Starting phenix.real_space_refine on Sun Jun 22 00:59:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t00_40930/06_2025/8t00_40930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t00_40930/06_2025/8t00_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_40930/06_2025/8t00_40930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t00_40930/06_2025/8t00_40930.map" model { file = "/net/cci-nas-00/data/ceres_data/8t00_40930/06_2025/8t00_40930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t00_40930/06_2025/8t00_40930.cif" } resolution = 4.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ARG:plan': 2} 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: 12.92, per 1000 atoms: 0.51 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: 7.18 Conformation dependent library (CDL) restraints added in 3.4 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: 10.38 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: 13.90 Time building geometry restraints manager: 7.92 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 1.490 1.535 -0.045 3.00e-02 1.11e+03 2.23e+00 bond pdb=" C1' DT B 118 " pdb=" N1 DT B 118 " ideal model delta sigma weight residual 1.490 1.533 -0.043 3.00e-02 1.11e+03 2.03e+00 bond pdb=" C1' DT B 103 " pdb=" N1 DT B 103 " ideal model delta sigma weight residual 1.490 1.532 -0.042 3.00e-02 1.11e+03 1.97e+00 bond pdb=" C MET I1319 " pdb=" N PRO I1320 " ideal model delta sigma weight residual 1.335 1.347 -0.012 8.70e-03 1.32e+04 1.93e+00 bond pdb=" CA PRO J1358 " pdb=" CB PRO J1358 " ideal model delta sigma weight residual 1.533 1.514 0.019 1.42e-02 4.96e+03 1.83e+00 ... (remaining 25693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 33866 1.63 - 3.27: 868 3.27 - 4.90: 167 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=" N GLY J 852 " pdb=" CA GLY J 852 " pdb=" C GLY J 852 " ideal model delta sigma weight residual 113.18 105.02 8.16 2.37e+00 1.78e-01 1.19e+01 angle pdb=" N ASP J1184 " pdb=" CA ASP J1184 " pdb=" C ASP J1184 " ideal model delta sigma weight residual 109.81 116.87 -7.06 2.21e+00 2.05e-01 1.02e+01 angle pdb=" C GLU H 17 " pdb=" CA GLU H 17 " pdb=" CB GLU H 17 " ideal model delta sigma weight residual 111.22 116.38 -5.16 1.72e+00 3.38e-01 9.00e+00 angle pdb=" N GLU I 625 " pdb=" CA GLU I 625 " pdb=" CB GLU I 625 " ideal model delta sigma weight residual 113.65 109.43 4.22 1.47e+00 4.63e-01 8.22e+00 ... (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: 2777 0.036 - 0.071: 787 0.071 - 0.107: 307 0.107 - 0.143: 108 0.143 - 0.178: 13 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=" CB THR H 222 " pdb=" CA THR H 222 " pdb=" OG1 THR H 222 " pdb=" CG2 THR H 222 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA ILE I 831 " pdb=" N ILE I 831 " pdb=" C ILE I 831 " pdb=" CB ILE I 831 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-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: 1.100 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: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 71.810 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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= 0.164 Angle : 1.002 79.924 34937 Z= 0.386 Chirality : 0.042 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 : 8.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (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 TRP 0.012 0.001 TRP I 183 HIS 0.007 0.001 HIS J1252 PHE 0.030 0.001 PHE J 773 TYR 0.014 0.002 TYR I1149 ARG 0.005 0.000 ARG J 515 Details of bonding type rmsd hydrogen bonds : bond 0.16656 ( 1057) hydrogen bonds : angle 6.90847 ( 2933) metal coordination : bond 0.06779 ( 8) metal coordination : angle 40.80901 ( 12) covalent geometry : bond 0.00347 (25698) covalent geometry : angle 0.65805 (34925) *********************** 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 : 2.986 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: 0.7973 (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: 0.9384 (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: 0.8613 (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: 0.9053 (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: 0.7148 (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: 0.7357 (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: 0.9213 (ttt-90) cc_final: 0.8506 (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: 0.8314 (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: 0.4771 time to fit residues: 718.4341 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 : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 80 optimal weight: 0.4980 chunk 159 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 chunk 282 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 GLN ** 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 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 951 GLN J1259 GLN J1367 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.069347 restraints weight = 89808.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.072428 restraints weight = 55912.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.074759 restraints weight = 39659.476| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2749 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= 0.175 Angle : 0.751 33.608 34937 Z= 0.368 Chirality : 0.045 0.164 3992 Planarity : 0.006 0.144 4386 Dihedral : 14.430 65.898 3992 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.06 % Favored : 93.91 % Rotamer: Outliers : 0.23 % Allowed : 4.80 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 3071 helix: 0.68 (0.15), residues: 1061 sheet: -1.03 (0.25), residues: 380 loop : -1.67 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 409 HIS 0.005 0.001 HIS J 450 PHE 0.025 0.002 PHE J1145 TYR 0.015 0.002 TYR J 46 ARG 0.013 0.001 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 1057) hydrogen bonds : angle 5.77744 ( 2933) metal coordination : bond 0.01853 ( 8) metal coordination : angle 16.58171 ( 12) covalent geometry : bond 0.00381 (25698) covalent geometry : angle 0.68484 (34925) *********************** 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 860 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 854 time to evaluate : 2.639 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: G 35 PHE cc_start: 0.9727 (m-80) cc_final: 0.9500 (m-80) REVERT: G 44 ARG cc_start: 0.9343 (ttt-90) cc_final: 0.8974 (ttt90) REVERT: G 45 ARG cc_start: 0.9479 (ttt90) cc_final: 0.9150 (mmt180) REVERT: G 84 ASN cc_start: 0.8722 (m-40) cc_final: 0.8518 (t0) REVERT: G 104 LYS cc_start: 0.8245 (tptp) cc_final: 0.7957 (tmtt) REVERT: G 121 VAL cc_start: 0.9797 (t) cc_final: 0.9141 (t) REVERT: H 29 GLU cc_start: 0.8277 (pm20) cc_final: 0.8019 (pm20) REVERT: H 46 ILE cc_start: 0.9702 (tp) cc_final: 0.9447 (tp) REVERT: H 71 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8820 (tptp) REVERT: H 95 LYS cc_start: 0.9486 (mppt) cc_final: 0.9276 (ptpp) REVERT: H 141 SER cc_start: 0.9654 (t) cc_final: 0.9342 (m) REVERT: H 142 MET cc_start: 0.9609 (ptm) cc_final: 0.9359 (ptm) REVERT: H 185 TYR cc_start: 0.8013 (p90) cc_final: 0.7454 (p90) REVERT: H 193 GLU cc_start: 0.8796 (tp30) cc_final: 0.7887 (tp30) REVERT: H 194 GLN cc_start: 0.9501 (tp40) cc_final: 0.8560 (mm-40) REVERT: H 200 LYS cc_start: 0.9075 (tmtt) cc_final: 0.8721 (tptp) REVERT: I 6 THR cc_start: 0.9305 (p) cc_final: 0.8749 (p) REVERT: I 9 LYS cc_start: 0.9126 (mttm) cc_final: 0.8565 (mttm) REVERT: I 32 LEU cc_start: 0.9599 (mt) cc_final: 0.9262 (pp) REVERT: I 53 PHE cc_start: 0.8459 (m-80) cc_final: 0.8063 (m-10) REVERT: I 57 PHE cc_start: 0.8880 (m-80) cc_final: 0.8662 (m-80) REVERT: I 69 GLN cc_start: 0.9562 (pt0) cc_final: 0.9242 (pm20) REVERT: I 92 TYR cc_start: 0.9390 (t80) cc_final: 0.8993 (t80) REVERT: I 124 MET cc_start: 0.9630 (tpp) cc_final: 0.9209 (tpp) REVERT: I 241 LEU cc_start: 0.9003 (tp) cc_final: 0.8797 (tp) REVERT: I 400 VAL cc_start: 0.9379 (t) cc_final: 0.8909 (t) REVERT: I 405 PHE cc_start: 0.9658 (t80) cc_final: 0.9344 (t80) REVERT: I 430 LYS cc_start: 0.9575 (mmtm) cc_final: 0.9319 (mmmt) REVERT: I 464 PHE cc_start: 0.9732 (t80) cc_final: 0.9515 (t80) REVERT: I 606 LEU cc_start: 0.9305 (mp) cc_final: 0.9104 (mp) REVERT: I 633 LEU cc_start: 0.9590 (pt) cc_final: 0.9249 (mm) REVERT: I 642 SER cc_start: 0.8957 (p) cc_final: 0.8650 (t) REVERT: I 681 MET cc_start: 0.9323 (mtp) cc_final: 0.8774 (mtt) REVERT: I 685 MET cc_start: 0.9450 (mtm) cc_final: 0.8770 (mtm) REVERT: I 734 ILE cc_start: 0.9247 (mp) cc_final: 0.8926 (mp) REVERT: I 748 ILE cc_start: 0.9129 (pt) cc_final: 0.8709 (pt) REVERT: I 799 ASN cc_start: 0.8882 (t0) cc_final: 0.8604 (t0) REVERT: I 805 MET cc_start: 0.9345 (ppp) cc_final: 0.9143 (ppp) REVERT: I 810 TYR cc_start: 0.9295 (m-10) cc_final: 0.9049 (m-10) REVERT: I 831 ILE cc_start: 0.8932 (mm) cc_final: 0.8538 (mm) REVERT: I 833 ILE cc_start: 0.9344 (mt) cc_final: 0.9058 (tp) REVERT: I 930 ASP cc_start: 0.9754 (t70) cc_final: 0.9478 (t70) REVERT: I 1025 PHE cc_start: 0.9524 (t80) cc_final: 0.9162 (t80) REVERT: I 1083 GLU cc_start: 0.8691 (mp0) cc_final: 0.7749 (mp0) REVERT: I 1106 ARG cc_start: 0.9277 (mmm-85) cc_final: 0.9009 (mmt180) REVERT: I 1107 MET cc_start: 0.9220 (mmm) cc_final: 0.7945 (tpp) REVERT: I 1119 MET cc_start: 0.9234 (mmm) cc_final: 0.9014 (mmm) REVERT: I 1122 LYS cc_start: 0.9670 (tptm) cc_final: 0.9140 (tppt) REVERT: I 1126 ASP cc_start: 0.9478 (m-30) cc_final: 0.8669 (m-30) REVERT: I 1214 ASP cc_start: 0.8833 (t0) cc_final: 0.8361 (t0) REVERT: I 1226 THR cc_start: 0.9506 (m) cc_final: 0.9210 (p) REVERT: I 1230 MET cc_start: 0.9372 (tpt) cc_final: 0.9116 (tpt) REVERT: I 1234 LYS cc_start: 0.9511 (tppp) cc_final: 0.9044 (tppp) REVERT: I 1237 HIS cc_start: 0.8855 (m-70) cc_final: 0.8517 (m90) REVERT: I 1270 PHE cc_start: 0.9142 (t80) cc_final: 0.8394 (t80) REVERT: I 1290 MET cc_start: 0.9451 (tmm) cc_final: 0.8974 (tmm) REVERT: I 1304 MET cc_start: 0.9696 (tmm) cc_final: 0.9253 (ptp) REVERT: I 1319 MET cc_start: 0.7999 (tpt) cc_final: 0.7050 (tpt) REVERT: I 1321 GLU cc_start: 0.9036 (pm20) cc_final: 0.8836 (pm20) REVERT: I 1329 GLU cc_start: 0.9877 (mt-10) cc_final: 0.9599 (mt-10) REVERT: J 102 MET cc_start: 0.7022 (tpt) cc_final: 0.6512 (tpt) REVERT: J 159 ILE cc_start: 0.9169 (pt) cc_final: 0.8565 (pt) REVERT: J 189 LEU cc_start: 0.9725 (mt) cc_final: 0.9494 (mt) REVERT: J 220 ARG cc_start: 0.9707 (ttm110) cc_final: 0.9498 (ptp-110) REVERT: J 242 LEU cc_start: 0.9481 (tt) cc_final: 0.9203 (tt) REVERT: J 243 PRO cc_start: 0.9631 (Cg_exo) cc_final: 0.9361 (Cg_endo) REVERT: J 325 LYS cc_start: 0.8023 (pttm) cc_final: 0.7519 (pttp) REVERT: J 329 ASP cc_start: 0.9638 (m-30) cc_final: 0.9343 (t0) REVERT: J 361 LEU cc_start: 0.9186 (mt) cc_final: 0.8753 (pp) REVERT: J 372 MET cc_start: 0.9501 (mpp) cc_final: 0.9129 (mmm) REVERT: J 374 LEU cc_start: 0.9423 (mt) cc_final: 0.9197 (mt) REVERT: J 409 TRP cc_start: 0.9033 (m100) cc_final: 0.8477 (m100) REVERT: J 437 PHE cc_start: 0.9589 (m-80) cc_final: 0.8654 (m-80) REVERT: J 452 LEU cc_start: 0.9709 (mt) cc_final: 0.9497 (mm) REVERT: J 478 LEU cc_start: 0.9661 (tt) cc_final: 0.9453 (mt) REVERT: J 487 THR cc_start: 0.9715 (p) cc_final: 0.9413 (p) REVERT: J 603 LYS cc_start: 0.9271 (pttt) cc_final: 0.8822 (ptpp) REVERT: J 627 THR cc_start: 0.9868 (t) cc_final: 0.9556 (t) REVERT: J 629 PHE cc_start: 0.9452 (m-80) cc_final: 0.9186 (m-80) REVERT: J 697 MET cc_start: 0.9701 (ppp) cc_final: 0.9354 (ppp) REVERT: J 743 MET cc_start: 0.9443 (ptm) cc_final: 0.9152 (ptm) REVERT: J 744 ARG cc_start: 0.8912 (ptm160) cc_final: 0.8339 (ptm-80) REVERT: J 764 ARG cc_start: 0.9096 (ttt-90) cc_final: 0.8715 (ttt-90) REVERT: J 772 TYR cc_start: 0.9125 (t80) cc_final: 0.8878 (t80) REVERT: J 822 MET cc_start: 0.8875 (tpt) cc_final: 0.8409 (tpp) REVERT: J 842 ARG cc_start: 0.9230 (mtm-85) cc_final: 0.8979 (mpt180) REVERT: J 892 PHE cc_start: 0.8967 (m-10) cc_final: 0.8743 (m-10) REVERT: J 1040 MET cc_start: 0.8027 (mmp) cc_final: 0.7390 (mmm) REVERT: J 1186 TYR cc_start: 0.9226 (t80) cc_final: 0.9010 (t80) REVERT: J 1194 ARG cc_start: 0.8208 (mtt180) cc_final: 0.7961 (mtt180) REVERT: J 1215 GLU cc_start: 0.9442 (mp0) cc_final: 0.9215 (mm-30) REVERT: J 1231 ARG cc_start: 0.9638 (mtp85) cc_final: 0.9398 (tpt-90) REVERT: J 1238 GLN cc_start: 0.9744 (mm110) cc_final: 0.9235 (tp40) REVERT: J 1242 ARG cc_start: 0.9037 (ttp80) cc_final: 0.8528 (ptp-170) REVERT: J 1260 MET cc_start: 0.9511 (tmm) cc_final: 0.9149 (tmm) REVERT: J 1266 ILE cc_start: 0.8165 (mt) cc_final: 0.7829 (mt) REVERT: J 1279 GLN cc_start: 0.7031 (tt0) cc_final: 0.6696 (tp40) REVERT: J 1286 LYS cc_start: 0.9635 (pttp) cc_final: 0.9279 (pttt) REVERT: J 1290 ARG cc_start: 0.9453 (mtm110) cc_final: 0.9162 (ptm160) REVERT: J 1307 LEU cc_start: 0.8845 (mm) cc_final: 0.8568 (mm) REVERT: J 1327 GLU cc_start: 0.7809 (tt0) cc_final: 0.7454 (pp20) REVERT: J 1331 VAL cc_start: 0.9019 (m) cc_final: 0.8814 (p) REVERT: J 1340 LYS cc_start: 0.8563 (tmtt) cc_final: 0.8288 (tttp) outliers start: 6 outliers final: 1 residues processed: 857 average time/residue: 0.5178 time to fit residues: 664.9956 Evaluate side-chains 701 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 700 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 85 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 264 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 241 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 111 optimal weight: 0.0980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN I 463 GLN I 517 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS I 834 GLN ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3712 r_free = 0.3712 target = 0.111057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.071493 restraints weight = 87632.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.074720 restraints weight = 54005.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.077176 restraints weight = 38018.881| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25706 Z= 0.139 Angle : 0.678 18.947 34937 Z= 0.350 Chirality : 0.045 0.278 3992 Planarity : 0.006 0.109 4386 Dihedral : 14.447 64.532 3992 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.70 % Favored : 94.27 % Rotamer: Outliers : 0.19 % Allowed : 4.26 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3071 helix: 0.64 (0.16), residues: 1072 sheet: -0.75 (0.27), residues: 357 loop : -1.69 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 183 HIS 0.004 0.001 HIS J1366 PHE 0.023 0.002 PHE J 62 TYR 0.026 0.001 TYR J 631 ARG 0.010 0.001 ARG I 88 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 1057) hydrogen bonds : angle 5.45200 ( 2933) metal coordination : bond 0.01102 ( 8) metal coordination : angle 8.06118 ( 12) covalent geometry : bond 0.00309 (25698) covalent geometry : angle 0.66141 (34925) *********************** 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 832 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 827 time to evaluate : 5.193 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: G 8 PHE cc_start: 0.8264 (m-80) cc_final: 0.7869 (m-80) REVERT: G 35 PHE cc_start: 0.9704 (m-80) cc_final: 0.9461 (m-80) REVERT: G 68 TYR cc_start: 0.8631 (m-10) cc_final: 0.8370 (m-10) REVERT: G 80 GLU cc_start: 0.9684 (tp30) cc_final: 0.9389 (tp30) REVERT: G 84 ASN cc_start: 0.9237 (m-40) cc_final: 0.8679 (m-40) REVERT: G 104 LYS cc_start: 0.8259 (tptp) cc_final: 0.7962 (tmtt) REVERT: G 207 THR cc_start: 0.7581 (t) cc_final: 0.7297 (t) REVERT: H 37 HIS cc_start: 0.9588 (m90) cc_final: 0.9328 (m90) REVERT: H 46 ILE cc_start: 0.9690 (tp) cc_final: 0.9482 (tp) REVERT: H 95 LYS cc_start: 0.9499 (mppt) cc_final: 0.9281 (ptpp) REVERT: H 141 SER cc_start: 0.9641 (t) cc_final: 0.9386 (m) REVERT: H 142 MET cc_start: 0.9606 (ptm) cc_final: 0.9347 (ptm) REVERT: H 147 GLN cc_start: 0.8991 (mp10) cc_final: 0.8605 (mp10) REVERT: H 185 TYR cc_start: 0.7937 (p90) cc_final: 0.7373 (p90) REVERT: I 6 THR cc_start: 0.9309 (p) cc_final: 0.8890 (p) REVERT: I 9 LYS cc_start: 0.8856 (mttm) cc_final: 0.8494 (mttm) REVERT: I 17 LYS cc_start: 0.9614 (mptt) cc_final: 0.9137 (mmtm) REVERT: I 32 LEU cc_start: 0.9578 (mt) cc_final: 0.9226 (pp) REVERT: I 53 PHE cc_start: 0.8616 (m-80) cc_final: 0.8274 (m-10) REVERT: I 74 ARG cc_start: 0.9559 (tmt170) cc_final: 0.9333 (ptm-80) REVERT: I 92 TYR cc_start: 0.9361 (t80) cc_final: 0.9039 (t80) REVERT: I 124 MET cc_start: 0.9610 (tpp) cc_final: 0.9281 (tpp) REVERT: I 215 TYR cc_start: 0.8592 (m-10) cc_final: 0.8299 (m-80) REVERT: I 240 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8660 (mp0) REVERT: I 277 LEU cc_start: 0.9684 (mt) cc_final: 0.9246 (pp) REVERT: I 342 ASP cc_start: 0.9066 (m-30) cc_final: 0.8769 (m-30) REVERT: I 396 ASP cc_start: 0.9142 (t0) cc_final: 0.8909 (t0) REVERT: I 405 PHE cc_start: 0.9606 (t80) cc_final: 0.9203 (t80) REVERT: I 464 PHE cc_start: 0.9803 (t80) cc_final: 0.9431 (t80) REVERT: I 465 ARG cc_start: 0.9063 (mtt-85) cc_final: 0.8808 (mtp85) REVERT: I 591 TYR cc_start: 0.9449 (m-80) cc_final: 0.8857 (m-80) REVERT: I 606 LEU cc_start: 0.9286 (mp) cc_final: 0.8631 (mp) REVERT: I 633 LEU cc_start: 0.9584 (pt) cc_final: 0.9225 (mm) REVERT: I 653 MET cc_start: 0.9478 (tpt) cc_final: 0.9234 (tpt) REVERT: I 659 GLN cc_start: 0.9609 (pp30) cc_final: 0.9030 (pp30) REVERT: I 668 ILE cc_start: 0.9554 (mm) cc_final: 0.9308 (mm) REVERT: I 672 GLU cc_start: 0.9328 (pm20) cc_final: 0.9076 (pm20) REVERT: I 681 MET cc_start: 0.9218 (mtp) cc_final: 0.8772 (mtt) REVERT: I 685 MET cc_start: 0.9393 (mtm) cc_final: 0.8900 (mtm) REVERT: I 762 ASN cc_start: 0.9164 (m-40) cc_final: 0.8899 (t0) REVERT: I 768 MET cc_start: 0.9314 (ppp) cc_final: 0.9089 (mpp) REVERT: I 799 ASN cc_start: 0.8781 (t0) cc_final: 0.8387 (t0) REVERT: I 800 MET cc_start: 0.9448 (mpp) cc_final: 0.8787 (mpp) REVERT: I 805 MET cc_start: 0.9364 (ppp) cc_final: 0.9157 (ppp) REVERT: I 816 ILE cc_start: 0.9443 (mt) cc_final: 0.8656 (mt) REVERT: I 817 LEU cc_start: 0.8499 (mm) cc_final: 0.7914 (mm) REVERT: I 827 ARG cc_start: 0.9288 (ptm160) cc_final: 0.8708 (ptm160) REVERT: I 833 ILE cc_start: 0.9447 (mt) cc_final: 0.9143 (tp) REVERT: I 930 ASP cc_start: 0.9721 (t70) cc_final: 0.8931 (t70) REVERT: I 1053 TYR cc_start: 0.8860 (m-80) cc_final: 0.8172 (m-80) REVERT: I 1056 VAL cc_start: 0.8691 (m) cc_final: 0.8096 (m) REVERT: I 1066 MET cc_start: 0.8926 (pmm) cc_final: 0.8176 (pmm) REVERT: I 1106 ARG cc_start: 0.9468 (mmm-85) cc_final: 0.9152 (mmt180) REVERT: I 1107 MET cc_start: 0.9196 (mmm) cc_final: 0.7867 (tpp) REVERT: I 1119 MET cc_start: 0.9184 (mmm) cc_final: 0.8971 (mmm) REVERT: I 1122 LYS cc_start: 0.9632 (tptm) cc_final: 0.9169 (tppt) REVERT: I 1126 ASP cc_start: 0.9448 (m-30) cc_final: 0.8701 (m-30) REVERT: I 1151 LEU cc_start: 0.9349 (tt) cc_final: 0.9123 (tp) REVERT: I 1187 PHE cc_start: 0.8887 (m-10) cc_final: 0.8513 (m-10) REVERT: I 1219 GLU cc_start: 0.9384 (pp20) cc_final: 0.8593 (pm20) REVERT: I 1226 THR cc_start: 0.9481 (m) cc_final: 0.9146 (m) REVERT: I 1234 LYS cc_start: 0.9443 (tppp) cc_final: 0.9010 (tppp) REVERT: I 1237 HIS cc_start: 0.8784 (m-70) cc_final: 0.8551 (m-70) REVERT: I 1265 PHE cc_start: 0.9156 (t80) cc_final: 0.8854 (t80) REVERT: I 1270 PHE cc_start: 0.9289 (t80) cc_final: 0.8500 (t80) REVERT: I 1290 MET cc_start: 0.9459 (tmm) cc_final: 0.8962 (tmm) REVERT: I 1304 MET cc_start: 0.9685 (tmm) cc_final: 0.9256 (ptp) REVERT: I 1319 MET cc_start: 0.7645 (tpt) cc_final: 0.6909 (tpt) REVERT: I 1321 GLU cc_start: 0.8888 (pm20) cc_final: 0.8687 (pm20) REVERT: I 1329 GLU cc_start: 0.9880 (mt-10) cc_final: 0.9598 (mt-10) REVERT: J 28 ASP cc_start: 0.9851 (t0) cc_final: 0.9558 (p0) REVERT: J 30 ILE cc_start: 0.9618 (mt) cc_final: 0.8744 (mt) REVERT: J 102 MET cc_start: 0.6824 (tpt) cc_final: 0.6562 (tpt) REVERT: J 180 MET cc_start: 0.9372 (ttm) cc_final: 0.8874 (ttt) REVERT: J 220 ARG cc_start: 0.9710 (ttm110) cc_final: 0.9505 (ptp-110) REVERT: J 242 LEU cc_start: 0.9461 (tt) cc_final: 0.9162 (tt) REVERT: J 243 PRO cc_start: 0.9672 (Cg_exo) cc_final: 0.9412 (Cg_endo) REVERT: J 335 GLN cc_start: 0.8973 (pp30) cc_final: 0.8613 (pp30) REVERT: J 361 LEU cc_start: 0.9089 (mt) cc_final: 0.8653 (pp) REVERT: J 423 LEU cc_start: 0.9799 (mp) cc_final: 0.9551 (mp) REVERT: J 437 PHE cc_start: 0.9616 (m-80) cc_final: 0.8691 (m-80) REVERT: J 452 LEU cc_start: 0.9692 (mt) cc_final: 0.9190 (mm) REVERT: J 454 CYS cc_start: 0.9268 (m) cc_final: 0.8980 (m) REVERT: J 487 THR cc_start: 0.9667 (p) cc_final: 0.9374 (p) REVERT: J 599 LYS cc_start: 0.9370 (pttm) cc_final: 0.9147 (ptmt) REVERT: J 603 LYS cc_start: 0.9262 (pttt) cc_final: 0.8964 (ptpp) REVERT: J 604 MET cc_start: 0.9702 (ttm) cc_final: 0.9377 (mmt) REVERT: J 625 MET cc_start: 0.9530 (ttp) cc_final: 0.9285 (tpp) REVERT: J 627 THR cc_start: 0.9861 (t) cc_final: 0.9393 (t) REVERT: J 697 MET cc_start: 0.9631 (ppp) cc_final: 0.9342 (ppp) REVERT: J 764 ARG cc_start: 0.9076 (ttt-90) cc_final: 0.8837 (ttt-90) REVERT: J 772 TYR cc_start: 0.9055 (t80) cc_final: 0.8664 (t80) REVERT: J 823 THR cc_start: 0.9603 (p) cc_final: 0.9399 (p) REVERT: J 1040 MET cc_start: 0.7951 (mmp) cc_final: 0.7261 (mmm) REVERT: J 1145 PHE cc_start: 0.9554 (m-80) cc_final: 0.9343 (m-80) REVERT: J 1215 GLU cc_start: 0.9470 (mp0) cc_final: 0.9241 (mm-30) REVERT: J 1231 ARG cc_start: 0.9696 (mtp85) cc_final: 0.9264 (tpt170) REVERT: J 1238 GLN cc_start: 0.9740 (mm110) cc_final: 0.9245 (tp40) REVERT: J 1242 ARG cc_start: 0.9012 (ttp80) cc_final: 0.8516 (ptp-170) REVERT: J 1260 MET cc_start: 0.9463 (tmm) cc_final: 0.8971 (tmm) REVERT: J 1279 GLN cc_start: 0.7439 (tt0) cc_final: 0.7134 (tp40) REVERT: J 1307 LEU cc_start: 0.8795 (mm) cc_final: 0.8497 (mm) REVERT: J 1331 VAL cc_start: 0.9046 (m) cc_final: 0.8841 (p) outliers start: 5 outliers final: 0 residues processed: 828 average time/residue: 0.8647 time to fit residues: 1116.4156 Evaluate side-chains 692 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 692 time to evaluate : 5.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 284 optimal weight: 4.9990 chunk 278 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 187 optimal weight: 40.0000 chunk 291 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 300 optimal weight: 10.0000 chunk 267 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1175 ASN I1209 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 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 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 667 GLN J 700 ASN ** J 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 954 ASN J1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.105029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.067153 restraints weight = 93614.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.070162 restraints weight = 58293.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.072431 restraints weight = 41107.430| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25706 Z= 0.224 Angle : 0.715 14.646 34937 Z= 0.376 Chirality : 0.045 0.214 3992 Planarity : 0.006 0.086 4386 Dihedral : 14.608 66.527 3992 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 0.15 % Allowed : 4.07 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3071 helix: 0.31 (0.15), residues: 1091 sheet: -1.19 (0.26), residues: 375 loop : -1.70 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 409 HIS 0.006 0.002 HIS J 364 PHE 0.034 0.003 PHE I 38 TYR 0.020 0.002 TYR J 537 ARG 0.014 0.001 ARG J 81 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 1057) hydrogen bonds : angle 5.65790 ( 2933) metal coordination : bond 0.01158 ( 8) metal coordination : angle 6.50676 ( 12) covalent geometry : bond 0.00459 (25698) covalent geometry : angle 0.70512 (34925) *********************** 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 773 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 769 time to evaluate : 3.320 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: G 35 PHE cc_start: 0.9561 (m-80) cc_final: 0.9352 (m-80) REVERT: G 71 LYS cc_start: 0.9560 (tmmt) cc_final: 0.9350 (tmtt) REVERT: G 80 GLU cc_start: 0.9717 (tp30) cc_final: 0.9358 (tm-30) REVERT: G 84 ASN cc_start: 0.9302 (m-40) cc_final: 0.8379 (m-40) REVERT: G 195 ARG cc_start: 0.9489 (tmt-80) cc_final: 0.9266 (tmt170) REVERT: G 227 GLN cc_start: 0.9849 (mt0) cc_final: 0.9587 (mt0) REVERT: H 37 HIS cc_start: 0.9731 (m90) cc_final: 0.8991 (m90) REVERT: H 46 ILE cc_start: 0.9775 (tp) cc_final: 0.9568 (tp) REVERT: H 83 LEU cc_start: 0.9576 (pp) cc_final: 0.9124 (mm) REVERT: H 95 LYS cc_start: 0.9466 (mppt) cc_final: 0.9233 (ptpp) REVERT: H 141 SER cc_start: 0.9642 (t) cc_final: 0.9322 (m) REVERT: H 142 MET cc_start: 0.9616 (ptm) cc_final: 0.9313 (ptm) REVERT: H 185 TYR cc_start: 0.7957 (p90) cc_final: 0.7255 (p90) REVERT: H 193 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8641 (tp30) REVERT: H 194 GLN cc_start: 0.9507 (tp-100) cc_final: 0.9204 (tp40) REVERT: I 5 TYR cc_start: 0.8997 (t80) cc_final: 0.8701 (t80) REVERT: I 9 LYS cc_start: 0.9003 (mttm) cc_final: 0.8662 (mttm) REVERT: I 32 LEU cc_start: 0.9541 (mt) cc_final: 0.9051 (pp) REVERT: I 35 PHE cc_start: 0.9388 (t80) cc_final: 0.8978 (t80) REVERT: I 69 GLN cc_start: 0.9508 (pt0) cc_final: 0.9258 (pm20) REVERT: I 92 TYR cc_start: 0.9474 (t80) cc_final: 0.8973 (t80) REVERT: I 100 LEU cc_start: 0.9740 (mt) cc_final: 0.9278 (pp) REVERT: I 124 MET cc_start: 0.9643 (tpp) cc_final: 0.9378 (tpp) REVERT: I 158 ASP cc_start: 0.9396 (t0) cc_final: 0.9008 (p0) REVERT: I 160 ASP cc_start: 0.9017 (m-30) cc_final: 0.7844 (m-30) REVERT: I 213 LEU cc_start: 0.9442 (mp) cc_final: 0.8761 (mp) REVERT: I 215 TYR cc_start: 0.8752 (m-10) cc_final: 0.8183 (m-80) REVERT: I 277 LEU cc_start: 0.9706 (mt) cc_final: 0.9233 (pp) REVERT: I 342 ASP cc_start: 0.9155 (m-30) cc_final: 0.8763 (m-30) REVERT: I 370 MET cc_start: 0.9602 (tmm) cc_final: 0.9384 (ppp) REVERT: I 396 ASP cc_start: 0.9108 (t0) cc_final: 0.8894 (t0) REVERT: I 405 PHE cc_start: 0.9650 (t80) cc_final: 0.9315 (t80) REVERT: I 419 ILE cc_start: 0.9304 (pt) cc_final: 0.8996 (pt) REVERT: I 464 PHE cc_start: 0.9796 (t80) cc_final: 0.9478 (t80) REVERT: I 465 ARG cc_start: 0.9079 (mtt-85) cc_final: 0.8857 (mtt-85) REVERT: I 606 LEU cc_start: 0.9369 (mp) cc_final: 0.9150 (mp) REVERT: I 633 LEU cc_start: 0.9543 (pt) cc_final: 0.9185 (mm) REVERT: I 672 GLU cc_start: 0.9349 (pm20) cc_final: 0.9043 (pm20) REVERT: I 681 MET cc_start: 0.9205 (mtp) cc_final: 0.8713 (mtt) REVERT: I 685 MET cc_start: 0.9289 (mtm) cc_final: 0.8954 (mtm) REVERT: I 741 MET cc_start: 0.9553 (mmt) cc_final: 0.9295 (mmm) REVERT: I 748 ILE cc_start: 0.8799 (pt) cc_final: 0.8371 (pt) REVERT: I 762 ASN cc_start: 0.9185 (m-40) cc_final: 0.8967 (t0) REVERT: I 789 THR cc_start: 0.9541 (m) cc_final: 0.9087 (p) REVERT: I 816 ILE cc_start: 0.9363 (mt) cc_final: 0.9161 (mt) REVERT: I 817 LEU cc_start: 0.8575 (mm) cc_final: 0.7600 (mm) REVERT: I 831 ILE cc_start: 0.8899 (mm) cc_final: 0.8359 (mm) REVERT: I 833 ILE cc_start: 0.9441 (mt) cc_final: 0.9232 (mt) REVERT: I 930 ASP cc_start: 0.9680 (t70) cc_final: 0.9027 (t70) REVERT: I 1053 TYR cc_start: 0.8707 (m-80) cc_final: 0.7983 (m-80) REVERT: I 1056 VAL cc_start: 0.8721 (m) cc_final: 0.8073 (m) REVERT: I 1061 GLN cc_start: 0.9464 (tt0) cc_final: 0.9003 (tm-30) REVERT: I 1085 MET cc_start: 0.8438 (mmt) cc_final: 0.7690 (mmt) REVERT: I 1106 ARG cc_start: 0.9551 (mmm-85) cc_final: 0.9212 (mmt180) REVERT: I 1107 MET cc_start: 0.9141 (mmm) cc_final: 0.8220 (tpp) REVERT: I 1119 MET cc_start: 0.9292 (mmm) cc_final: 0.9048 (mmm) REVERT: I 1122 LYS cc_start: 0.9638 (tptm) cc_final: 0.9203 (tppt) REVERT: I 1126 ASP cc_start: 0.9432 (m-30) cc_final: 0.8641 (m-30) REVERT: I 1216 ARG cc_start: 0.9164 (mtp-110) cc_final: 0.8321 (mmm-85) REVERT: I 1234 LYS cc_start: 0.9495 (tppp) cc_final: 0.9000 (tppp) REVERT: I 1237 HIS cc_start: 0.8969 (m-70) cc_final: 0.8624 (m90) REVERT: I 1264 GLN cc_start: 0.9413 (tp-100) cc_final: 0.9050 (tm-30) REVERT: I 1270 PHE cc_start: 0.8968 (t80) cc_final: 0.8236 (t80) REVERT: I 1274 GLU cc_start: 0.9038 (mp0) cc_final: 0.8755 (mp0) REVERT: I 1290 MET cc_start: 0.9508 (tmm) cc_final: 0.9052 (tmm) REVERT: I 1304 MET cc_start: 0.9690 (tmm) cc_final: 0.9308 (ptp) REVERT: I 1319 MET cc_start: 0.8149 (tpt) cc_final: 0.7123 (tpt) REVERT: I 1321 GLU cc_start: 0.9051 (pm20) cc_final: 0.8831 (pm20) REVERT: I 1329 GLU cc_start: 0.9886 (mt-10) cc_final: 0.9583 (mt-10) REVERT: J 28 ASP cc_start: 0.9866 (t0) cc_final: 0.9605 (p0) REVERT: J 30 ILE cc_start: 0.9359 (mt) cc_final: 0.8908 (mt) REVERT: J 102 MET cc_start: 0.6837 (tpt) cc_final: 0.6262 (tpt) REVERT: J 207 GLU cc_start: 0.9436 (mm-30) cc_final: 0.9159 (mm-30) REVERT: J 242 LEU cc_start: 0.9511 (tt) cc_final: 0.9258 (tt) REVERT: J 325 LYS cc_start: 0.8018 (pttp) cc_final: 0.7578 (pttp) REVERT: J 329 ASP cc_start: 0.9625 (m-30) cc_final: 0.9190 (t0) REVERT: J 361 LEU cc_start: 0.9127 (mt) cc_final: 0.8732 (pp) REVERT: J 374 LEU cc_start: 0.9423 (mt) cc_final: 0.9208 (mt) REVERT: J 409 TRP cc_start: 0.9180 (m100) cc_final: 0.8291 (m100) REVERT: J 423 LEU cc_start: 0.9809 (mp) cc_final: 0.9580 (mp) REVERT: J 437 PHE cc_start: 0.9598 (m-80) cc_final: 0.8640 (m-80) REVERT: J 445 LYS cc_start: 0.8799 (mmpt) cc_final: 0.8597 (mmtm) REVERT: J 454 CYS cc_start: 0.9268 (m) cc_final: 0.9012 (m) REVERT: J 513 MET cc_start: 0.9332 (mmp) cc_final: 0.9102 (mmp) REVERT: J 603 LYS cc_start: 0.9284 (pttt) cc_final: 0.9014 (ptpp) REVERT: J 627 THR cc_start: 0.9868 (t) cc_final: 0.9455 (t) REVERT: J 631 TYR cc_start: 0.9593 (m-80) cc_final: 0.9367 (m-80) REVERT: J 644 MET cc_start: 0.9594 (mpp) cc_final: 0.9370 (mpp) REVERT: J 645 VAL cc_start: 0.8617 (p) cc_final: 0.8237 (m) REVERT: J 697 MET cc_start: 0.9658 (ppp) cc_final: 0.9418 (ppp) REVERT: J 743 MET cc_start: 0.9452 (ptm) cc_final: 0.9080 (ptm) REVERT: J 744 ARG cc_start: 0.8729 (ptm-80) cc_final: 0.8379 (ptm-80) REVERT: J 763 PHE cc_start: 0.9460 (m-80) cc_final: 0.8075 (m-80) REVERT: J 764 ARG cc_start: 0.9108 (ttt-90) cc_final: 0.8819 (ttt-90) REVERT: J 772 TYR cc_start: 0.9218 (t80) cc_final: 0.8913 (t80) REVERT: J 822 MET cc_start: 0.8958 (tpt) cc_final: 0.8587 (tpp) REVERT: J 1040 MET cc_start: 0.7869 (mmp) cc_final: 0.7150 (mmm) REVERT: J 1194 ARG cc_start: 0.7573 (mtt180) cc_final: 0.7367 (mtt180) REVERT: J 1215 GLU cc_start: 0.9535 (mp0) cc_final: 0.9254 (mm-30) REVERT: J 1238 GLN cc_start: 0.9783 (mm110) cc_final: 0.9246 (tp40) REVERT: J 1242 ARG cc_start: 0.9043 (ttp80) cc_final: 0.8545 (ptp-170) REVERT: J 1254 GLU cc_start: 0.9487 (mt-10) cc_final: 0.9273 (mt-10) REVERT: J 1334 GLU cc_start: 0.9366 (tm-30) cc_final: 0.9058 (tm-30) outliers start: 4 outliers final: 0 residues processed: 769 average time/residue: 0.5455 time to fit residues: 645.6406 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 : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 71 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 40 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 289 optimal weight: 0.0070 overall best weight: 1.0604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN I 69 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** ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1175 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 435 GLN ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 667 GLN J 700 ASN ** J 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 907 HIS J 954 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.109510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.070439 restraints weight = 88872.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.073613 restraints weight = 55597.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.076031 restraints weight = 39431.978| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25706 Z= 0.133 Angle : 0.662 10.786 34937 Z= 0.343 Chirality : 0.045 0.287 3992 Planarity : 0.005 0.102 4386 Dihedral : 14.442 66.570 3992 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.83 % Favored : 94.14 % Rotamer: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 3071 helix: 0.49 (0.15), residues: 1094 sheet: -1.13 (0.27), residues: 356 loop : -1.62 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 997 HIS 0.005 0.001 HIS I 551 PHE 0.020 0.002 PHE J1145 TYR 0.027 0.002 TYR J 631 ARG 0.023 0.001 ARG J 634 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 1057) hydrogen bonds : angle 5.38050 ( 2933) metal coordination : bond 0.00856 ( 8) metal coordination : angle 5.80913 ( 12) covalent geometry : bond 0.00297 (25698) covalent geometry : angle 0.65314 (34925) *********************** 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 780 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 777 time to evaluate : 2.767 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: G 35 PHE cc_start: 0.9578 (m-80) cc_final: 0.9338 (m-80) REVERT: G 80 GLU cc_start: 0.9703 (tp30) cc_final: 0.9410 (tp30) REVERT: G 84 ASN cc_start: 0.9259 (m-40) cc_final: 0.8631 (m-40) REVERT: G 131 CYS cc_start: 0.9460 (p) cc_final: 0.9174 (t) REVERT: G 133 LEU cc_start: 0.9343 (mm) cc_final: 0.8634 (tp) REVERT: G 205 MET cc_start: 0.9654 (ppp) cc_final: 0.9428 (ppp) REVERT: G 227 GLN cc_start: 0.9822 (mt0) cc_final: 0.9534 (mt0) REVERT: H 46 ILE cc_start: 0.9753 (tp) cc_final: 0.9550 (tp) REVERT: H 83 LEU cc_start: 0.9552 (pp) cc_final: 0.9089 (mm) REVERT: H 95 LYS cc_start: 0.9461 (mppt) cc_final: 0.9231 (pttm) REVERT: H 141 SER cc_start: 0.9646 (t) cc_final: 0.9341 (m) REVERT: H 142 MET cc_start: 0.9611 (ptm) cc_final: 0.9333 (ptm) REVERT: H 185 TYR cc_start: 0.7841 (p90) cc_final: 0.7616 (p90) REVERT: H 193 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8722 (tp30) REVERT: H 194 GLN cc_start: 0.9448 (tp-100) cc_final: 0.9243 (tp40) REVERT: I 6 THR cc_start: 0.9281 (p) cc_final: 0.8731 (p) REVERT: I 9 LYS cc_start: 0.8996 (mttm) cc_final: 0.8711 (mttm) REVERT: I 32 LEU cc_start: 0.9499 (mt) cc_final: 0.9070 (pp) REVERT: I 53 PHE cc_start: 0.8529 (m-80) cc_final: 0.8250 (m-10) REVERT: I 74 ARG cc_start: 0.9554 (tmt170) cc_final: 0.9271 (ptm-80) REVERT: I 92 TYR cc_start: 0.9387 (t80) cc_final: 0.9047 (t80) REVERT: I 124 MET cc_start: 0.9666 (tpp) cc_final: 0.9276 (tpp) REVERT: I 213 LEU cc_start: 0.9404 (mp) cc_final: 0.8745 (mp) REVERT: I 215 TYR cc_start: 0.8671 (m-10) cc_final: 0.8353 (m-80) REVERT: I 277 LEU cc_start: 0.9682 (mt) cc_final: 0.9226 (pp) REVERT: I 291 TYR cc_start: 0.9564 (t80) cc_final: 0.9309 (t80) REVERT: I 342 ASP cc_start: 0.9050 (m-30) cc_final: 0.8725 (m-30) REVERT: I 405 PHE cc_start: 0.9582 (t80) cc_final: 0.9157 (t80) REVERT: I 419 ILE cc_start: 0.9357 (pt) cc_final: 0.9097 (pt) REVERT: I 430 LYS cc_start: 0.9487 (mmtm) cc_final: 0.9268 (mmmt) REVERT: I 591 TYR cc_start: 0.9476 (m-80) cc_final: 0.8894 (m-80) REVERT: I 606 LEU cc_start: 0.9283 (mp) cc_final: 0.8669 (mp) REVERT: I 633 LEU cc_start: 0.9593 (pt) cc_final: 0.9299 (mm) REVERT: I 668 ILE cc_start: 0.9545 (mm) cc_final: 0.9263 (mm) REVERT: I 671 LEU cc_start: 0.9795 (tp) cc_final: 0.9507 (tp) REVERT: I 672 GLU cc_start: 0.9446 (pm20) cc_final: 0.8748 (pm20) REVERT: I 681 MET cc_start: 0.9210 (mtp) cc_final: 0.8693 (mtt) REVERT: I 685 MET cc_start: 0.9223 (mtm) cc_final: 0.8945 (mtm) REVERT: I 741 MET cc_start: 0.9596 (mmt) cc_final: 0.9334 (mmm) REVERT: I 748 ILE cc_start: 0.8687 (pt) cc_final: 0.7865 (pt) REVERT: I 762 ASN cc_start: 0.9106 (m-40) cc_final: 0.8888 (t0) REVERT: I 790 ASP cc_start: 0.9475 (t0) cc_final: 0.8984 (p0) REVERT: I 799 ASN cc_start: 0.8873 (t0) cc_final: 0.8600 (t0) REVERT: I 805 MET cc_start: 0.9282 (ppp) cc_final: 0.9002 (ppp) REVERT: I 817 LEU cc_start: 0.8670 (mm) cc_final: 0.7873 (mm) REVERT: I 827 ARG cc_start: 0.9034 (ptm160) cc_final: 0.8540 (ptm160) REVERT: I 831 ILE cc_start: 0.8751 (mm) cc_final: 0.8329 (mm) REVERT: I 833 ILE cc_start: 0.9545 (mt) cc_final: 0.9232 (tp) REVERT: I 930 ASP cc_start: 0.9687 (t70) cc_final: 0.8976 (t0) REVERT: I 1053 TYR cc_start: 0.8708 (m-80) cc_final: 0.7968 (m-80) REVERT: I 1056 VAL cc_start: 0.8724 (m) cc_final: 0.8010 (m) REVERT: I 1061 GLN cc_start: 0.9450 (tt0) cc_final: 0.9048 (tm-30) REVERT: I 1085 MET cc_start: 0.8568 (mmt) cc_final: 0.7729 (mmt) REVERT: I 1095 ASP cc_start: 0.9637 (m-30) cc_final: 0.9155 (t70) REVERT: I 1106 ARG cc_start: 0.9538 (mmm-85) cc_final: 0.9222 (mmt180) REVERT: I 1107 MET cc_start: 0.9100 (mmm) cc_final: 0.8269 (tpp) REVERT: I 1119 MET cc_start: 0.9167 (mmm) cc_final: 0.8921 (mmm) REVERT: I 1122 LYS cc_start: 0.9615 (tptm) cc_final: 0.9163 (tppt) REVERT: I 1126 ASP cc_start: 0.9386 (m-30) cc_final: 0.8597 (m-30) REVERT: I 1132 LEU cc_start: 0.9476 (tp) cc_final: 0.9098 (tp) REVERT: I 1226 THR cc_start: 0.9417 (m) cc_final: 0.9175 (p) REVERT: I 1230 MET cc_start: 0.9441 (tpt) cc_final: 0.9183 (tmm) REVERT: I 1234 LYS cc_start: 0.9395 (tppp) cc_final: 0.8966 (tppp) REVERT: I 1237 HIS cc_start: 0.8746 (m-70) cc_final: 0.8434 (m90) REVERT: I 1265 PHE cc_start: 0.9162 (t80) cc_final: 0.8844 (t80) REVERT: I 1270 PHE cc_start: 0.9052 (t80) cc_final: 0.8313 (t80) REVERT: I 1290 MET cc_start: 0.9431 (tmm) cc_final: 0.8972 (tmm) REVERT: I 1304 MET cc_start: 0.9700 (tmm) cc_final: 0.9314 (ptp) REVERT: I 1319 MET cc_start: 0.8247 (tpt) cc_final: 0.7140 (tpt) REVERT: I 1329 GLU cc_start: 0.9893 (mt-10) cc_final: 0.9567 (mt-10) REVERT: J 28 ASP cc_start: 0.9870 (t0) cc_final: 0.9580 (p0) REVERT: J 61 ILE cc_start: 0.8835 (tp) cc_final: 0.8514 (pt) REVERT: J 102 MET cc_start: 0.7114 (tpt) cc_final: 0.4993 (ttt) REVERT: J 180 MET cc_start: 0.9024 (ttt) cc_final: 0.8793 (ttt) REVERT: J 207 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9181 (mm-30) REVERT: J 220 ARG cc_start: 0.9691 (mtp-110) cc_final: 0.9459 (ptm160) REVERT: J 268 LEU cc_start: 0.9382 (mt) cc_final: 0.9135 (mt) REVERT: J 325 LYS cc_start: 0.7790 (pttm) cc_final: 0.7528 (pttp) REVERT: J 335 GLN cc_start: 0.9013 (pp30) cc_final: 0.8704 (pp30) REVERT: J 361 LEU cc_start: 0.9176 (mt) cc_final: 0.8649 (pp) REVERT: J 365 GLN cc_start: 0.9722 (pt0) cc_final: 0.9443 (pt0) REVERT: J 409 TRP cc_start: 0.9067 (m100) cc_final: 0.8211 (m100) REVERT: J 437 PHE cc_start: 0.9627 (m-80) cc_final: 0.9027 (m-80) REVERT: J 454 CYS cc_start: 0.9265 (m) cc_final: 0.9022 (m) REVERT: J 484 MET cc_start: 0.8950 (mpp) cc_final: 0.8749 (mpp) REVERT: J 512 TYR cc_start: 0.9269 (t80) cc_final: 0.9007 (t80) REVERT: J 526 VAL cc_start: 0.8963 (p) cc_final: 0.8693 (p) REVERT: J 587 LEU cc_start: 0.9153 (mm) cc_final: 0.8750 (mm) REVERT: J 603 LYS cc_start: 0.9297 (pttt) cc_final: 0.9033 (ptpp) REVERT: J 604 MET cc_start: 0.9734 (ttm) cc_final: 0.9486 (mmt) REVERT: J 627 THR cc_start: 0.9856 (t) cc_final: 0.9431 (t) REVERT: J 645 VAL cc_start: 0.8621 (p) cc_final: 0.8184 (m) REVERT: J 697 MET cc_start: 0.9653 (ppp) cc_final: 0.9426 (ppp) REVERT: J 739 GLN cc_start: 0.9105 (mt0) cc_final: 0.8710 (mt0) REVERT: J 763 PHE cc_start: 0.9440 (m-80) cc_final: 0.8061 (m-80) REVERT: J 777 HIS cc_start: 0.8966 (m-70) cc_final: 0.7741 (m-70) REVERT: J 792 ASN cc_start: 0.9386 (m110) cc_final: 0.9175 (m-40) REVERT: J 822 MET cc_start: 0.8903 (tpt) cc_final: 0.8500 (tpp) REVERT: J 932 MET cc_start: 0.5527 (tpp) cc_final: 0.5197 (tpp) REVERT: J 1040 MET cc_start: 0.7856 (mmp) cc_final: 0.7143 (mmm) REVERT: J 1194 ARG cc_start: 0.7477 (mtt180) cc_final: 0.7263 (mtt180) REVERT: J 1215 GLU cc_start: 0.9537 (mp0) cc_final: 0.9262 (mm-30) REVERT: J 1242 ARG cc_start: 0.9037 (ttp80) cc_final: 0.8781 (ptp-170) REVERT: J 1260 MET cc_start: 0.9466 (tmm) cc_final: 0.9082 (tmm) REVERT: J 1334 GLU cc_start: 0.9348 (tm-30) cc_final: 0.9021 (tm-30) outliers start: 3 outliers final: 1 residues processed: 779 average time/residue: 0.4359 time to fit residues: 514.5201 Evaluate side-chains 662 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 661 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 132 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 284 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS H 194 GLN I 60 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 GLN I 148 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 832 HIS ** 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 341 ASN 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 700 ASN ** J 771 GLN ** 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 = 0.3658 r_free = 0.3658 target = 0.106230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.067530 restraints weight = 91828.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.070562 restraints weight = 57527.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.072879 restraints weight = 41009.723| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25706 Z= 0.182 Angle : 0.682 9.417 34937 Z= 0.360 Chirality : 0.045 0.231 3992 Planarity : 0.005 0.070 4386 Dihedral : 14.449 65.814 3992 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.74 % Favored : 93.23 % Rotamer: Outliers : 0.04 % Allowed : 2.25 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 3071 helix: 0.33 (0.15), residues: 1109 sheet: -1.32 (0.26), residues: 362 loop : -1.66 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 183 HIS 0.009 0.001 HIS J 907 PHE 0.026 0.002 PHE J1319 TYR 0.019 0.002 TYR J 537 ARG 0.012 0.001 ARG J 634 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 1057) hydrogen bonds : angle 5.47314 ( 2933) metal coordination : bond 0.01125 ( 8) metal coordination : angle 5.14117 ( 12) covalent geometry : bond 0.00386 (25698) covalent geometry : angle 0.67567 (34925) *********************** 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 743 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 742 time to evaluate : 2.702 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: G 35 PHE cc_start: 0.9592 (m-80) cc_final: 0.9384 (m-80) REVERT: G 84 ASN cc_start: 0.9269 (m-40) cc_final: 0.8447 (t0) REVERT: G 131 CYS cc_start: 0.9519 (p) cc_final: 0.9297 (t) REVERT: G 195 ARG cc_start: 0.9517 (tmt-80) cc_final: 0.9285 (tmt170) REVERT: G 227 GLN cc_start: 0.9833 (mt0) cc_final: 0.9557 (mp10) REVERT: H 16 ILE cc_start: 0.8081 (pt) cc_final: 0.7582 (mp) REVERT: H 37 HIS cc_start: 0.9601 (m-70) cc_final: 0.8835 (m90) REVERT: H 41 ASN cc_start: 0.9440 (t0) cc_final: 0.9074 (m-40) REVERT: H 46 ILE cc_start: 0.9753 (tp) cc_final: 0.9525 (tp) REVERT: H 83 LEU cc_start: 0.9546 (pp) cc_final: 0.9086 (mm) REVERT: H 95 LYS cc_start: 0.9413 (mppt) cc_final: 0.9170 (pttm) REVERT: H 133 LEU cc_start: 0.8986 (tp) cc_final: 0.8765 (tp) REVERT: H 141 SER cc_start: 0.9631 (t) cc_final: 0.9136 (m) REVERT: H 142 MET cc_start: 0.9618 (ptm) cc_final: 0.9004 (tmm) REVERT: H 193 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8452 (tp30) REVERT: H 194 GLN cc_start: 0.9440 (tp40) cc_final: 0.9220 (tp40) REVERT: I 32 LEU cc_start: 0.9495 (mt) cc_final: 0.9203 (pp) REVERT: I 74 ARG cc_start: 0.9588 (tmt170) cc_final: 0.9325 (ptm-80) REVERT: I 92 TYR cc_start: 0.9432 (t80) cc_final: 0.9023 (t80) REVERT: I 100 LEU cc_start: 0.9711 (mt) cc_final: 0.9329 (pp) REVERT: I 193 ASN cc_start: 0.9490 (m-40) cc_final: 0.9189 (m-40) REVERT: I 213 LEU cc_start: 0.9409 (mp) cc_final: 0.8781 (mp) REVERT: I 215 TYR cc_start: 0.8730 (m-10) cc_final: 0.8207 (m-80) REVERT: I 235 ASN cc_start: 0.9441 (t0) cc_final: 0.9130 (p0) REVERT: I 240 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8640 (tp30) REVERT: I 277 LEU cc_start: 0.9699 (mt) cc_final: 0.9235 (pp) REVERT: I 291 TYR cc_start: 0.9553 (t80) cc_final: 0.9325 (t80) REVERT: I 342 ASP cc_start: 0.9065 (m-30) cc_final: 0.8714 (m-30) REVERT: I 405 PHE cc_start: 0.9626 (t80) cc_final: 0.9290 (t80) REVERT: I 419 ILE cc_start: 0.9366 (pt) cc_final: 0.9090 (pt) REVERT: I 446 ASP cc_start: 0.9234 (p0) cc_final: 0.8893 (p0) REVERT: I 452 ARG cc_start: 0.9401 (ttt90) cc_final: 0.8996 (mmm-85) REVERT: I 464 PHE cc_start: 0.9767 (t80) cc_final: 0.9399 (t80) REVERT: I 606 LEU cc_start: 0.9340 (mp) cc_final: 0.9105 (mp) REVERT: I 671 LEU cc_start: 0.9792 (tp) cc_final: 0.9538 (tp) REVERT: I 672 GLU cc_start: 0.9500 (pm20) cc_final: 0.8712 (pm20) REVERT: I 681 MET cc_start: 0.9177 (mtp) cc_final: 0.8691 (mtt) REVERT: I 685 MET cc_start: 0.9264 (mtm) cc_final: 0.8970 (mtm) REVERT: I 688 GLN cc_start: 0.9292 (mp10) cc_final: 0.9032 (mp10) REVERT: I 741 MET cc_start: 0.9567 (mmt) cc_final: 0.9301 (mmm) REVERT: I 748 ILE cc_start: 0.8160 (pt) cc_final: 0.7736 (pt) REVERT: I 805 MET cc_start: 0.9321 (ppp) cc_final: 0.9032 (ppp) REVERT: I 812 PHE cc_start: 0.9123 (t80) cc_final: 0.8763 (t80) REVERT: I 817 LEU cc_start: 0.8673 (mm) cc_final: 0.7926 (mm) REVERT: I 831 ILE cc_start: 0.8847 (mm) cc_final: 0.8371 (mm) REVERT: I 833 ILE cc_start: 0.9469 (mt) cc_final: 0.9210 (mt) REVERT: I 882 ILE cc_start: 0.9299 (mp) cc_final: 0.9087 (mp) REVERT: I 930 ASP cc_start: 0.9652 (t70) cc_final: 0.8957 (t0) REVERT: I 1053 TYR cc_start: 0.8688 (m-80) cc_final: 0.7977 (m-80) REVERT: I 1056 VAL cc_start: 0.8666 (m) cc_final: 0.7999 (m) REVERT: I 1085 MET cc_start: 0.8422 (mmt) cc_final: 0.7684 (mmt) REVERT: I 1095 ASP cc_start: 0.9674 (m-30) cc_final: 0.9222 (t70) REVERT: I 1106 ARG cc_start: 0.9545 (mmm-85) cc_final: 0.9235 (mmt180) REVERT: I 1107 MET cc_start: 0.9141 (mmm) cc_final: 0.7939 (tpp) REVERT: I 1119 MET cc_start: 0.9219 (mmm) cc_final: 0.8988 (mmm) REVERT: I 1122 LYS cc_start: 0.9631 (tptm) cc_final: 0.9186 (tppt) REVERT: I 1126 ASP cc_start: 0.9390 (m-30) cc_final: 0.8597 (m-30) REVERT: I 1216 ARG cc_start: 0.9329 (mtp-110) cc_final: 0.8551 (mmm-85) REVERT: I 1237 HIS cc_start: 0.8825 (m90) cc_final: 0.8553 (m90) REVERT: I 1242 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7751 (mmtt) REVERT: I 1265 PHE cc_start: 0.9195 (t80) cc_final: 0.8874 (t80) REVERT: I 1270 PHE cc_start: 0.9046 (t80) cc_final: 0.8113 (t80) REVERT: I 1273 MET cc_start: 0.8170 (ptt) cc_final: 0.7957 (ptt) REVERT: I 1290 MET cc_start: 0.9430 (tmm) cc_final: 0.9035 (tmm) REVERT: I 1304 MET cc_start: 0.9702 (tmm) cc_final: 0.9335 (ptp) REVERT: I 1319 MET cc_start: 0.8119 (tpt) cc_final: 0.7092 (tpt) REVERT: I 1321 GLU cc_start: 0.8889 (pm20) cc_final: 0.8675 (pm20) REVERT: I 1329 GLU cc_start: 0.9891 (mt-10) cc_final: 0.9565 (mt-10) REVERT: J 28 ASP cc_start: 0.9874 (t0) cc_final: 0.9588 (p0) REVERT: J 61 ILE cc_start: 0.9015 (tp) cc_final: 0.8782 (pt) REVERT: J 102 MET cc_start: 0.7203 (tpt) cc_final: 0.4881 (ttt) REVERT: J 180 MET cc_start: 0.9048 (ttt) cc_final: 0.8754 (ttt) REVERT: J 207 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9160 (mm-30) REVERT: J 220 ARG cc_start: 0.9644 (mtp-110) cc_final: 0.9361 (ptm160) REVERT: J 325 LYS cc_start: 0.7967 (pttm) cc_final: 0.7357 (pttp) REVERT: J 329 ASP cc_start: 0.9637 (m-30) cc_final: 0.9330 (t0) REVERT: J 332 LYS cc_start: 0.9148 (mmtt) cc_final: 0.8917 (mmtt) REVERT: J 361 LEU cc_start: 0.9206 (mt) cc_final: 0.8803 (pp) REVERT: J 365 GLN cc_start: 0.9708 (pt0) cc_final: 0.9479 (pt0) REVERT: J 409 TRP cc_start: 0.8970 (m100) cc_final: 0.8001 (m100) REVERT: J 437 PHE cc_start: 0.9647 (m-80) cc_final: 0.9077 (m-80) REVERT: J 454 CYS cc_start: 0.9302 (m) cc_final: 0.8918 (m) REVERT: J 512 TYR cc_start: 0.9386 (t80) cc_final: 0.9085 (t80) REVERT: J 587 LEU cc_start: 0.9192 (mm) cc_final: 0.8817 (mm) REVERT: J 603 LYS cc_start: 0.9277 (pttt) cc_final: 0.8911 (ptpp) REVERT: J 627 THR cc_start: 0.9847 (t) cc_final: 0.9497 (t) REVERT: J 629 PHE cc_start: 0.9434 (m-80) cc_final: 0.9009 (m-80) REVERT: J 631 TYR cc_start: 0.9573 (m-80) cc_final: 0.9259 (m-80) REVERT: J 645 VAL cc_start: 0.8502 (p) cc_final: 0.8164 (m) REVERT: J 697 MET cc_start: 0.9682 (ppp) cc_final: 0.9431 (ppp) REVERT: J 743 MET cc_start: 0.9275 (ptm) cc_final: 0.9019 (ptm) REVERT: J 792 ASN cc_start: 0.9393 (m110) cc_final: 0.9181 (m110) REVERT: J 821 MET cc_start: 0.9402 (mmp) cc_final: 0.9041 (tpp) REVERT: J 823 THR cc_start: 0.9619 (p) cc_final: 0.9337 (p) REVERT: J 932 MET cc_start: 0.5615 (tpp) cc_final: 0.5341 (tpp) REVERT: J 1040 MET cc_start: 0.7965 (mmp) cc_final: 0.7283 (mmm) REVERT: J 1215 GLU cc_start: 0.9560 (mp0) cc_final: 0.9246 (mm-30) REVERT: J 1238 GLN cc_start: 0.9641 (tp-100) cc_final: 0.9086 (tp-100) REVERT: J 1254 GLU cc_start: 0.9513 (mt-10) cc_final: 0.9312 (mt-10) REVERT: J 1334 GLU cc_start: 0.9447 (tm-30) cc_final: 0.9183 (tm-30) outliers start: 1 outliers final: 0 residues processed: 742 average time/residue: 0.3962 time to fit residues: 447.7556 Evaluate side-chains 636 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 636 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 126 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 chunk 132 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 30.0000 chunk 156 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN ** I 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1175 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN J 365 GLN ** J 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 ASN J 700 ASN ** J 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 954 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.103090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.063516 restraints weight = 89060.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.066664 restraints weight = 55687.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069107 restraints weight = 39577.310| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25706 Z= 0.136 Angle : 0.690 9.214 34937 Z= 0.360 Chirality : 0.046 0.219 3992 Planarity : 0.005 0.068 4386 Dihedral : 14.311 63.945 3992 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.94 % Rotamer: Outliers : 0.04 % Allowed : 1.56 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.15), residues: 3071 helix: 0.40 (0.15), residues: 1094 sheet: -1.21 (0.28), residues: 352 loop : -1.59 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 183 HIS 0.019 0.001 HIS J 419 PHE 0.029 0.002 PHE J1274 TYR 0.050 0.002 TYR I 5 ARG 0.017 0.001 ARG J1284 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 1057) hydrogen bonds : angle 5.32639 ( 2933) metal coordination : bond 0.00745 ( 8) metal coordination : angle 4.06236 ( 12) covalent geometry : bond 0.00302 (25698) covalent geometry : angle 0.68559 (34925) *********************** 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 755 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 754 time to evaluate : 2.936 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: G 35 PHE cc_start: 0.9582 (m-80) cc_final: 0.9369 (m-80) REVERT: G 84 ASN cc_start: 0.9255 (m-40) cc_final: 0.8404 (t0) REVERT: G 130 ILE cc_start: 0.9571 (mp) cc_final: 0.9187 (mp) REVERT: G 141 SER cc_start: 0.9354 (t) cc_final: 0.8931 (t) REVERT: G 142 MET cc_start: 0.9530 (mtt) cc_final: 0.9315 (mtt) REVERT: G 143 ARG cc_start: 0.9196 (mpp-170) cc_final: 0.8739 (mmp80) REVERT: G 205 MET cc_start: 0.9605 (ppp) cc_final: 0.9338 (ppp) REVERT: H 16 ILE cc_start: 0.8022 (pt) cc_final: 0.7607 (mp) REVERT: H 37 HIS cc_start: 0.9496 (m-70) cc_final: 0.8738 (m90) REVERT: H 46 ILE cc_start: 0.9713 (tp) cc_final: 0.9499 (tp) REVERT: H 83 LEU cc_start: 0.9518 (pp) cc_final: 0.9058 (mm) REVERT: H 95 LYS cc_start: 0.9462 (mppt) cc_final: 0.9250 (pttm) REVERT: H 141 SER cc_start: 0.9518 (t) cc_final: 0.9068 (m) REVERT: H 142 MET cc_start: 0.9582 (ptm) cc_final: 0.8990 (tmm) REVERT: H 185 TYR cc_start: 0.7509 (p90) cc_final: 0.6821 (p90) REVERT: H 193 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8474 (tp30) REVERT: H 194 GLN cc_start: 0.9398 (tp40) cc_final: 0.9156 (tp40) REVERT: I 5 TYR cc_start: 0.9094 (t80) cc_final: 0.8847 (t80) REVERT: I 39 ILE cc_start: 0.9261 (pt) cc_final: 0.8695 (pt) REVERT: I 74 ARG cc_start: 0.9607 (tmt170) cc_final: 0.9335 (ptm-80) REVERT: I 80 PHE cc_start: 0.9149 (m-80) cc_final: 0.8813 (m-10) REVERT: I 92 TYR cc_start: 0.9380 (t80) cc_final: 0.9051 (t80) REVERT: I 100 LEU cc_start: 0.9674 (mt) cc_final: 0.9282 (pp) REVERT: I 172 TYR cc_start: 0.7991 (m-80) cc_final: 0.7716 (m-80) REVERT: I 192 ASP cc_start: 0.9844 (m-30) cc_final: 0.9570 (m-30) REVERT: I 193 ASN cc_start: 0.9557 (m-40) cc_final: 0.9338 (t0) REVERT: I 197 ARG cc_start: 0.9127 (ttt180) cc_final: 0.8731 (tmm-80) REVERT: I 213 LEU cc_start: 0.9430 (mp) cc_final: 0.8779 (mp) REVERT: I 215 TYR cc_start: 0.8719 (m-10) cc_final: 0.8371 (m-80) REVERT: I 224 PHE cc_start: 0.9712 (m-80) cc_final: 0.9487 (m-80) REVERT: I 240 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8611 (tp30) REVERT: I 291 TYR cc_start: 0.9510 (t80) cc_final: 0.9277 (t80) REVERT: I 342 ASP cc_start: 0.9010 (m-30) cc_final: 0.8665 (m-30) REVERT: I 405 PHE cc_start: 0.9562 (t80) cc_final: 0.9130 (t80) REVERT: I 419 ILE cc_start: 0.9388 (pt) cc_final: 0.9114 (pt) REVERT: I 430 LYS cc_start: 0.9515 (mptt) cc_final: 0.9308 (mmtt) REVERT: I 446 ASP cc_start: 0.9259 (p0) cc_final: 0.8938 (p0) REVERT: I 452 ARG cc_start: 0.9375 (ttt90) cc_final: 0.9020 (mmm-85) REVERT: I 464 PHE cc_start: 0.9748 (t80) cc_final: 0.9458 (t80) REVERT: I 578 TYR cc_start: 0.8728 (m-80) cc_final: 0.8005 (m-80) REVERT: I 591 TYR cc_start: 0.9496 (m-80) cc_final: 0.8732 (m-80) REVERT: I 606 LEU cc_start: 0.9333 (mp) cc_final: 0.8730 (mp) REVERT: I 633 LEU cc_start: 0.9592 (pt) cc_final: 0.9293 (mm) REVERT: I 671 LEU cc_start: 0.9780 (tp) cc_final: 0.9458 (tp) REVERT: I 672 GLU cc_start: 0.9483 (pm20) cc_final: 0.8819 (pm20) REVERT: I 681 MET cc_start: 0.9197 (mtp) cc_final: 0.8704 (mtt) REVERT: I 685 MET cc_start: 0.9111 (mtm) cc_final: 0.8876 (mtm) REVERT: I 741 MET cc_start: 0.9528 (mmt) cc_final: 0.9266 (mmm) REVERT: I 748 ILE cc_start: 0.7985 (pt) cc_final: 0.7531 (pt) REVERT: I 790 ASP cc_start: 0.9470 (t0) cc_final: 0.8984 (p0) REVERT: I 799 ASN cc_start: 0.8635 (t0) cc_final: 0.8365 (m-40) REVERT: I 805 MET cc_start: 0.9372 (ppp) cc_final: 0.9141 (ppp) REVERT: I 812 PHE cc_start: 0.8970 (t80) cc_final: 0.8689 (t80) REVERT: I 816 ILE cc_start: 0.9358 (mt) cc_final: 0.8696 (mt) REVERT: I 817 LEU cc_start: 0.8785 (mm) cc_final: 0.7933 (mm) REVERT: I 827 ARG cc_start: 0.8968 (ptm160) cc_final: 0.8571 (ptm160) REVERT: I 831 ILE cc_start: 0.8761 (mm) cc_final: 0.8307 (mm) REVERT: I 865 LEU cc_start: 0.7181 (mm) cc_final: 0.6760 (tp) REVERT: I 930 ASP cc_start: 0.9669 (t70) cc_final: 0.8961 (t70) REVERT: I 1053 TYR cc_start: 0.8713 (m-80) cc_final: 0.7933 (m-80) REVERT: I 1066 MET cc_start: 0.8939 (pmm) cc_final: 0.7962 (pmm) REVERT: I 1085 MET cc_start: 0.8538 (mmt) cc_final: 0.7920 (mmt) REVERT: I 1119 MET cc_start: 0.9101 (mmm) cc_final: 0.8852 (mmm) REVERT: I 1122 LYS cc_start: 0.9623 (tptm) cc_final: 0.9103 (tppt) REVERT: I 1126 ASP cc_start: 0.9354 (m-30) cc_final: 0.8593 (m-30) REVERT: I 1216 ARG cc_start: 0.9288 (mtp-110) cc_final: 0.8554 (mmm-85) REVERT: I 1226 THR cc_start: 0.9446 (m) cc_final: 0.9140 (p) REVERT: I 1230 MET cc_start: 0.9323 (tpt) cc_final: 0.9038 (tmm) REVERT: I 1265 PHE cc_start: 0.9155 (t80) cc_final: 0.8816 (t80) REVERT: I 1270 PHE cc_start: 0.9096 (t80) cc_final: 0.8391 (t80) REVERT: I 1290 MET cc_start: 0.9383 (tmm) cc_final: 0.8905 (tmm) REVERT: I 1304 MET cc_start: 0.9692 (tmm) cc_final: 0.9317 (ptp) REVERT: I 1319 MET cc_start: 0.8173 (tpt) cc_final: 0.7278 (tpt) REVERT: I 1329 GLU cc_start: 0.9886 (mt-10) cc_final: 0.9545 (mt-10) REVERT: J 28 ASP cc_start: 0.9864 (t0) cc_final: 0.9576 (p0) REVERT: J 38 VAL cc_start: 0.8508 (t) cc_final: 0.8152 (t) REVERT: J 61 ILE cc_start: 0.8763 (tp) cc_final: 0.8549 (pt) REVERT: J 102 MET cc_start: 0.7396 (tpt) cc_final: 0.5141 (ttt) REVERT: J 140 TYR cc_start: 0.9740 (m-80) cc_final: 0.9506 (m-80) REVERT: J 158 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8539 (tm-30) REVERT: J 180 MET cc_start: 0.8936 (ttt) cc_final: 0.8707 (ttt) REVERT: J 220 ARG cc_start: 0.9635 (mtp-110) cc_final: 0.9391 (ptm160) REVERT: J 325 LYS cc_start: 0.7915 (pttm) cc_final: 0.7187 (pttp) REVERT: J 329 ASP cc_start: 0.9743 (m-30) cc_final: 0.9310 (t0) REVERT: J 330 MET cc_start: 0.9149 (mmp) cc_final: 0.8877 (mmm) REVERT: J 361 LEU cc_start: 0.9184 (mt) cc_final: 0.8732 (pp) REVERT: J 365 GLN cc_start: 0.9724 (pt0) cc_final: 0.9481 (pt0) REVERT: J 385 LEU cc_start: 0.9407 (tt) cc_final: 0.9142 (pp) REVERT: J 409 TRP cc_start: 0.8916 (m100) cc_final: 0.8004 (m100) REVERT: J 434 ILE cc_start: 0.9501 (tp) cc_final: 0.9154 (tp) REVERT: J 437 PHE cc_start: 0.9567 (m-80) cc_final: 0.9015 (m-80) REVERT: J 454 CYS cc_start: 0.9259 (m) cc_final: 0.8883 (m) REVERT: J 484 MET cc_start: 0.8908 (mpp) cc_final: 0.8662 (mpp) REVERT: J 512 TYR cc_start: 0.9409 (t80) cc_final: 0.9122 (t80) REVERT: J 513 MET cc_start: 0.9074 (mmp) cc_final: 0.8858 (mmm) REVERT: J 526 VAL cc_start: 0.8910 (p) cc_final: 0.8664 (p) REVERT: J 534 GLU cc_start: 0.9445 (tm-30) cc_final: 0.9026 (mp0) REVERT: J 581 MET cc_start: 0.9539 (ppp) cc_final: 0.9223 (ppp) REVERT: J 587 LEU cc_start: 0.9144 (mm) cc_final: 0.8724 (mm) REVERT: J 603 LYS cc_start: 0.9243 (pttt) cc_final: 0.8976 (ptpp) REVERT: J 604 MET cc_start: 0.9727 (ttm) cc_final: 0.9411 (mmt) REVERT: J 627 THR cc_start: 0.9808 (t) cc_final: 0.9352 (t) REVERT: J 631 TYR cc_start: 0.9549 (m-80) cc_final: 0.9020 (m-80) REVERT: J 644 MET cc_start: 0.9385 (mpp) cc_final: 0.9180 (mpp) REVERT: J 645 VAL cc_start: 0.8519 (p) cc_final: 0.8119 (m) REVERT: J 697 MET cc_start: 0.9689 (ppp) cc_final: 0.9468 (ppp) REVERT: J 698 MET cc_start: 0.9664 (tpt) cc_final: 0.9463 (tpp) REVERT: J 764 ARG cc_start: 0.8990 (ttt-90) cc_final: 0.8554 (ttt-90) REVERT: J 765 GLU cc_start: 0.9279 (mp0) cc_final: 0.9042 (mp0) REVERT: J 767 LEU cc_start: 0.9068 (mp) cc_final: 0.8188 (tp) REVERT: J 770 LEU cc_start: 0.9801 (mt) cc_final: 0.9566 (mt) REVERT: J 915 ILE cc_start: 0.9527 (pt) cc_final: 0.9016 (mp) REVERT: J 1040 MET cc_start: 0.8007 (mmp) cc_final: 0.7373 (mmm) REVERT: J 1194 ARG cc_start: 0.7875 (mtt180) cc_final: 0.7477 (mtt180) REVERT: J 1238 GLN cc_start: 0.9618 (tp-100) cc_final: 0.9180 (tp-100) REVERT: J 1254 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9304 (mt-10) REVERT: J 1260 MET cc_start: 0.9542 (tmm) cc_final: 0.9177 (tmm) REVERT: J 1302 TYR cc_start: 0.9341 (p90) cc_final: 0.9043 (p90) REVERT: J 1307 LEU cc_start: 0.9013 (mm) cc_final: 0.8793 (mm) REVERT: J 1334 GLU cc_start: 0.9426 (tm-30) cc_final: 0.9175 (tm-30) REVERT: J 1373 ARG cc_start: 0.5928 (ptm160) cc_final: 0.5643 (ptm160) outliers start: 1 outliers final: 1 residues processed: 754 average time/residue: 0.3898 time to fit residues: 447.6077 Evaluate side-chains 658 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 657 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 220 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 235 optimal weight: 0.7980 chunk 53 optimal weight: 30.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 GLN I 148 GLN ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 658 GLN ** I 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 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** ** 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 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 ASN ** J 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 667 GLN J 700 ASN ** J 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 954 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.102499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.065001 restraints weight = 93812.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.067864 restraints weight = 59033.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.070041 restraints weight = 42310.362| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25706 Z= 0.229 Angle : 0.742 10.310 34937 Z= 0.393 Chirality : 0.046 0.256 3992 Planarity : 0.006 0.068 4386 Dihedral : 14.440 64.674 3992 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 25.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.03 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 3071 helix: 0.21 (0.15), residues: 1108 sheet: -1.40 (0.26), residues: 375 loop : -1.69 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP J 236 HIS 0.021 0.002 HIS J 419 PHE 0.031 0.003 PHE I 38 TYR 0.043 0.003 TYR J 631 ARG 0.015 0.001 ARG I 101 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 1057) hydrogen bonds : angle 5.63622 ( 2933) metal coordination : bond 0.01136 ( 8) metal coordination : angle 4.57509 ( 12) covalent geometry : bond 0.00467 (25698) covalent geometry : angle 0.73717 (34925) *********************** 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 741 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 741 time to evaluate : 3.057 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: G 76 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8732 (mt-10) REVERT: G 84 ASN cc_start: 0.9292 (m-40) cc_final: 0.8411 (t0) REVERT: G 130 ILE cc_start: 0.9671 (mp) cc_final: 0.9340 (mp) REVERT: G 131 CYS cc_start: 0.9342 (p) cc_final: 0.8749 (p) REVERT: G 227 GLN cc_start: 0.9834 (mt0) cc_final: 0.9514 (mt0) REVERT: H 16 ILE cc_start: 0.8166 (pt) cc_final: 0.7756 (mp) REVERT: H 37 HIS cc_start: 0.9598 (m-70) cc_final: 0.8762 (m90) REVERT: H 83 LEU cc_start: 0.9539 (pp) cc_final: 0.9083 (mm) REVERT: H 95 LYS cc_start: 0.9470 (mppt) cc_final: 0.9221 (pttm) REVERT: H 102 LEU cc_start: 0.9444 (tp) cc_final: 0.9143 (tp) REVERT: H 133 LEU cc_start: 0.9001 (tp) cc_final: 0.8793 (tp) REVERT: H 141 SER cc_start: 0.9471 (t) cc_final: 0.9262 (m) REVERT: H 193 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8506 (tp30) REVERT: I 5 TYR cc_start: 0.9191 (t80) cc_final: 0.8956 (t80) REVERT: I 81 ASP cc_start: 0.9355 (p0) cc_final: 0.8969 (p0) REVERT: I 92 TYR cc_start: 0.9489 (t80) cc_final: 0.8924 (t80) REVERT: I 100 LEU cc_start: 0.9665 (mt) cc_final: 0.9234 (pp) REVERT: I 172 TYR cc_start: 0.8065 (m-80) cc_final: 0.7807 (m-80) REVERT: I 192 ASP cc_start: 0.9844 (m-30) cc_final: 0.9531 (m-30) REVERT: I 193 ASN cc_start: 0.9534 (m-40) cc_final: 0.9273 (t0) REVERT: I 213 LEU cc_start: 0.9456 (mp) cc_final: 0.8839 (mp) REVERT: I 215 TYR cc_start: 0.8804 (m-10) cc_final: 0.8281 (m-80) REVERT: I 235 ASN cc_start: 0.9400 (t0) cc_final: 0.9090 (p0) REVERT: I 240 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8661 (tp30) REVERT: I 291 TYR cc_start: 0.9524 (t80) cc_final: 0.9284 (t80) REVERT: I 342 ASP cc_start: 0.9098 (m-30) cc_final: 0.8770 (m-30) REVERT: I 368 ARG cc_start: 0.9564 (mtm180) cc_final: 0.9281 (mmm-85) REVERT: I 405 PHE cc_start: 0.9612 (t80) cc_final: 0.9234 (t80) REVERT: I 419 ILE cc_start: 0.9446 (pt) cc_final: 0.9155 (pt) REVERT: I 430 LYS cc_start: 0.9501 (mptt) cc_final: 0.9244 (mmtt) REVERT: I 446 ASP cc_start: 0.9331 (p0) cc_final: 0.9073 (p0) REVERT: I 464 PHE cc_start: 0.9691 (t80) cc_final: 0.9232 (t80) REVERT: I 492 MET cc_start: 0.8740 (mmp) cc_final: 0.8505 (mmm) REVERT: I 548 ARG cc_start: 0.9574 (mtt180) cc_final: 0.9181 (mmm160) REVERT: I 606 LEU cc_start: 0.9377 (mp) cc_final: 0.9094 (mp) REVERT: I 636 CYS cc_start: 0.9301 (m) cc_final: 0.8979 (m) REVERT: I 668 ILE cc_start: 0.9588 (mm) cc_final: 0.9365 (mm) REVERT: I 671 LEU cc_start: 0.9791 (tp) cc_final: 0.9498 (tp) REVERT: I 681 MET cc_start: 0.9128 (mtp) cc_final: 0.8670 (mtt) REVERT: I 685 MET cc_start: 0.9213 (mtm) cc_final: 0.8972 (mtm) REVERT: I 767 GLN cc_start: 0.6898 (mt0) cc_final: 0.6396 (mt0) REVERT: I 790 ASP cc_start: 0.9588 (t0) cc_final: 0.9194 (p0) REVERT: I 799 ASN cc_start: 0.8606 (t0) cc_final: 0.8387 (m-40) REVERT: I 812 PHE cc_start: 0.9093 (t80) cc_final: 0.8844 (t80) REVERT: I 817 LEU cc_start: 0.8776 (mm) cc_final: 0.7868 (mm) REVERT: I 831 ILE cc_start: 0.8989 (mm) cc_final: 0.8719 (mm) REVERT: I 876 GLU cc_start: 0.9596 (tm-30) cc_final: 0.9257 (tp30) REVERT: I 930 ASP cc_start: 0.9605 (t70) cc_final: 0.8912 (t0) REVERT: I 1053 TYR cc_start: 0.8636 (m-80) cc_final: 0.7932 (m-80) REVERT: I 1085 MET cc_start: 0.8571 (mmt) cc_final: 0.7858 (mmt) REVERT: I 1107 MET cc_start: 0.9126 (mmm) cc_final: 0.8122 (tpp) REVERT: I 1119 MET cc_start: 0.9230 (mmm) cc_final: 0.8968 (mmm) REVERT: I 1122 LYS cc_start: 0.9649 (tptm) cc_final: 0.9208 (tppt) REVERT: I 1126 ASP cc_start: 0.9381 (m-30) cc_final: 0.8583 (m-30) REVERT: I 1187 PHE cc_start: 0.8953 (m-10) cc_final: 0.8480 (m-10) REVERT: I 1216 ARG cc_start: 0.9279 (mtp-110) cc_final: 0.8392 (mmm-85) REVERT: I 1234 LYS cc_start: 0.9512 (tppp) cc_final: 0.9149 (tppp) REVERT: I 1237 HIS cc_start: 0.9034 (m90) cc_final: 0.8499 (m90) REVERT: I 1242 LYS cc_start: 0.8293 (mptt) cc_final: 0.8035 (mmtt) REVERT: I 1264 GLN cc_start: 0.9385 (tp-100) cc_final: 0.8963 (tm-30) REVERT: I 1270 PHE cc_start: 0.8888 (t80) cc_final: 0.8107 (t80) REVERT: I 1290 MET cc_start: 0.9339 (tmm) cc_final: 0.8940 (tmm) REVERT: I 1319 MET cc_start: 0.8508 (tpt) cc_final: 0.7353 (tpt) REVERT: I 1321 GLU cc_start: 0.8978 (pm20) cc_final: 0.8725 (pm20) REVERT: I 1329 GLU cc_start: 0.9894 (mt-10) cc_final: 0.9535 (mt-10) REVERT: J 28 ASP cc_start: 0.9871 (t0) cc_final: 0.9590 (p0) REVERT: J 102 MET cc_start: 0.7221 (tpt) cc_final: 0.4658 (ttt) REVERT: J 140 TYR cc_start: 0.9754 (m-80) cc_final: 0.9520 (m-80) REVERT: J 158 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8646 (tm-30) REVERT: J 180 MET cc_start: 0.8950 (ttt) cc_final: 0.8705 (ttt) REVERT: J 207 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9149 (mm-30) REVERT: J 325 LYS cc_start: 0.8032 (pttm) cc_final: 0.7385 (pttp) REVERT: J 329 ASP cc_start: 0.9726 (m-30) cc_final: 0.9350 (t0) REVERT: J 330 MET cc_start: 0.9100 (mmp) cc_final: 0.8852 (mmm) REVERT: J 332 LYS cc_start: 0.9288 (mmtt) cc_final: 0.9059 (mmtt) REVERT: J 361 LEU cc_start: 0.9210 (mt) cc_final: 0.8868 (pp) REVERT: J 365 GLN cc_start: 0.9686 (pt0) cc_final: 0.9461 (pt0) REVERT: J 380 PHE cc_start: 0.9727 (m-80) cc_final: 0.9467 (m-80) REVERT: J 409 TRP cc_start: 0.8878 (m100) cc_final: 0.8209 (m100) REVERT: J 412 LEU cc_start: 0.9718 (tt) cc_final: 0.9479 (pp) REVERT: J 437 PHE cc_start: 0.9590 (m-80) cc_final: 0.9034 (m-80) REVERT: J 454 CYS cc_start: 0.9339 (m) cc_final: 0.9027 (m) REVERT: J 478 LEU cc_start: 0.9697 (tt) cc_final: 0.9451 (mt) REVERT: J 512 TYR cc_start: 0.9425 (t80) cc_final: 0.9136 (t80) REVERT: J 587 LEU cc_start: 0.9213 (mm) cc_final: 0.8836 (mm) REVERT: J 603 LYS cc_start: 0.9232 (pttt) cc_final: 0.8962 (ptpp) REVERT: J 604 MET cc_start: 0.9761 (ttm) cc_final: 0.9491 (mmt) REVERT: J 627 THR cc_start: 0.9757 (t) cc_final: 0.9349 (t) REVERT: J 629 PHE cc_start: 0.9270 (m-80) cc_final: 0.8945 (m-80) REVERT: J 631 TYR cc_start: 0.9504 (m-80) cc_final: 0.9115 (m-80) REVERT: J 645 VAL cc_start: 0.8561 (p) cc_final: 0.8177 (m) REVERT: J 686 TRP cc_start: 0.9189 (m100) cc_final: 0.8828 (m100) REVERT: J 697 MET cc_start: 0.9657 (ppp) cc_final: 0.9415 (ppp) REVERT: J 698 MET cc_start: 0.9672 (tpt) cc_final: 0.9471 (tpp) REVERT: J 743 MET cc_start: 0.9289 (ptm) cc_final: 0.9051 (ptm) REVERT: J 764 ARG cc_start: 0.9096 (ttt-90) cc_final: 0.8696 (ttt-90) REVERT: J 798 ARG cc_start: 0.9434 (ptp-170) cc_final: 0.9163 (ptt-90) REVERT: J 1040 MET cc_start: 0.8089 (mmp) cc_final: 0.7405 (mmm) REVERT: J 1194 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7583 (mtt180) REVERT: J 1238 GLN cc_start: 0.9548 (tp-100) cc_final: 0.8925 (tp-100) REVERT: J 1242 ARG cc_start: 0.9255 (pmt-80) cc_final: 0.8875 (pmt-80) REVERT: J 1254 GLU cc_start: 0.9476 (mt-10) cc_final: 0.9248 (mt-10) REVERT: J 1259 GLN cc_start: 0.9233 (mm110) cc_final: 0.8886 (mt0) REVERT: J 1334 GLU cc_start: 0.9508 (tm-30) cc_final: 0.9266 (tm-30) REVERT: J 1373 ARG cc_start: 0.6280 (ptm160) cc_final: 0.6056 (ptm160) outliers start: 0 outliers final: 0 residues processed: 741 average time/residue: 0.3904 time to fit residues: 442.2920 Evaluate side-chains 647 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 647 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 7.9990 chunk 164 optimal weight: 0.0570 chunk 165 optimal weight: 6.9990 chunk 305 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 GLN I 148 GLN ** I 526 HIS ** 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 659 GLN I 832 HIS ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1220 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1307 ASN ** 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 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 667 GLN J 700 ASN ** J 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 954 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.108410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.069085 restraints weight = 89515.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.072230 restraints weight = 55908.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074641 restraints weight = 39610.007| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25706 Z= 0.135 Angle : 0.708 10.486 34937 Z= 0.368 Chirality : 0.046 0.291 3992 Planarity : 0.005 0.068 4386 Dihedral : 14.322 63.204 3992 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.28 % Favored : 93.68 % Rotamer: Outliers : 0.04 % Allowed : 0.65 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3071 helix: 0.36 (0.16), residues: 1091 sheet: -1.22 (0.26), residues: 384 loop : -1.59 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.117 0.004 TRP J 236 HIS 0.012 0.001 HIS J 419 PHE 0.024 0.002 PHE J 629 TYR 0.033 0.002 TYR I 5 ARG 0.012 0.001 ARG J1330 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 1057) hydrogen bonds : angle 5.32246 ( 2933) metal coordination : bond 0.00752 ( 8) metal coordination : angle 4.29624 ( 12) covalent geometry : bond 0.00306 (25698) covalent geometry : angle 0.70381 (34925) *********************** 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 755 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 754 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 58 GLU cc_start: 0.9353 (pm20) cc_final: 0.8856 (pm20) REVERT: G 84 ASN cc_start: 0.9268 (m-40) cc_final: 0.8413 (t0) REVERT: G 130 ILE cc_start: 0.9590 (mp) cc_final: 0.9209 (mp) REVERT: G 148 ARG cc_start: 0.8349 (mtt180) cc_final: 0.8149 (mtt180) REVERT: G 195 ARG cc_start: 0.9553 (tmt-80) cc_final: 0.9322 (tmt170) REVERT: G 205 MET cc_start: 0.9562 (ppp) cc_final: 0.9230 (ppp) REVERT: G 227 GLN cc_start: 0.9831 (mt0) cc_final: 0.9481 (mt0) REVERT: H 16 ILE cc_start: 0.8131 (pt) cc_final: 0.7750 (mp) REVERT: H 37 HIS cc_start: 0.9427 (m-70) cc_final: 0.8663 (m90) REVERT: H 46 ILE cc_start: 0.9626 (tp) cc_final: 0.9340 (tp) REVERT: H 83 LEU cc_start: 0.9513 (pp) cc_final: 0.9046 (mm) REVERT: H 95 LYS cc_start: 0.9490 (mppt) cc_final: 0.9257 (ptpp) REVERT: H 141 SER cc_start: 0.9633 (t) cc_final: 0.9303 (m) REVERT: H 193 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8506 (tp30) REVERT: I 27 LEU cc_start: 0.9691 (mt) cc_final: 0.9376 (mt) REVERT: I 32 LEU cc_start: 0.9525 (mt) cc_final: 0.9251 (pp) REVERT: I 33 ASP cc_start: 0.9357 (m-30) cc_final: 0.9134 (m-30) REVERT: I 39 ILE cc_start: 0.9336 (pt) cc_final: 0.8793 (pt) REVERT: I 49 LEU cc_start: 0.9371 (mm) cc_final: 0.9168 (mm) REVERT: I 74 ARG cc_start: 0.9662 (tmt170) cc_final: 0.9388 (ptm-80) REVERT: I 80 PHE cc_start: 0.9113 (m-80) cc_final: 0.8616 (m-10) REVERT: I 81 ASP cc_start: 0.9362 (p0) cc_final: 0.9030 (p0) REVERT: I 92 TYR cc_start: 0.9379 (t80) cc_final: 0.9162 (t80) REVERT: I 100 LEU cc_start: 0.9662 (mt) cc_final: 0.9243 (pp) REVERT: I 172 TYR cc_start: 0.7979 (m-80) cc_final: 0.7674 (m-80) REVERT: I 192 ASP cc_start: 0.9823 (m-30) cc_final: 0.9472 (m-30) REVERT: I 193 ASN cc_start: 0.9494 (m-40) cc_final: 0.9257 (t0) REVERT: I 213 LEU cc_start: 0.9428 (mp) cc_final: 0.8772 (mp) REVERT: I 215 TYR cc_start: 0.8691 (m-10) cc_final: 0.8378 (m-80) REVERT: I 224 PHE cc_start: 0.9668 (m-80) cc_final: 0.9398 (m-80) REVERT: I 235 ASN cc_start: 0.9379 (t0) cc_final: 0.9071 (p0) REVERT: I 240 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8651 (tp30) REVERT: I 291 TYR cc_start: 0.9508 (t80) cc_final: 0.9262 (t80) REVERT: I 342 ASP cc_start: 0.9085 (m-30) cc_final: 0.8751 (m-30) REVERT: I 405 PHE cc_start: 0.9551 (t80) cc_final: 0.9113 (t80) REVERT: I 419 ILE cc_start: 0.9410 (pt) cc_final: 0.9173 (pt) REVERT: I 430 LYS cc_start: 0.9419 (mptt) cc_final: 0.9168 (mmmt) REVERT: I 446 ASP cc_start: 0.9292 (p0) cc_final: 0.8934 (p0) REVERT: I 452 ARG cc_start: 0.9385 (ttt90) cc_final: 0.8937 (mmm-85) REVERT: I 461 GLU cc_start: 0.9537 (mm-30) cc_final: 0.8993 (tp30) REVERT: I 464 PHE cc_start: 0.9717 (t80) cc_final: 0.9227 (t80) REVERT: I 491 ASP cc_start: 0.9289 (m-30) cc_final: 0.9002 (p0) REVERT: I 492 MET cc_start: 0.8699 (mmp) cc_final: 0.8107 (mmm) REVERT: I 510 GLN cc_start: 0.9577 (mp10) cc_final: 0.9186 (pm20) REVERT: I 578 TYR cc_start: 0.8629 (m-80) cc_final: 0.8004 (m-80) REVERT: I 601 ASP cc_start: 0.9342 (p0) cc_final: 0.9114 (m-30) REVERT: I 606 LEU cc_start: 0.9273 (mp) cc_final: 0.9048 (mp) REVERT: I 633 LEU cc_start: 0.9586 (pt) cc_final: 0.9291 (mm) REVERT: I 636 CYS cc_start: 0.9322 (m) cc_final: 0.8939 (m) REVERT: I 668 ILE cc_start: 0.9505 (mm) cc_final: 0.9245 (mm) REVERT: I 671 LEU cc_start: 0.9764 (tp) cc_final: 0.9467 (tp) REVERT: I 672 GLU cc_start: 0.9496 (pm20) cc_final: 0.8978 (pm20) REVERT: I 681 MET cc_start: 0.9134 (mtp) cc_final: 0.8657 (mtt) REVERT: I 685 MET cc_start: 0.9051 (mtm) cc_final: 0.8751 (mtm) REVERT: I 741 MET cc_start: 0.9497 (mmt) cc_final: 0.9169 (mmm) REVERT: I 748 ILE cc_start: 0.7930 (pt) cc_final: 0.7448 (pt) REVERT: I 790 ASP cc_start: 0.9510 (t0) cc_final: 0.9083 (p0) REVERT: I 799 ASN cc_start: 0.8503 (t0) cc_final: 0.8197 (m-40) REVERT: I 817 LEU cc_start: 0.8845 (mm) cc_final: 0.7987 (mm) REVERT: I 827 ARG cc_start: 0.8988 (ptm160) cc_final: 0.8566 (ptm160) REVERT: I 831 ILE cc_start: 0.8825 (mm) cc_final: 0.8302 (mm) REVERT: I 930 ASP cc_start: 0.9620 (t70) cc_final: 0.8841 (t70) REVERT: I 1053 TYR cc_start: 0.8653 (m-80) cc_final: 0.7909 (m-80) REVERT: I 1054 LEU cc_start: 0.9784 (mm) cc_final: 0.9582 (mm) REVERT: I 1085 MET cc_start: 0.8574 (mmt) cc_final: 0.7759 (mmt) REVERT: I 1107 MET cc_start: 0.8987 (mmm) cc_final: 0.7951 (tmm) REVERT: I 1119 MET cc_start: 0.9143 (mmm) cc_final: 0.8933 (mmm) REVERT: I 1122 LYS cc_start: 0.9586 (tptm) cc_final: 0.9103 (tppt) REVERT: I 1126 ASP cc_start: 0.9300 (m-30) cc_final: 0.8672 (m-30) REVERT: I 1187 PHE cc_start: 0.8776 (m-10) cc_final: 0.8276 (m-10) REVERT: I 1216 ARG cc_start: 0.9297 (mtp-110) cc_final: 0.8458 (mmm-85) REVERT: I 1226 THR cc_start: 0.9404 (m) cc_final: 0.9076 (p) REVERT: I 1230 MET cc_start: 0.9321 (tpt) cc_final: 0.8558 (tmm) REVERT: I 1237 HIS cc_start: 0.8872 (m90) cc_final: 0.8505 (m90) REVERT: I 1264 GLN cc_start: 0.9433 (tp-100) cc_final: 0.8980 (tm-30) REVERT: I 1265 PHE cc_start: 0.9188 (t80) cc_final: 0.8736 (t80) REVERT: I 1270 PHE cc_start: 0.8980 (t80) cc_final: 0.8060 (t80) REVERT: I 1290 MET cc_start: 0.9314 (tmm) cc_final: 0.8933 (tmm) REVERT: I 1304 MET cc_start: 0.9738 (tmm) cc_final: 0.9374 (ptp) REVERT: I 1319 MET cc_start: 0.8494 (tpt) cc_final: 0.7366 (tpt) REVERT: I 1321 GLU cc_start: 0.8910 (pm20) cc_final: 0.8706 (pm20) REVERT: I 1329 GLU cc_start: 0.9890 (mt-10) cc_final: 0.9527 (mt-10) REVERT: J 33 TRP cc_start: 0.8832 (m100) cc_final: 0.8546 (m100) REVERT: J 102 MET cc_start: 0.7169 (tpt) cc_final: 0.4842 (ttt) REVERT: J 158 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8520 (tm-30) REVERT: J 207 GLU cc_start: 0.9475 (mm-30) cc_final: 0.9183 (mm-30) REVERT: J 325 LYS cc_start: 0.7922 (pttm) cc_final: 0.7126 (pttp) REVERT: J 329 ASP cc_start: 0.9696 (m-30) cc_final: 0.9301 (t0) REVERT: J 330 MET cc_start: 0.9081 (mmp) cc_final: 0.8816 (mmm) REVERT: J 335 GLN cc_start: 0.9208 (pm20) cc_final: 0.8968 (pm20) REVERT: J 361 LEU cc_start: 0.9236 (mt) cc_final: 0.8763 (pp) REVERT: J 362 ARG cc_start: 0.9246 (mpt180) cc_final: 0.9025 (mpp80) REVERT: J 368 LEU cc_start: 0.9654 (tt) cc_final: 0.9427 (tt) REVERT: J 409 TRP cc_start: 0.8881 (m100) cc_final: 0.8036 (m100) REVERT: J 415 VAL cc_start: 0.8889 (p) cc_final: 0.8625 (m) REVERT: J 431 ARG cc_start: 0.9400 (ttm170) cc_final: 0.9193 (tpt-90) REVERT: J 437 PHE cc_start: 0.9506 (m-80) cc_final: 0.8952 (m-80) REVERT: J 454 CYS cc_start: 0.9299 (m) cc_final: 0.8934 (m) REVERT: J 512 TYR cc_start: 0.9428 (t80) cc_final: 0.9104 (t80) REVERT: J 526 VAL cc_start: 0.8792 (p) cc_final: 0.8548 (p) REVERT: J 581 MET cc_start: 0.9561 (ppp) cc_final: 0.9358 (ppp) REVERT: J 587 LEU cc_start: 0.9129 (mm) cc_final: 0.8709 (mm) REVERT: J 603 LYS cc_start: 0.9219 (pttt) cc_final: 0.8966 (ptpp) REVERT: J 604 MET cc_start: 0.9740 (ttm) cc_final: 0.9425 (mmt) REVERT: J 627 THR cc_start: 0.9765 (t) cc_final: 0.9514 (t) REVERT: J 629 PHE cc_start: 0.9035 (m-80) cc_final: 0.8800 (m-80) REVERT: J 645 VAL cc_start: 0.8595 (p) cc_final: 0.8241 (m) REVERT: J 686 TRP cc_start: 0.9231 (m100) cc_final: 0.8915 (m100) REVERT: J 697 MET cc_start: 0.9670 (ppp) cc_final: 0.9455 (ppp) REVERT: J 727 ASP cc_start: 0.9126 (t70) cc_final: 0.8919 (m-30) REVERT: J 763 PHE cc_start: 0.9320 (m-80) cc_final: 0.8394 (m-10) REVERT: J 764 ARG cc_start: 0.9022 (ttt-90) cc_final: 0.8821 (ttt-90) REVERT: J 765 GLU cc_start: 0.9329 (mp0) cc_final: 0.9086 (mp0) REVERT: J 767 LEU cc_start: 0.9163 (mp) cc_final: 0.8451 (tp) REVERT: J 792 ASN cc_start: 0.9352 (m110) cc_final: 0.9147 (m110) REVERT: J 798 ARG cc_start: 0.9387 (ptp-170) cc_final: 0.9138 (ptt-90) REVERT: J 863 LEU cc_start: 0.8964 (tt) cc_final: 0.8643 (tp) REVERT: J 864 LEU cc_start: 0.9415 (mm) cc_final: 0.9209 (mm) REVERT: J 1040 MET cc_start: 0.7779 (mmp) cc_final: 0.7087 (mmm) REVERT: J 1194 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7562 (mtt180) REVERT: J 1238 GLN cc_start: 0.9536 (tp-100) cc_final: 0.8827 (tp-100) REVERT: J 1242 ARG cc_start: 0.9198 (pmt-80) cc_final: 0.8827 (pmt-80) REVERT: J 1259 GLN cc_start: 0.9166 (mm110) cc_final: 0.8866 (mt0) REVERT: J 1331 VAL cc_start: 0.9560 (m) cc_final: 0.8968 (p) REVERT: J 1334 GLU cc_start: 0.9499 (tm-30) cc_final: 0.9262 (tm-30) outliers start: 1 outliers final: 1 residues processed: 754 average time/residue: 0.3922 time to fit residues: 452.3957 Evaluate side-chains 659 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 658 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 300 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 302 optimal weight: 7.9990 chunk 282 optimal weight: 30.0000 chunk 162 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN ** I 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** 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 700 ASN ** J 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 954 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.106989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.068621 restraints weight = 89669.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071674 restraints weight = 56271.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.074011 restraints weight = 40007.613| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25706 Z= 0.145 Angle : 0.716 13.580 34937 Z= 0.372 Chirality : 0.046 0.313 3992 Planarity : 0.005 0.075 4386 Dihedral : 14.285 62.654 3992 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.38 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 3071 helix: 0.26 (0.15), residues: 1098 sheet: -1.13 (0.27), residues: 354 loop : -1.63 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.004 TRP J 236 HIS 0.013 0.001 HIS J 419 PHE 0.032 0.002 PHE I 812 TYR 0.033 0.002 TYR I 5 ARG 0.014 0.001 ARG J1330 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 1057) hydrogen bonds : angle 5.34804 ( 2933) metal coordination : bond 0.00778 ( 8) metal coordination : angle 3.76340 ( 12) covalent geometry : bond 0.00327 (25698) covalent geometry : angle 0.71259 (34925) ********************** 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 743 residues out of total 2633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 743 time to evaluate : 2.749 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 84 ASN cc_start: 0.9278 (m-40) cc_final: 0.8426 (t0) REVERT: G 130 ILE cc_start: 0.9603 (mp) cc_final: 0.9203 (mp) REVERT: G 148 ARG cc_start: 0.8366 (mtt180) cc_final: 0.8154 (mtt180) REVERT: G 195 ARG cc_start: 0.9570 (tmt-80) cc_final: 0.9339 (tmt170) REVERT: G 205 MET cc_start: 0.9569 (ppp) cc_final: 0.9210 (ppp) REVERT: G 227 GLN cc_start: 0.9843 (mt0) cc_final: 0.9494 (mt0) REVERT: H 16 ILE cc_start: 0.8168 (pt) cc_final: 0.7794 (mp) REVERT: H 35 PHE cc_start: 0.8913 (m-80) cc_final: 0.8658 (m-80) REVERT: H 37 HIS cc_start: 0.9399 (m-70) cc_final: 0.8681 (m90) REVERT: H 46 ILE cc_start: 0.9617 (tp) cc_final: 0.9361 (tp) REVERT: H 83 LEU cc_start: 0.9500 (pp) cc_final: 0.9031 (mm) REVERT: H 95 LYS cc_start: 0.9498 (mppt) cc_final: 0.9295 (pttm) REVERT: H 133 LEU cc_start: 0.8963 (tp) cc_final: 0.8755 (tp) REVERT: H 141 SER cc_start: 0.9607 (t) cc_final: 0.9279 (m) REVERT: H 193 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8489 (tp30) REVERT: I 32 LEU cc_start: 0.9560 (mt) cc_final: 0.9234 (pp) REVERT: I 33 ASP cc_start: 0.9388 (m-30) cc_final: 0.9178 (m-30) REVERT: I 39 ILE cc_start: 0.9243 (pt) cc_final: 0.8972 (pt) REVERT: I 74 ARG cc_start: 0.9655 (tmt170) cc_final: 0.9353 (ttp80) REVERT: I 80 PHE cc_start: 0.9195 (m-80) cc_final: 0.8618 (m-10) REVERT: I 81 ASP cc_start: 0.9373 (p0) cc_final: 0.8997 (p0) REVERT: I 92 TYR cc_start: 0.9358 (t80) cc_final: 0.9021 (t80) REVERT: I 100 LEU cc_start: 0.9633 (mt) cc_final: 0.9178 (pp) REVERT: I 160 ASP cc_start: 0.8781 (m-30) cc_final: 0.8579 (m-30) REVERT: I 172 TYR cc_start: 0.8030 (m-80) cc_final: 0.7722 (m-80) REVERT: I 192 ASP cc_start: 0.9821 (m-30) cc_final: 0.9482 (m-30) REVERT: I 193 ASN cc_start: 0.9515 (m-40) cc_final: 0.9219 (t0) REVERT: I 213 LEU cc_start: 0.9442 (mp) cc_final: 0.8804 (mp) REVERT: I 215 TYR cc_start: 0.8717 (m-10) cc_final: 0.8388 (m-80) REVERT: I 235 ASN cc_start: 0.9369 (t0) cc_final: 0.9006 (p0) REVERT: I 240 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8598 (tp30) REVERT: I 291 TYR cc_start: 0.9495 (t80) cc_final: 0.9263 (t80) REVERT: I 342 ASP cc_start: 0.9042 (m-30) cc_final: 0.8729 (m-30) REVERT: I 368 ARG cc_start: 0.9552 (mtm180) cc_final: 0.9320 (mmm-85) REVERT: I 405 PHE cc_start: 0.9573 (t80) cc_final: 0.9206 (t80) REVERT: I 419 ILE cc_start: 0.9465 (pt) cc_final: 0.9201 (pt) REVERT: I 430 LYS cc_start: 0.9450 (mptt) cc_final: 0.9211 (mmmt) REVERT: I 446 ASP cc_start: 0.9289 (p0) cc_final: 0.8975 (p0) REVERT: I 461 GLU cc_start: 0.9602 (mm-30) cc_final: 0.8877 (tp30) REVERT: I 464 PHE cc_start: 0.9715 (t80) cc_final: 0.9235 (t80) REVERT: I 492 MET cc_start: 0.8779 (mmp) cc_final: 0.8566 (mmm) REVERT: I 510 GLN cc_start: 0.9611 (mp10) cc_final: 0.9227 (pm20) REVERT: I 548 ARG cc_start: 0.9532 (mtt180) cc_final: 0.9167 (mmm160) REVERT: I 578 TYR cc_start: 0.8791 (m-80) cc_final: 0.7895 (m-80) REVERT: I 591 TYR cc_start: 0.9629 (m-80) cc_final: 0.9277 (m-80) REVERT: I 601 ASP cc_start: 0.9344 (p0) cc_final: 0.9113 (m-30) REVERT: I 606 LEU cc_start: 0.9328 (mp) cc_final: 0.8810 (mp) REVERT: I 633 LEU cc_start: 0.9570 (pt) cc_final: 0.9271 (mm) REVERT: I 636 CYS cc_start: 0.9172 (m) cc_final: 0.8819 (m) REVERT: I 668 ILE cc_start: 0.9494 (mm) cc_final: 0.9231 (mm) REVERT: I 681 MET cc_start: 0.9138 (mtp) cc_final: 0.8653 (mtt) REVERT: I 685 MET cc_start: 0.9041 (mtm) cc_final: 0.8771 (mtm) REVERT: I 741 MET cc_start: 0.9520 (mmt) cc_final: 0.9181 (mmm) REVERT: I 748 ILE cc_start: 0.7954 (pt) cc_final: 0.7751 (pt) REVERT: I 790 ASP cc_start: 0.9524 (t0) cc_final: 0.9100 (p0) REVERT: I 817 LEU cc_start: 0.8823 (mm) cc_final: 0.7970 (mm) REVERT: I 827 ARG cc_start: 0.9092 (ptm160) cc_final: 0.8603 (ptm160) REVERT: I 930 ASP cc_start: 0.9608 (t70) cc_final: 0.8815 (t0) REVERT: I 1053 TYR cc_start: 0.8672 (m-80) cc_final: 0.8104 (m-80) REVERT: I 1054 LEU cc_start: 0.9778 (mm) cc_final: 0.9545 (mm) REVERT: I 1085 MET cc_start: 0.8528 (mmt) cc_final: 0.7715 (mmt) REVERT: I 1107 MET cc_start: 0.8960 (mmm) cc_final: 0.7901 (tmm) REVERT: I 1119 MET cc_start: 0.9164 (mmm) cc_final: 0.8937 (mmm) REVERT: I 1122 LYS cc_start: 0.9609 (tptm) cc_final: 0.9132 (tppt) REVERT: I 1126 ASP cc_start: 0.9353 (m-30) cc_final: 0.8777 (m-30) REVERT: I 1187 PHE cc_start: 0.8857 (m-10) cc_final: 0.8554 (m-10) REVERT: I 1216 ARG cc_start: 0.9243 (mtp-110) cc_final: 0.8311 (mmm-85) REVERT: I 1226 THR cc_start: 0.9390 (m) cc_final: 0.9092 (p) REVERT: I 1230 MET cc_start: 0.9315 (tpt) cc_final: 0.8587 (tmm) REVERT: I 1237 HIS cc_start: 0.8890 (m90) cc_final: 0.8278 (m90) REVERT: I 1242 LYS cc_start: 0.8142 (mptt) cc_final: 0.7852 (mmtt) REVERT: I 1264 GLN cc_start: 0.9376 (tp-100) cc_final: 0.8918 (tm-30) REVERT: I 1265 PHE cc_start: 0.9208 (t80) cc_final: 0.8851 (t80) REVERT: I 1270 PHE cc_start: 0.9193 (t80) cc_final: 0.8217 (t80) REVERT: I 1290 MET cc_start: 0.9352 (tmm) cc_final: 0.8884 (tmm) REVERT: I 1304 MET cc_start: 0.9739 (tmm) cc_final: 0.9287 (ptp) REVERT: I 1319 MET cc_start: 0.8562 (tpt) cc_final: 0.7154 (tpt) REVERT: I 1329 GLU cc_start: 0.9885 (mt-10) cc_final: 0.9540 (mt-10) REVERT: J 33 TRP cc_start: 0.8890 (m100) cc_final: 0.8589 (m100) REVERT: J 102 MET cc_start: 0.7139 (tpt) cc_final: 0.4885 (ttt) REVERT: J 158 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8542 (tm-30) REVERT: J 207 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9213 (mm-30) REVERT: J 220 ARG cc_start: 0.9405 (mtp180) cc_final: 0.8999 (mtp85) REVERT: J 325 LYS cc_start: 0.7946 (pttm) cc_final: 0.7370 (pttp) REVERT: J 329 ASP cc_start: 0.9689 (m-30) cc_final: 0.9300 (t0) REVERT: J 335 GLN cc_start: 0.9204 (pm20) cc_final: 0.8963 (pm20) REVERT: J 361 LEU cc_start: 0.9183 (mt) cc_final: 0.8741 (pp) REVERT: J 409 TRP cc_start: 0.8838 (m100) cc_final: 0.7930 (m100) REVERT: J 415 VAL cc_start: 0.8896 (p) cc_final: 0.8635 (m) REVERT: J 437 PHE cc_start: 0.9514 (m-80) cc_final: 0.8976 (m-80) REVERT: J 454 CYS cc_start: 0.9360 (m) cc_final: 0.9078 (m) REVERT: J 475 GLU cc_start: 0.8980 (mp0) cc_final: 0.8766 (mp0) REVERT: J 484 MET cc_start: 0.8866 (mpp) cc_final: 0.8622 (mpp) REVERT: J 512 TYR cc_start: 0.9434 (t80) cc_final: 0.9106 (t80) REVERT: J 525 MET cc_start: 0.9423 (pmm) cc_final: 0.9168 (pmm) REVERT: J 587 LEU cc_start: 0.9097 (mm) cc_final: 0.8674 (mm) REVERT: J 603 LYS cc_start: 0.9190 (pttt) cc_final: 0.8940 (ptpp) REVERT: J 604 MET cc_start: 0.9758 (ttm) cc_final: 0.9462 (mmt) REVERT: J 627 THR cc_start: 0.9780 (t) cc_final: 0.9521 (t) REVERT: J 629 PHE cc_start: 0.9126 (m-80) cc_final: 0.8823 (m-80) REVERT: J 645 VAL cc_start: 0.8501 (p) cc_final: 0.8147 (m) REVERT: J 686 TRP cc_start: 0.9224 (m100) cc_final: 0.8871 (m100) REVERT: J 697 MET cc_start: 0.9699 (ppp) cc_final: 0.9479 (ppp) REVERT: J 724 MET cc_start: 0.9352 (mtt) cc_final: 0.9124 (mtt) REVERT: J 727 ASP cc_start: 0.9166 (t70) cc_final: 0.8895 (m-30) REVERT: J 763 PHE cc_start: 0.9364 (m-80) cc_final: 0.8382 (m-10) REVERT: J 764 ARG cc_start: 0.9049 (ttt-90) cc_final: 0.8699 (ttt-90) REVERT: J 792 ASN cc_start: 0.9346 (m110) cc_final: 0.9142 (m-40) REVERT: J 798 ARG cc_start: 0.9387 (ptp-170) cc_final: 0.9148 (ptt-90) REVERT: J 822 MET cc_start: 0.8801 (tpp) cc_final: 0.8555 (tpp) REVERT: J 863 LEU cc_start: 0.8784 (tt) cc_final: 0.8414 (tp) REVERT: J 1040 MET cc_start: 0.7624 (mmp) cc_final: 0.6841 (mmm) REVERT: J 1194 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7634 (mtt180) REVERT: J 1238 GLN cc_start: 0.9414 (tp-100) cc_final: 0.9072 (tp-100) REVERT: J 1254 GLU cc_start: 0.9499 (mt-10) cc_final: 0.9270 (mt-10) REVERT: J 1259 GLN cc_start: 0.9172 (mm110) cc_final: 0.8828 (mt0) REVERT: J 1334 GLU cc_start: 0.9500 (tm-30) cc_final: 0.9271 (tm-30) REVERT: J 1373 ARG cc_start: 0.5845 (ptm160) cc_final: 0.5581 (ptm160) outliers start: 0 outliers final: 0 residues processed: 743 average time/residue: 0.3912 time to fit residues: 444.1176 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 : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 165 optimal weight: 10.0000 chunk 303 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 chunk 248 optimal weight: 0.9980 chunk 282 optimal weight: 30.0000 chunk 177 optimal weight: 0.9980 chunk 273 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 ASN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN ** I 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** 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 700 ASN J 771 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 = 0.3683 r_free = 0.3683 target = 0.103562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.064477 restraints weight = 90112.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067457 restraints weight = 57585.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.069730 restraints weight = 41344.353| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25706 Z= 0.146 Angle : 0.701 9.475 34937 Z= 0.366 Chirality : 0.046 0.282 3992 Planarity : 0.005 0.067 4386 Dihedral : 14.271 62.580 3992 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 3071 helix: 0.25 (0.15), residues: 1104 sheet: -1.25 (0.26), residues: 373 loop : -1.64 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP J 236 HIS 0.012 0.001 HIS J 419 PHE 0.025 0.002 PHE I 812 TYR 0.034 0.002 TYR I 5 ARG 0.008 0.001 ARG I 394 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 1057) hydrogen bonds : angle 5.34011 ( 2933) metal coordination : bond 0.00778 ( 8) metal coordination : angle 3.70607 ( 12) covalent geometry : bond 0.00327 (25698) covalent geometry : angle 0.69746 (34925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12252.43 seconds wall clock time: 217 minutes 8.66 seconds (13028.66 seconds total)