GLU cc_start: 0.9550 (tp30) cc_final: 0.8878 (tp30) REVERT: I 464 PHE cc_start: 0.9774 (t80) cc_final: 0.9299 (t80) REVERT: I 548 ARG cc_start: 0.9351 (mmt180) cc_final: 0.9101 (mmm160) REVERT: I 591 TYR cc_start: 0.9520 (m-80) cc_final: 0.8888 (m-80) REVERT: I 606 LEU cc_start: 0.9302 (mp) cc_final: 0.8656 (mp) REVERT: I 633 LEU cc_start: 0.9573 (pt) cc_final: 0.9267 (mm) REVERT: I 668 ILE cc_start: 0.9537 (mm) cc_final: 0.9256 (mm) REVERT: I 671 LEU cc_start: 0.9762 (tp) cc_final: 0.9538 (tp) REVERT: I 672 GLU cc_start: 0.9548 (pm20) cc_final: 0.8964 (pm20) REVERT: I 681 MET cc_start: 0.9288 (mtp) cc_final: 0.8965 (mtt) REVERT: I 685 MET cc_start: 0.9438 (mtp) cc_final: 0.9054 (mtp) REVERT: I 805 MET cc_start: 0.9314 (ppp) cc_final: 0.9018 (ppp) REVERT: I 812 PHE cc_start: 0.8844 (t80) cc_final: 0.8615 (t80) REVERT: I 816 ILE cc_start: 0.9420 (mt) cc_final: 0.8984 (mt) REVERT: I 817 LEU cc_start: 0.8407 (mm) cc_final: 0.7810 (mm) REVERT: I 831 ILE cc_start: 0.8966 (mm) cc_final: 0.8472 (mm) REVERT: I 957 LYS cc_start: 0.9588 (pptt) cc_final: 0.9291 (ptpp) REVERT: I 1056 VAL cc_start: 0.8768 (m) cc_final: 0.8465 (m) REVERT: I 1066 MET cc_start: 0.8854 (pmm) cc_final: 0.8553 (pmm) REVERT: I 1080 ASN cc_start: 0.9017 (m-40) cc_final: 0.8329 (t0) REVERT: I 1106 ARG cc_start: 0.9522 (mmm-85) cc_final: 0.9221 (mmt180) REVERT: I 1107 MET cc_start: 0.9027 (mmm) cc_final: 0.7849 (tmm) REVERT: I 1122 LYS cc_start: 0.9639 (tptm) cc_final: 0.9150 (tppt) REVERT: I 1126 ASP cc_start: 0.9355 (m-30) cc_final: 0.8736 (m-30) REVERT: I 1187 PHE cc_start: 0.8969 (m-10) cc_final: 0.8456 (m-10) REVERT: I 1216 ARG cc_start: 0.9234 (mtp180) cc_final: 0.8791 (mmm-85) REVERT: I 1234 LYS cc_start: 0.9451 (tppp) cc_final: 0.9038 (tppp) REVERT: I 1237 HIS cc_start: 0.8516 (m90) cc_final: 0.8283 (m90) REVERT: I 1265 PHE cc_start: 0.9177 (t80) cc_final: 0.8882 (t80) REVERT: I 1270 PHE cc_start: 0.9008 (t80) cc_final: 0.8223 (t80) REVERT: I 1290 MET cc_start: 0.9442 (tmm) cc_final: 0.9079 (tmm) REVERT: I 1304 MET cc_start: 0.9671 (tmm) cc_final: 0.9289 (ptp) REVERT: I 1319 MET cc_start: 0.7757 (tpt) cc_final: 0.6934 (tpt) REVERT: I 1321 GLU cc_start: 0.8898 (pm20) cc_final: 0.8683 (pm20) REVERT: I 1329 GLU cc_start: 0.9898 (mt-10) cc_final: 0.9499 (mt-10) REVERT: J 24 LEU cc_start: 0.8430 (tt) cc_final: 0.7990 (tt) REVERT: J 33 TRP cc_start: 0.9007 (m100) cc_final: 0.8787 (m100) REVERT: J 38 VAL cc_start: 0.8690 (t) cc_final: 0.8465 (t) REVERT: J 91 GLU cc_start: 0.8746 (pp20) cc_final: 0.8509 (tp30) REVERT: J 102 MET cc_start: 0.7482 (tpt) cc_final: 0.5083 (ttt) REVERT: J 140 TYR cc_start: 0.9737 (m-80) cc_final: 0.9484 (m-80) REVERT: J 207 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9164 (mm-30) REVERT: J 237 MET cc_start: 0.9413 (mpp) cc_final: 0.9104 (mpp) REVERT: J 327 LEU cc_start: 0.9803 (mp) cc_final: 0.9536 (mp) REVERT: J 330 MET cc_start: 0.9391 (mpp) cc_final: 0.9084 (ppp) REVERT: J 331 ILE cc_start: 0.9008 (pt) cc_final: 0.8618 (pt) REVERT: J 332 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8633 (mmmt) REVERT: J 361 LEU cc_start: 0.9232 (mt) cc_final: 0.8771 (pp) REVERT: J 365 GLN cc_start: 0.9601 (pt0) cc_final: 0.9377 (pt0) REVERT: J 372 MET cc_start: 0.9508 (mpp) cc_final: 0.9081 (ptp) REVERT: J 405 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8618 (mt-10) REVERT: J 409 TRP cc_start: 0.8970 (m100) cc_final: 0.8251 (m100) REVERT: J 437 PHE cc_start: 0.9585 (m-80) cc_final: 0.8987 (m-80) REVERT: J 454 CYS cc_start: 0.9311 (m) cc_final: 0.8963 (m) REVERT: J 499 ILE cc_start: 0.9411 (tp) cc_final: 0.9200 (mm) REVERT: J 512 TYR cc_start: 0.9385 (t80) cc_final: 0.8934 (t80) REVERT: J 513 MET cc_start: 0.9371 (mmp) cc_final: 0.9136 (mmp) REVERT: J 544 LEU cc_start: 0.9444 (tp) cc_final: 0.8918 (tp) REVERT: J 594 GLN cc_start: 0.9342 (tm-30) cc_final: 0.9008 (tm-30) REVERT: J 603 LYS cc_start: 0.9349 (pttt) cc_final: 0.9090 (ptpp) REVERT: J 631 TYR cc_start: 0.9560 (m-80) cc_final: 0.9296 (m-80) REVERT: J 645 VAL cc_start: 0.8566 (p) cc_final: 0.8197 (m) REVERT: J 697 MET cc_start: 0.9678 (ppp) cc_final: 0.9409 (ppp) REVERT: J 739 GLN cc_start: 0.9059 (mt0) cc_final: 0.8823 (mt0) REVERT: J 743 MET cc_start: 0.9088 (ptm) cc_final: 0.8764 (ptm) REVERT: J 763 PHE cc_start: 0.9390 (m-80) cc_final: 0.8954 (m-80) REVERT: J 764 ARG cc_start: 0.9081 (ttt-90) cc_final: 0.8814 (ttt-90) REVERT: J 792 ASN cc_start: 0.9345 (m110) cc_final: 0.9118 (m110) REVERT: J 822 MET cc_start: 0.8653 (tpt) cc_final: 0.8452 (tpp) REVERT: J 1040 MET cc_start: 0.7804 (mmp) cc_final: 0.7107 (mmm) REVERT: J 1194 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7926 (mtt180) REVERT: J 1199 PHE cc_start: 0.9596 (m-80) cc_final: 0.9379 (m-80) REVERT: J 1231 ARG cc_start: 0.9677 (mtp85) cc_final: 0.9301 (tpt-90) REVERT: J 1238 GLN cc_start: 0.9106 (pp30) cc_final: 0.8808 (pp30) REVERT: J 1239 ASP cc_start: 0.9457 (t0) cc_final: 0.9193 (t0) REVERT: J 1242 ARG cc_start: 0.9259 (pmt-80) cc_final: 0.8939 (pmt-80) REVERT: J 1254 GLU cc_start: 0.9542 (mt-10) cc_final: 0.9301 (mt-10) REVERT: J 1260 MET cc_start: 0.9506 (tmm) cc_final: 0.9152 (tmm) REVERT: J 1307 LEU cc_start: 0.8922 (mm) cc_final: 0.8686 (mm) REVERT: J 1328 THR cc_start: 0.8861 (m) cc_final: 0.8624 (m) REVERT: J 1330 ARG cc_start: 0.9545 (ptm-80) cc_final: 0.9191 (ptm-80) REVERT: J 1334 GLU cc_start: 0.9375 (tm-30) cc_final: 0.8978 (tm-30) REVERT: J 1373 ARG cc_start: 0.6196 (ptm160) cc_final: 0.5910 (ptm160) outliers start: 0 outliers final: 0 residues processed: 739 average time/residue: 0.1620 time to fit residues: 186.9076 Evaluate side-chains 650 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 650 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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: 20.0000 chunk 109 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 chunk 296 optimal weight: 9.9990 chunk 4 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 37 HIS I 148 GLN ** I 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 526 HIS ** 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** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN J 365 GLN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 700 ASN J 921 GLN J 954 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.105641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067356 restraints weight = 90156.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070372 restraints weight = 55662.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072672 restraints weight = 39259.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074454 restraints weight = 29889.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.075757 restraints weight = 24100.304| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 25706 Z= 0.175 Angle : 0.756 12.109 34937 Z= 0.397 Chirality : 0.048 0.321 3992 Planarity : 0.006 0.083 4386 Dihedral : 14.705 63.920 3992 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.97 % Rotamer: Outliers : 0.04 % Allowed : 0.53 % Favored : 99.43 % 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: -1.62 (0.14), residues: 3071 helix: -0.03 (0.15), residues: 1094 sheet: -1.47 (0.26), residues: 369 loop : -1.74 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG I 368 TYR 0.040 0.002 TYR I 756 PHE 0.029 0.003 PHE J1274 TRP 0.021 0.002 TRP I 807 HIS 0.011 0.001 HIS J 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (25698) covalent geometry : angle 0.75151 / 0.40 (34925) hydrogen bonds : bond 0.04763 / 3.27 ( 1057) hydrogen bonds : angle 5.79372 / 4.01 ( 2933) metal coordination : bond 0.00870 / 0.39 ( 8) metal coordination : angle 4.63897 / 2.43 ( 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 735 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 734 time to evaluate : 0.939 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: G 44 ARG cc_start: 0.9426 (ttt-90) cc_final: 0.9087 (ttt90) REVERT: G 84 ASN cc_start: 0.8788 (t0) cc_final: 0.8473 (t0) REVERT: G 104 LYS cc_start: 0.8290 (tptp) cc_final: 0.7869 (tmtt) REVERT: G 130 ILE cc_start: 0.9633 (mp) cc_final: 0.9315 (mp) REVERT: G 133 LEU cc_start: 0.9337 (mm) cc_final: 0.9105 (mm) REVERT: G 199 ASP cc_start: 0.7726 (m-30) cc_final: 0.7305 (m-30) REVERT: G 205 MET cc_start: 0.9562 (ppp) cc_final: 0.9186 (ppp) REVERT: G 227 GLN cc_start: 0.9607 (mm-40) cc_final: 0.9318 (mt0) REVERT: H 16 ILE cc_start: 0.8364 (pt) cc_final: 0.8000 (mp) REVERT: H 35 PHE cc_start: 0.9106 (m-80) cc_final: 0.8881 (m-80) REVERT: H 37 HIS cc_start: 0.9645 (m-70) cc_final: 0.9393 (m90) REVERT: H 46 ILE cc_start: 0.9645 (tp) cc_final: 0.9411 (tp) REVERT: H 68 TYR cc_start: 0.9541 (m-10) cc_final: 0.9238 (m-10) REVERT: H 79 LEU cc_start: 0.9293 (mp) cc_final: 0.9001 (mp) REVERT: H 83 LEU cc_start: 0.9556 (pp) cc_final: 0.9118 (mm) REVERT: H 95 LYS cc_start: 0.9500 (mppt) cc_final: 0.9250 (ptpp) REVERT: H 102 LEU cc_start: 0.9371 (tp) cc_final: 0.8971 (tt) REVERT: H 193 GLU cc_start: 0.8557 (tp30) cc_final: 0.8168 (tp30) REVERT: I 5 TYR cc_start: 0.8977 (t80) cc_final: 0.8619 (t80) REVERT: I 6 THR cc_start: 0.9233 (p) cc_final: 0.8741 (p) REVERT: I 9 LYS cc_start: 0.8939 (mttm) cc_final: 0.8531 (mttm) REVERT: I 32 LEU cc_start: 0.9478 (mt) cc_final: 0.8959 (pp) REVERT: I 39 ILE cc_start: 0.9353 (pt) cc_final: 0.8916 (pt) REVERT: I 80 PHE cc_start: 0.9180 (m-80) cc_final: 0.8668 (m-10) REVERT: I 124 MET cc_start: 0.9682 (tpp) cc_final: 0.9476 (tpp) REVERT: I 151 ARG cc_start: 0.9413 (mmp80) cc_final: 0.9173 (mmp80) REVERT: I 213 LEU cc_start: 0.9401 (mp) cc_final: 0.8773 (mp) REVERT: I 215 TYR cc_start: 0.8721 (m-10) cc_final: 0.8433 (m-80) REVERT: I 235 ASN cc_start: 0.9366 (t0) cc_final: 0.9033 (p0) REVERT: I 240 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8588 (tp30) REVERT: I 277 LEU cc_start: 0.9653 (mt) cc_final: 0.9169 (pp) REVERT: I 291 TYR cc_start: 0.9501 (t80) cc_final: 0.9247 (t80) REVERT: I 342 ASP cc_start: 0.9059 (m-30) cc_final: 0.8713 (m-30) REVERT: I 405 PHE cc_start: 0.9608 (t80) cc_final: 0.9218 (t80) REVERT: I 430 LYS cc_start: 0.9354 (mptt) cc_final: 0.9147 (mmmt) REVERT: I 452 ARG cc_start: 0.9524 (tpt-90) cc_final: 0.8895 (tpt90) REVERT: I 461 GLU cc_start: 0.9579 (tp30) cc_final: 0.8955 (tp30) REVERT: I 464 PHE cc_start: 0.9774 (t80) cc_final: 0.9292 (t80) REVERT: I 548 ARG cc_start: 0.9350 (mmt180) cc_final: 0.9087 (mmm160) REVERT: I 591 TYR cc_start: 0.9512 (m-80) cc_final: 0.8872 (m-80) REVERT: I 606 LEU cc_start: 0.9285 (mp) cc_final: 0.8663 (mp) REVERT: I 668 ILE cc_start: 0.9560 (mm) cc_final: 0.9281 (mm) REVERT: I 671 LEU cc_start: 0.9760 (tp) cc_final: 0.9508 (tp) REVERT: I 672 GLU cc_start: 0.9534 (pm20) cc_final: 0.9059 (pm20) REVERT: I 681 MET cc_start: 0.9278 (mtp) cc_final: 0.8953 (mtt) REVERT: I 685 MET cc_start: 0.9446 (mtp) cc_final: 0.9026 (mtp) REVERT: I 748 ILE cc_start: 0.8527 (pt) cc_final: 0.8127 (pt) REVERT: I 805 MET cc_start: 0.9299 (ppp) cc_final: 0.9001 (ppp) REVERT: I 817 LEU cc_start: 0.8520 (mm) cc_final: 0.7799 (mm) REVERT: I 831 ILE cc_start: 0.8960 (mm) cc_final: 0.8429 (mm) REVERT: I 833 ILE cc_start: 0.9498 (tp) cc_final: 0.9239 (mt) REVERT: I 957 LYS cc_start: 0.9568 (pptt) cc_final: 0.9288 (ptpp) REVERT: I 1056 VAL cc_start: 0.8810 (m) cc_final: 0.8473 (m) REVERT: I 1080 ASN cc_start: 0.9003 (m-40) cc_final: 0.8380 (t0) REVERT: I 1085 MET cc_start: 0.8300 (tpt) cc_final: 0.8091 (tpp) REVERT: I 1095 ASP cc_start: 0.9714 (m-30) cc_final: 0.9293 (t70) REVERT: I 1096 ILE cc_start: 0.9634 (mp) cc_final: 0.9372 (mp) REVERT: I 1106 ARG cc_start: 0.9514 (mmm-85) cc_final: 0.9214 (mmt180) REVERT: I 1107 MET cc_start: 0.9028 (mmm) cc_final: 0.7811 (tmm) REVERT: I 1119 MET cc_start: 0.8808 (mmp) cc_final: 0.8596 (mmp) REVERT: I 1122 LYS cc_start: 0.9624 (tptm) cc_final: 0.9131 (tppt) REVERT: I 1126 ASP cc_start: 0.9374 (m-30) cc_final: 0.8794 (m-30) REVERT: I 1187 PHE cc_start: 0.8978 (m-10) cc_final: 0.8555 (m-10) REVERT: I 1216 ARG cc_start: 0.9202 (mtp180) cc_final: 0.8736 (mmm-85) REVERT: I 1234 LYS cc_start: 0.9464 (tppp) cc_final: 0.8982 (tppp) REVERT: I 1265 PHE cc_start: 0.9163 (t80) cc_final: 0.8876 (t80) REVERT: I 1270 PHE cc_start: 0.8974 (t80) cc_final: 0.8192 (t80) REVERT: I 1290 MET cc_start: 0.9355 (tmm) cc_final: 0.9022 (tmm) REVERT: I 1304 MET cc_start: 0.9674 (tmm) cc_final: 0.9297 (ptp) REVERT: I 1319 MET cc_start: 0.7952 (tpt) cc_final: 0.7074 (tpt) REVERT: I 1321 GLU cc_start: 0.8941 (pm20) cc_final: 0.8728 (pm20) REVERT: I 1329 GLU cc_start: 0.9905 (mt-10) cc_final: 0.9504 (mt-10) REVERT: J 24 LEU cc_start: 0.8619 (tt) cc_final: 0.8230 (tt) REVERT: J 33 TRP cc_start: 0.8962 (m100) cc_final: 0.8753 (m100) REVERT: J 91 GLU cc_start: 0.8761 (pp20) cc_final: 0.8544 (tp30) REVERT: J 102 MET cc_start: 0.7412 (tpt) cc_final: 0.4937 (ttt) REVERT: J 140 TYR cc_start: 0.9741 (m-80) cc_final: 0.9479 (m-80) REVERT: J 207 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9169 (mm-30) REVERT: J 237 MET cc_start: 0.9392 (mpp) cc_final: 0.9109 (mpp) REVERT: J 327 LEU cc_start: 0.9789 (mp) cc_final: 0.9493 (mp) REVERT: J 330 MET cc_start: 0.9430 (mpp) cc_final: 0.9123 (ppp) REVERT: J 331 ILE cc_start: 0.9012 (pt) cc_final: 0.8597 (pt) REVERT: J 332 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8635 (mmmt) REVERT: J 361 LEU cc_start: 0.9231 (mt) cc_final: 0.8753 (pp) REVERT: J 365 GLN cc_start: 0.9630 (pt0) cc_final: 0.9405 (pt0) REVERT: J 372 MET cc_start: 0.9445 (mpp) cc_final: 0.9229 (ptp) REVERT: J 405 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8631 (mt-10) REVERT: J 409 TRP cc_start: 0.8950 (m100) cc_final: 0.8252 (m100) REVERT: J 415 VAL cc_start: 0.9160 (p) cc_final: 0.8957 (m) REVERT: J 437 PHE cc_start: 0.9561 (m-80) cc_final: 0.8975 (m-80) REVERT: J 454 CYS cc_start: 0.9311 (m) cc_final: 0.8956 (m) REVERT: J 499 ILE cc_start: 0.9391 (tp) cc_final: 0.9175 (mm) REVERT: J 512 TYR cc_start: 0.9391 (t80) cc_final: 0.8954 (t80) REVERT: J 526 VAL cc_start: 0.8977 (p) cc_final: 0.8663 (p) REVERT: J 544 LEU cc_start: 0.9449 (tp) cc_final: 0.8917 (tp) REVERT: J 594 GLN cc_start: 0.9309 (tm-30) cc_final: 0.8990 (tm-30) REVERT: J 603 LYS cc_start: 0.9354 (pttt) cc_final: 0.9002 (ptpp) REVERT: J 631 TYR cc_start: 0.9444 (m-80) cc_final: 0.9243 (m-80) REVERT: J 645 VAL cc_start: 0.8585 (p) cc_final: 0.8216 (m) REVERT: J 686 TRP cc_start: 0.9146 (m100) cc_final: 0.8691 (m100) REVERT: J 697 MET cc_start: 0.9679 (ppp) cc_final: 0.9412 (ppp) REVERT: J 739 GLN cc_start: 0.9082 (mt0) cc_final: 0.8853 (mt0) REVERT: J 743 MET cc_start: 0.9018 (ptm) cc_final: 0.8776 (ptm) REVERT: J 763 PHE cc_start: 0.9362 (m-80) cc_final: 0.8948 (m-80) REVERT: J 764 ARG cc_start: 0.9032 (ttt-90) cc_final: 0.8781 (ttt-90) REVERT: J 792 ASN cc_start: 0.9359 (m110) cc_final: 0.9124 (m110) REVERT: J 813 ASP cc_start: 0.9107 (p0) cc_final: 0.8645 (t70) REVERT: J 821 MET cc_start: 0.9350 (mmp) cc_final: 0.8846 (tpp) REVERT: J 1040 MET cc_start: 0.7705 (mmp) cc_final: 0.6962 (mmm) REVERT: J 1194 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7881 (mtt180) REVERT: J 1199 PHE cc_start: 0.9590 (m-80) cc_final: 0.9363 (m-80) REVERT: J 1231 ARG cc_start: 0.9667 (mtp85) cc_final: 0.9336 (ttt180) REVERT: J 1238 GLN cc_start: 0.9107 (pp30) cc_final: 0.8900 (pp30) REVERT: J 1242 ARG cc_start: 0.9000 (pmt-80) cc_final: 0.8710 (pmt-80) REVERT: J 1254 GLU cc_start: 0.9529 (mt-10) cc_final: 0.9278 (mt-10) REVERT: J 1260 MET cc_start: 0.9502 (tmm) cc_final: 0.9146 (tmm) REVERT: J 1302 TYR cc_start: 0.9373 (p90) cc_final: 0.8965 (p90) REVERT: J 1307 LEU cc_start: 0.8884 (mm) cc_final: 0.8682 (mm) REVERT: J 1328 THR cc_start: 0.8849 (m) cc_final: 0.8628 (m) REVERT: J 1330 ARG cc_start: 0.9545 (ptm-80) cc_final: 0.9199 (ptm-80) REVERT: J 1334 GLU cc_start: 0.9409 (tm-30) cc_final: 0.9041 (tm-30) REVERT: J 1373 ARG cc_start: 0.6109 (ptm160) cc_final: 0.5827 (ptm160) outliers start: 1 outliers final: 1 residues processed: 734 average time/residue: 0.1717 time to fit residues: 197.0317 Evaluate side-chains 651 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 650 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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: 10.0000 chunk 90 optimal weight: 8.9990 chunk 181 optimal weight: 40.0000 chunk 194 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 300 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 66 HIS ** 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 628 HIS ** 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** ** I1236 ASN ** 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 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** 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 667 GLN J 700 ASN J 921 GLN J 954 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.101752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.064238 restraints weight = 93602.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.067089 restraints weight = 58610.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069287 restraints weight = 41704.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070865 restraints weight = 31949.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.072156 restraints weight = 26069.120| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 25706 Z= 0.241 Angle : 0.792 10.407 34937 Z= 0.418 Chirality : 0.048 0.305 3992 Planarity : 0.006 0.075 4386 Dihedral : 14.792 65.067 3992 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 26.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.62 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -1.76 (0.14), residues: 3071 helix: -0.16 (0.15), residues: 1094 sheet: -1.57 (0.25), residues: 369 loop : -1.80 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 764 TYR 0.034 0.002 TYR I1231 PHE 0.032 0.003 PHE I 136 TRP 0.023 0.003 TRP I 807 HIS 0.013 0.002 HIS J 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.24 (25698) covalent geometry : angle 0.78693 / 0.42 (34925) hydrogen bonds : bond 0.04966 / 3.46 ( 1057) hydrogen bonds : angle 5.94375 / 4.12 ( 2933) metal coordination : bond 0.01126 / 0.53 ( 8) metal coordination : angle 4.91868 / 2.56 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5324.28 seconds wall clock time: 92 minutes 49.24 seconds (5569.24 seconds total)