Starting phenix.real_space_refine on Sun Jun 22 20:30:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xug_33468/06_2025/7xug_33468.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xug_33468/06_2025/7xug_33468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xug_33468/06_2025/7xug_33468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xug_33468/06_2025/7xug_33468.map" model { file = "/net/cci-nas-00/data/ceres_data/7xug_33468/06_2025/7xug_33468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xug_33468/06_2025/7xug_33468.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 59 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16125 2.51 5 N 4601 2.21 5 O 5132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.45s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26026 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 421 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "B" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 606 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1686 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1315, 10372 Classifications: {'peptide': 1315} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1259} Chain breaks: 1 Chain: "J" Number of atoms: 10414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10414 Classifications: {'peptide': 1339} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1283} Chain breaks: 2 Chain: "K" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 631 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} 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 15427 SG CYS J 70 53.069 120.026 62.720 1.00 99.60 S ATOM 15441 SG CYS J 72 54.012 123.479 62.554 1.00103.88 S ATOM 15549 SG CYS J 85 51.704 122.159 59.861 1.00103.61 S ATOM 15573 SG CYS J 88 55.120 120.719 59.764 1.00100.15 S ATOM 21261 SG CYS J 814 50.534 53.596 48.938 1.00 63.68 S ATOM 21826 SG CYS J 888 52.909 56.131 50.397 1.00 54.43 S ATOM 21877 SG CYS J 895 50.353 54.594 52.692 1.00 45.78 S ATOM 21898 SG CYS J 898 53.214 52.612 51.518 1.00 48.56 S Time building chain proxies: 14.62, per 1000 atoms: 0.56 Number of scatterers: 26026 At special positions: 0 Unit cell: (149.46, 139.92, 148.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 59 15.00 Mg 1 11.99 O 5132 8.00 N 4601 7.00 C 16125 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: 6.53 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " Number of angles added : 12 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5854 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 49 sheets defined 37.1% alpha, 15.9% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 8.93 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 4.005A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.845A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) 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 158 Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'G' and resid 230 through 232 No H-bonds generated for 'chain 'G' and resid 230 through 232' Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.747A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.540A pdb=" N LYS H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.816A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE I 39 " --> pdb=" O PHE I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.607A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 212 removed outlier: 4.195A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.953A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 removed outlier: 3.788A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.952A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.212A 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 455 through 480 removed outlier: 3.598A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 487 Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 520 through 528 removed outlier: 3.868A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 820 through 825 removed outlier: 3.559A pdb=" N GLU I 825 " --> pdb=" O ARG I 821 " (cutoff:3.500A) Processing helix chain 'I' and resid 860 through 865 removed outlier: 3.728A pdb=" N SER I 863 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU I 865 " --> pdb=" O LEU I 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 860 through 865' Processing helix chain 'I' and resid 942 through 963 Processing helix chain 'I' and resid 966 through 979 Processing helix chain 'I' and resid 986 through 990 removed outlier: 3.646A pdb=" N LEU I 989 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP I 990 " --> pdb=" O GLU I 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 986 through 990' Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.607A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS I1028 " --> pdb=" O GLU I1024 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA I1031 " --> pdb=" O LYS I1027 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS I1032 " --> pdb=" O LYS I1028 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG I1033 " --> pdb=" O LEU I1029 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG I1034 " --> pdb=" O GLU I1030 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.426A 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: 3.573A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1175 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 1282 removed outlier: 3.531A pdb=" N VAL I1275 " --> pdb=" O GLY I1271 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.761A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1322 through 1332 removed outlier: 3.958A pdb=" N LEU I1326 " --> pdb=" O SER I1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.531A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (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 removed outlier: 3.605A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 194 through 207 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 removed outlier: 3.503A pdb=" N LEU J 249 " --> pdb=" O PRO J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 286 removed outlier: 3.545A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.525A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 332 Processing helix chain 'J' and resid 336 through 341 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 406 through 416 removed outlier: 4.541A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 538 Processing helix chain 'J' and resid 574 through 581 Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.666A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.628A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.588A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.526A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.020A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.610A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.623A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.767A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1072 Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 removed outlier: 3.533A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) Processing helix chain 'J' and resid 1226 through 1243 removed outlier: 3.505A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 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 removed outlier: 3.695A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.873A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 16 removed outlier: 7.001A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 98 through 105 removed outlier: 3.767A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 removed outlier: 3.516A pdb=" N ARG G 91 " --> pdb=" O GLU G 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 removed outlier: 3.548A pdb=" N ALA G 175 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 16 through 20 removed outlier: 6.344A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 16 through 20 removed outlier: 6.344A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 97 through 104 removed outlier: 7.553A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN H 147 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.578A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 66 through 75 removed outlier: 5.344A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 453 removed outlier: 3.586A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB8, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB9, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AC1, first strand: chain 'I' and resid 249 through 250 removed outlier: 3.678A pdb=" N GLU I 249 " --> pdb=" O ILE I 269 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.017A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.577A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (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 580 through 581 Processing sheet with id=AC6, first strand: chain 'I' and resid 634 through 637 Processing sheet with id=AC7, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.565A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET I 768 " --> pdb=" O ASP I 785 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 749 through 751 removed outlier: 6.493A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.562A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.542A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 830 through 831 Processing sheet with id=AD3, first strand: chain 'I' and resid 834 through 841 removed outlier: 5.677A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD5, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.665A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD7, first strand: chain 'J' and resid 103 through 112 removed outlier: 6.649A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.651A pdb=" N VAL J 145 " --> pdb=" O LYS J 179 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS J 179 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 253 through 254 removed outlier: 4.194A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA J 261 " --> pdb=" O VAL J 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'J' and resid 350 through 357 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 708 Processing sheet with id=AE4, first strand: chain 'J' and resid 809 through 811 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 949 through 951 removed outlier: 4.652A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 958 through 961 removed outlier: 6.787A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE9, first strand: chain 'J' and resid 1024 through 1026 removed outlier: 4.368A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AF2, first strand: chain 'J' and resid 1156 through 1157 removed outlier: 3.607A pdb=" N ALA J1157 " --> pdb=" O ASP J1208 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP J1208 " --> pdb=" O ALA J1157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'J' and resid 1162 through 1168 removed outlier: 5.340A pdb=" N ARG J1174 " --> pdb=" O GLY J1166 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU J1168 " --> pdb=" O LYS J1172 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS J1172 " --> pdb=" O GLU J1168 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.218A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 2838 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 11.96 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7318 1.33 - 1.45: 4423 1.45 - 1.57: 14494 1.57 - 1.70: 115 1.70 - 1.82: 184 Bond restraints: 26534 Sorted by residual: bond pdb=" C ILE I 145 " pdb=" N VAL I 146 " ideal model delta sigma weight residual 1.334 1.297 0.036 1.24e-02 6.50e+03 8.49e+00 bond pdb=" CA SER J 590 " pdb=" C SER J 590 " ideal model delta sigma weight residual 1.522 1.483 0.039 1.38e-02 5.25e+03 8.03e+00 bond pdb=" N VAL I1155 " pdb=" CA VAL I1155 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.83e+00 bond pdb=" N THR I 754 " pdb=" CA THR I 754 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.33e-02 5.65e+03 6.55e+00 bond pdb=" C LYS I 17 " pdb=" N ARG I 18 " ideal model delta sigma weight residual 1.328 1.287 0.041 1.67e-02 3.59e+03 6.03e+00 ... (remaining 26529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 33799 1.63 - 3.26: 1918 3.26 - 4.89: 298 4.89 - 6.52: 64 6.52 - 8.14: 12 Bond angle restraints: 36091 Sorted by residual: angle pdb=" C VAL I1103 " pdb=" CA VAL I1103 " pdb=" CB VAL I1103 " ideal model delta sigma weight residual 114.00 108.62 5.38 1.31e+00 5.83e-01 1.69e+01 angle pdb=" CA ARG I 201 " pdb=" CB ARG I 201 " pdb=" CG ARG I 201 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CA TYR I1018 " pdb=" CB TYR I1018 " pdb=" CG TYR I1018 " ideal model delta sigma weight residual 113.90 120.48 -6.58 1.80e+00 3.09e-01 1.34e+01 angle pdb=" CA TYR I 756 " pdb=" C TYR I 756 " pdb=" O TYR I 756 " ideal model delta sigma weight residual 122.45 117.71 4.74 1.30e+00 5.92e-01 1.33e+01 angle pdb=" CB ARG G 170 " pdb=" CG ARG G 170 " pdb=" CD ARG G 170 " ideal model delta sigma weight residual 111.30 118.82 -7.52 2.30e+00 1.89e-01 1.07e+01 ... (remaining 36086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.71: 15513 30.71 - 61.42: 669 61.42 - 92.12: 62 92.12 - 122.83: 0 122.83 - 153.54: 1 Dihedral angle restraints: 16245 sinusoidal: 7144 harmonic: 9101 Sorted by residual: dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual -180.00 -151.51 -28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ASN I 519 " pdb=" C ASN I 519 " pdb=" N PRO I 520 " pdb=" CA PRO I 520 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA PRO J 502 " pdb=" C PRO J 502 " pdb=" N SER J 503 " pdb=" CA SER J 503 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 16242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2703 0.045 - 0.089: 1064 0.089 - 0.134: 301 0.134 - 0.179: 52 0.179 - 0.223: 9 Chirality restraints: 4129 Sorted by residual: chirality pdb=" CB VAL J 415 " pdb=" CA VAL J 415 " pdb=" CG1 VAL J 415 " pdb=" CG2 VAL J 415 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB ILE I 765 " pdb=" CA ILE I 765 " pdb=" CG1 ILE I 765 " pdb=" CG2 ILE I 765 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA GLN J 504 " pdb=" N GLN J 504 " pdb=" C GLN J 504 " pdb=" CB GLN J 504 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 4126 not shown) Planarity restraints: 4519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 519 " 0.046 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PRO I 520 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO I 520 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 520 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " 0.044 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO I 190 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I1018 " 0.026 2.00e-02 2.50e+03 1.72e-02 5.91e+00 pdb=" CG TYR I1018 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR I1018 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR I1018 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR I1018 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR I1018 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR I1018 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR I1018 " 0.001 2.00e-02 2.50e+03 ... (remaining 4516 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 193 2.53 - 3.12: 21054 3.12 - 3.72: 38463 3.72 - 4.31: 53490 4.31 - 4.90: 90717 Nonbonded interactions: 203917 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 1.938 2.170 nonbonded pdb=" OG1 THR I 91 " pdb=" O ILE I 138 " model vdw 1.958 3.040 nonbonded pdb=" OD2 ASP G 62 " pdb=" OG SER G 141 " model vdw 1.988 3.040 nonbonded pdb=" OG1 THR I 216 " pdb=" OE1 GLN I 219 " model vdw 1.992 3.040 nonbonded pdb=" OG SER J1318 " pdb=" OD1 ASP J1342 " model vdw 2.038 3.040 ... (remaining 203912 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 7 through 158 or resid 169 through 232)) selection = (chain 'H' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 69.610 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 26542 Z= 0.390 Angle : 0.874 13.559 36103 Z= 0.485 Chirality : 0.051 0.223 4129 Planarity : 0.005 0.070 4519 Dihedral : 16.496 153.540 10391 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.91 % Favored : 91.02 % Rotamer: Outliers : 0.11 % Allowed : 0.45 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 3152 helix: -0.14 (0.15), residues: 1077 sheet: -1.95 (0.23), residues: 413 loop : -2.28 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J1193 HIS 0.009 0.002 HIS J 80 PHE 0.027 0.003 PHE J 17 TYR 0.040 0.003 TYR I1018 ARG 0.023 0.001 ARG I1033 Details of bonding type rmsd hydrogen bonds : bond 0.15059 ( 1068) hydrogen bonds : angle 6.44076 ( 2966) metal coordination : bond 0.01755 ( 8) metal coordination : angle 5.29015 ( 12) covalent geometry : bond 0.00883 (26534) covalent geometry : angle 0.86931 (36091) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 473 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 347 ILE cc_start: 0.8271 (mm) cc_final: 0.8032 (mm) REVERT: I 369 MET cc_start: 0.8088 (tmm) cc_final: 0.7869 (tmm) REVERT: I 371 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7913 (mtm-85) REVERT: I 514 PHE cc_start: 0.8741 (t80) cc_final: 0.8374 (t80) REVERT: I 524 ILE cc_start: 0.9190 (tp) cc_final: 0.8963 (tp) REVERT: I 588 GLU cc_start: 0.7930 (mp0) cc_final: 0.7720 (mp0) REVERT: I 628 HIS cc_start: 0.7380 (m-70) cc_final: 0.7133 (m-70) REVERT: I 1171 ARG cc_start: 0.7696 (ttp-170) cc_final: 0.7453 (ttp-170) REVERT: I 1188 ASP cc_start: 0.8836 (p0) cc_final: 0.8574 (p0) REVERT: J 81 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7964 (ptm-80) REVERT: J 136 GLU cc_start: 0.8231 (pp20) cc_final: 0.7979 (pp20) REVERT: J 298 MET cc_start: 0.7176 (ttt) cc_final: 0.6939 (ttm) REVERT: J 679 TYR cc_start: 0.7463 (t80) cc_final: 0.7160 (t80) REVERT: J 788 LEU cc_start: 0.8878 (mt) cc_final: 0.8288 (tt) REVERT: J 811 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7199 (mt-10) REVERT: J 862 THR cc_start: 0.8489 (p) cc_final: 0.8276 (p) REVERT: J 983 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8118 (mptt) REVERT: K 56 GLU cc_start: 0.7830 (pt0) cc_final: 0.7534 (pt0) outliers start: 3 outliers final: 0 residues processed: 475 average time/residue: 0.4153 time to fit residues: 299.9659 Evaluate side-chains 395 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 0.8980 chunk 242 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 152 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.171479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124328 restraints weight = 34001.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121845 restraints weight = 35663.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123466 restraints weight = 33240.977| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26542 Z= 0.153 Angle : 0.668 9.516 36103 Z= 0.347 Chirality : 0.045 0.211 4129 Planarity : 0.005 0.068 4519 Dihedral : 13.393 151.484 4202 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 1.04 % Allowed : 8.42 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3152 helix: 0.69 (0.16), residues: 1075 sheet: -1.42 (0.25), residues: 401 loop : -2.03 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP J1020 HIS 0.007 0.001 HIS G 23 PHE 0.018 0.002 PHE I 337 TYR 0.024 0.001 TYR I1018 ARG 0.009 0.001 ARG G 170 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 1068) hydrogen bonds : angle 5.04683 ( 2966) metal coordination : bond 0.01016 ( 8) metal coordination : angle 3.42975 ( 12) covalent geometry : bond 0.00351 (26534) covalent geometry : angle 0.66530 (36091) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 471 time to evaluate : 2.965 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: G 10 LYS cc_start: 0.8851 (mtmm) cc_final: 0.8618 (mppt) REVERT: H 51 MET cc_start: 0.8019 (tpp) cc_final: 0.7749 (ttm) REVERT: H 75 GLN cc_start: 0.7777 (tt0) cc_final: 0.7473 (tt0) REVERT: I 14 ASP cc_start: 0.8608 (t0) cc_final: 0.8382 (t0) REVERT: I 239 MET cc_start: 0.6669 (tmm) cc_final: 0.6374 (tmm) REVERT: I 299 LYS cc_start: 0.7372 (tptp) cc_final: 0.7083 (tptp) REVERT: I 369 MET cc_start: 0.8083 (tmm) cc_final: 0.7794 (tmm) REVERT: I 628 HIS cc_start: 0.7118 (m-70) cc_final: 0.6810 (m-70) REVERT: I 1188 ASP cc_start: 0.8800 (p0) cc_final: 0.8588 (p0) REVERT: I 1211 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7477 (ttm110) REVERT: J 134 ASP cc_start: 0.7274 (p0) cc_final: 0.6108 (p0) REVERT: J 136 GLU cc_start: 0.8095 (pp20) cc_final: 0.7880 (pp20) REVERT: J 140 TYR cc_start: 0.7678 (m-80) cc_final: 0.6567 (m-80) REVERT: J 141 PHE cc_start: 0.8084 (m-80) cc_final: 0.7420 (m-80) REVERT: J 602 SER cc_start: 0.8732 (t) cc_final: 0.8301 (p) REVERT: J 788 LEU cc_start: 0.8606 (mt) cc_final: 0.7931 (tt) REVERT: J 811 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7138 (mt-10) REVERT: J 918 ILE cc_start: 0.8833 (pt) cc_final: 0.8467 (mt) REVERT: K 11 GLU cc_start: 0.7733 (pp20) cc_final: 0.7522 (pp20) outliers start: 28 outliers final: 20 residues processed: 479 average time/residue: 0.4009 time to fit residues: 297.6459 Evaluate side-chains 414 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 394 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 225 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 221 optimal weight: 0.0370 chunk 89 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 307 optimal weight: 0.4980 chunk 254 optimal weight: 0.8980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 618 GLN ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I 955 GLN J 702 GLN J1279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.171020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122934 restraints weight = 33949.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120016 restraints weight = 35217.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121622 restraints weight = 33529.840| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26542 Z= 0.133 Angle : 0.620 12.093 36103 Z= 0.320 Chirality : 0.043 0.214 4129 Planarity : 0.004 0.057 4519 Dihedral : 13.293 151.240 4202 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 1.56 % Allowed : 12.02 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 3152 helix: 1.01 (0.16), residues: 1075 sheet: -1.20 (0.25), residues: 411 loop : -1.89 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J1020 HIS 0.006 0.001 HIS I 628 PHE 0.023 0.001 PHE I 337 TYR 0.025 0.001 TYR I1018 ARG 0.009 0.000 ARG G 170 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 1068) hydrogen bonds : angle 4.78248 ( 2966) metal coordination : bond 0.01466 ( 8) metal coordination : angle 4.69340 ( 12) covalent geometry : bond 0.00304 (26534) covalent geometry : angle 0.61407 (36091) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 420 time to evaluate : 2.843 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: G 10 LYS cc_start: 0.8839 (mtmm) cc_final: 0.8626 (mppt) REVERT: G 77 ASP cc_start: 0.7704 (m-30) cc_final: 0.7392 (m-30) REVERT: G 200 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8277 (ttpt) REVERT: H 51 MET cc_start: 0.8064 (tpp) cc_final: 0.7832 (ttm) REVERT: I 239 MET cc_start: 0.6689 (tmm) cc_final: 0.6424 (tmm) REVERT: I 369 MET cc_start: 0.8147 (tmm) cc_final: 0.7862 (tmm) REVERT: I 628 HIS cc_start: 0.7092 (m-70) cc_final: 0.6708 (m-70) REVERT: I 1095 ASP cc_start: 0.8793 (t0) cc_final: 0.8583 (t0) REVERT: J 602 SER cc_start: 0.8683 (t) cc_final: 0.8255 (p) REVERT: J 788 LEU cc_start: 0.8390 (mt) cc_final: 0.7787 (tt) REVERT: J 918 ILE cc_start: 0.8942 (pt) cc_final: 0.8556 (mt) REVERT: J 1317 GLU cc_start: 0.6381 (pt0) cc_final: 0.6139 (pm20) REVERT: K 75 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8102 (tm-30) outliers start: 42 outliers final: 24 residues processed: 441 average time/residue: 0.4056 time to fit residues: 278.3556 Evaluate side-chains 414 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 390 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 110 optimal weight: 3.9990 chunk 21 optimal weight: 0.0060 chunk 103 optimal weight: 0.9980 chunk 74 optimal weight: 30.0000 chunk 294 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 308 optimal weight: 0.0000 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1268 GLN J 702 GLN ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.171347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123977 restraints weight = 34196.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121737 restraints weight = 36538.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122916 restraints weight = 36364.273| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26542 Z= 0.126 Angle : 0.609 9.545 36103 Z= 0.313 Chirality : 0.042 0.290 4129 Planarity : 0.004 0.057 4519 Dihedral : 13.245 151.442 4202 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 1.93 % Allowed : 13.84 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3152 helix: 1.18 (0.16), residues: 1073 sheet: -1.01 (0.25), residues: 413 loop : -1.79 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J1020 HIS 0.006 0.001 HIS H 66 PHE 0.016 0.001 PHE I 337 TYR 0.014 0.001 TYR I1018 ARG 0.009 0.000 ARG J1345 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 1068) hydrogen bonds : angle 4.63374 ( 2966) metal coordination : bond 0.00776 ( 8) metal coordination : angle 3.87688 ( 12) covalent geometry : bond 0.00291 (26534) covalent geometry : angle 0.60501 (36091) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 423 time to evaluate : 3.716 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: G 114 ASP cc_start: 0.7696 (t70) cc_final: 0.7488 (t0) REVERT: G 200 LYS cc_start: 0.8573 (ttpt) cc_final: 0.8303 (ttpt) REVERT: H 226 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7329 (tm-30) REVERT: I 202 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7674 (ttp-110) REVERT: I 369 MET cc_start: 0.8269 (tmm) cc_final: 0.8047 (tmm) REVERT: I 524 ILE cc_start: 0.8659 (tp) cc_final: 0.8396 (tp) REVERT: I 1095 ASP cc_start: 0.8832 (t0) cc_final: 0.8587 (t0) REVERT: J 140 TYR cc_start: 0.6979 (m-80) cc_final: 0.6705 (m-80) REVERT: J 602 SER cc_start: 0.8729 (t) cc_final: 0.8275 (p) REVERT: J 788 LEU cc_start: 0.8348 (mt) cc_final: 0.7737 (tt) REVERT: J 918 ILE cc_start: 0.8895 (pt) cc_final: 0.8466 (mt) REVERT: K 75 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8086 (tm-30) outliers start: 52 outliers final: 35 residues processed: 451 average time/residue: 0.3993 time to fit residues: 280.3022 Evaluate side-chains 424 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 389 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 172 optimal weight: 2.9990 chunk 279 optimal weight: 8.9990 chunk 315 optimal weight: 0.5980 chunk 286 optimal weight: 30.0000 chunk 64 optimal weight: 0.2980 chunk 307 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 283 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 139 ASN J 266 ASN J 702 GLN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.175463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.127255 restraints weight = 33992.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125142 restraints weight = 35123.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126225 restraints weight = 34962.216| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26542 Z= 0.122 Angle : 0.608 9.702 36103 Z= 0.309 Chirality : 0.042 0.206 4129 Planarity : 0.004 0.061 4519 Dihedral : 13.199 151.587 4202 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.73 % Rotamer: Outliers : 1.78 % Allowed : 15.39 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 3152 helix: 1.31 (0.16), residues: 1072 sheet: -0.99 (0.25), residues: 429 loop : -1.75 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J1020 HIS 0.005 0.001 HIS H 66 PHE 0.013 0.001 PHE I 405 TYR 0.024 0.001 TYR I1018 ARG 0.009 0.000 ARG J1290 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 1068) hydrogen bonds : angle 4.56254 ( 2966) metal coordination : bond 0.00739 ( 8) metal coordination : angle 3.76245 ( 12) covalent geometry : bond 0.00283 (26534) covalent geometry : angle 0.60419 (36091) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 428 time to evaluate : 3.098 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: G 8 PHE cc_start: 0.7858 (m-80) cc_final: 0.7610 (m-10) REVERT: G 76 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: G 200 LYS cc_start: 0.8560 (ttpt) cc_final: 0.8345 (ttpt) REVERT: H 18 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7520 (mm-40) REVERT: H 51 MET cc_start: 0.7925 (tpp) cc_final: 0.7713 (ttm) REVERT: H 127 GLN cc_start: 0.8060 (pm20) cc_final: 0.7842 (pm20) REVERT: I 70 TYR cc_start: 0.8425 (t80) cc_final: 0.8065 (t80) REVERT: I 202 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7711 (ttp-110) REVERT: I 369 MET cc_start: 0.8370 (tmm) cc_final: 0.8133 (tmm) REVERT: I 524 ILE cc_start: 0.8620 (tp) cc_final: 0.8363 (tp) REVERT: I 1095 ASP cc_start: 0.8772 (t0) cc_final: 0.8557 (t0) REVERT: J 214 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7722 (mtm-85) REVERT: J 235 GLU cc_start: 0.6878 (pm20) cc_final: 0.6639 (pm20) REVERT: J 312 ARG cc_start: 0.6498 (ptm160) cc_final: 0.6269 (ptp-170) REVERT: J 602 SER cc_start: 0.8764 (t) cc_final: 0.8269 (p) REVERT: J 625 MET cc_start: 0.8199 (ttp) cc_final: 0.7994 (ttp) REVERT: J 698 MET cc_start: 0.8683 (tpp) cc_final: 0.8458 (mmm) REVERT: J 788 LEU cc_start: 0.8205 (mt) cc_final: 0.7649 (tt) REVERT: J 918 ILE cc_start: 0.8864 (pt) cc_final: 0.8429 (mt) REVERT: J 1317 GLU cc_start: 0.6499 (pm20) cc_final: 0.6236 (pm20) REVERT: J 1345 ARG cc_start: 0.7795 (ptt-90) cc_final: 0.7468 (ptt90) outliers start: 48 outliers final: 38 residues processed: 455 average time/residue: 0.4033 time to fit residues: 287.6260 Evaluate side-chains 437 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 398 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 111 optimal weight: 0.0000 chunk 34 optimal weight: 9.9990 chunk 309 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 955 GLN J 702 GLN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.174169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125601 restraints weight = 33862.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122851 restraints weight = 34998.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124349 restraints weight = 33273.937| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26542 Z= 0.155 Angle : 0.621 9.756 36103 Z= 0.316 Chirality : 0.043 0.222 4129 Planarity : 0.004 0.064 4519 Dihedral : 13.188 151.885 4202 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 2.08 % Allowed : 16.36 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3152 helix: 1.29 (0.16), residues: 1078 sheet: -0.96 (0.25), residues: 429 loop : -1.72 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J1193 HIS 0.007 0.001 HIS J 104 PHE 0.017 0.001 PHE I 80 TYR 0.014 0.001 TYR H 152 ARG 0.007 0.000 ARG I 175 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 1068) hydrogen bonds : angle 4.53269 ( 2966) metal coordination : bond 0.00957 ( 8) metal coordination : angle 3.89673 ( 12) covalent geometry : bond 0.00367 (26534) covalent geometry : angle 0.61737 (36091) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 415 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: G 10 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8450 (mmmm) REVERT: G 76 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: G 127 GLN cc_start: 0.8121 (mp10) cc_final: 0.7882 (pm20) REVERT: G 200 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8357 (ttpt) REVERT: H 18 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7517 (mm-40) REVERT: H 51 MET cc_start: 0.7928 (tpp) cc_final: 0.7710 (ttm) REVERT: H 226 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7237 (tm-30) REVERT: I 70 TYR cc_start: 0.8458 (t80) cc_final: 0.8126 (t80) REVERT: I 202 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7832 (ttp80) REVERT: I 369 MET cc_start: 0.8388 (tmm) cc_final: 0.8101 (tmm) REVERT: I 1095 ASP cc_start: 0.8846 (t0) cc_final: 0.8589 (t0) REVERT: J 172 PHE cc_start: 0.6439 (m-80) cc_final: 0.5726 (m-80) REVERT: J 214 ARG cc_start: 0.8084 (mtt180) cc_final: 0.7812 (mtm-85) REVERT: J 235 GLU cc_start: 0.6911 (pm20) cc_final: 0.6647 (pm20) REVERT: J 625 MET cc_start: 0.8228 (ttp) cc_final: 0.8025 (ttp) REVERT: J 698 MET cc_start: 0.8708 (tpp) cc_final: 0.8496 (mmm) REVERT: J 788 LEU cc_start: 0.8292 (mt) cc_final: 0.7663 (tt) REVERT: J 1345 ARG cc_start: 0.7910 (ptt-90) cc_final: 0.7592 (ptt-90) REVERT: K 69 ARG cc_start: 0.6885 (ttp80) cc_final: 0.6619 (ttp80) REVERT: K 75 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8110 (tm-30) outliers start: 56 outliers final: 49 residues processed: 446 average time/residue: 0.4218 time to fit residues: 292.3256 Evaluate side-chains 444 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 394 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 216 optimal weight: 0.9980 chunk 300 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 231 optimal weight: 0.8980 chunk 263 optimal weight: 7.9990 chunk 312 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 702 GLN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1326 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.172846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124030 restraints weight = 34079.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121191 restraints weight = 35301.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122633 restraints weight = 34585.760| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26542 Z= 0.184 Angle : 0.640 10.198 36103 Z= 0.325 Chirality : 0.043 0.189 4129 Planarity : 0.004 0.062 4519 Dihedral : 13.202 151.975 4202 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.90 % Favored : 94.07 % Rotamer: Outliers : 2.45 % Allowed : 16.80 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3152 helix: 1.27 (0.16), residues: 1079 sheet: -1.02 (0.24), residues: 443 loop : -1.68 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J1193 HIS 0.007 0.001 HIS J 104 PHE 0.014 0.001 PHE I 405 TYR 0.022 0.001 TYR I1018 ARG 0.007 0.000 ARG I 473 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 1068) hydrogen bonds : angle 4.55847 ( 2966) metal coordination : bond 0.01096 ( 8) metal coordination : angle 3.59573 ( 12) covalent geometry : bond 0.00440 (26534) covalent geometry : angle 0.63635 (36091) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 405 time to evaluate : 4.494 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: G 10 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8323 (mmmm) REVERT: G 76 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: G 120 ASP cc_start: 0.8028 (p0) cc_final: 0.7540 (p0) REVERT: G 200 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8357 (ttpt) REVERT: H 18 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7548 (mm-40) REVERT: H 51 MET cc_start: 0.7940 (tpp) cc_final: 0.7706 (ttm) REVERT: H 226 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7120 (tm-30) REVERT: I 70 TYR cc_start: 0.8452 (t80) cc_final: 0.8057 (t80) REVERT: I 369 MET cc_start: 0.8319 (tmm) cc_final: 0.8074 (tmm) REVERT: I 1095 ASP cc_start: 0.8883 (t0) cc_final: 0.8595 (t0) REVERT: J 172 PHE cc_start: 0.6425 (m-80) cc_final: 0.5698 (m-80) REVERT: J 214 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7826 (mtm-85) REVERT: J 235 GLU cc_start: 0.6905 (pm20) cc_final: 0.6629 (pm20) REVERT: J 327 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8264 (mm) REVERT: J 535 ARG cc_start: 0.8076 (ptm-80) cc_final: 0.7830 (ttt-90) REVERT: J 788 LEU cc_start: 0.8427 (mt) cc_final: 0.7731 (tt) REVERT: J 1317 GLU cc_start: 0.6732 (pm20) cc_final: 0.6315 (pm20) REVERT: J 1345 ARG cc_start: 0.7863 (ptt-90) cc_final: 0.7507 (ptt90) REVERT: K 75 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8165 (tm-30) outliers start: 66 outliers final: 53 residues processed: 445 average time/residue: 0.4819 time to fit residues: 338.9356 Evaluate side-chains 443 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 388 time to evaluate : 4.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 220 optimal weight: 0.7980 chunk 242 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 278 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 chunk 273 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 167 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 702 GLN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.175151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126797 restraints weight = 33867.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124300 restraints weight = 34763.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125693 restraints weight = 33710.317| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26542 Z= 0.125 Angle : 0.621 11.517 36103 Z= 0.315 Chirality : 0.042 0.228 4129 Planarity : 0.004 0.064 4519 Dihedral : 13.144 151.683 4202 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 1.63 % Allowed : 17.77 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3152 helix: 1.36 (0.16), residues: 1078 sheet: -0.93 (0.25), residues: 438 loop : -1.59 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J1193 HIS 0.006 0.001 HIS J 104 PHE 0.013 0.001 PHE I 405 TYR 0.017 0.001 TYR J 144 ARG 0.008 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 1068) hydrogen bonds : angle 4.46502 ( 2966) metal coordination : bond 0.00761 ( 8) metal coordination : angle 3.14147 ( 12) covalent geometry : bond 0.00291 (26534) covalent geometry : angle 0.61851 (36091) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 423 time to evaluate : 3.471 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: G 76 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: G 120 ASP cc_start: 0.8047 (p0) cc_final: 0.7586 (p0) REVERT: H 18 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7532 (mm-40) REVERT: H 51 MET cc_start: 0.7951 (tpp) cc_final: 0.7729 (ttm) REVERT: H 226 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7349 (tm-30) REVERT: I 14 ASP cc_start: 0.8506 (t0) cc_final: 0.8267 (t0) REVERT: I 70 TYR cc_start: 0.8426 (t80) cc_final: 0.8035 (t80) REVERT: I 524 ILE cc_start: 0.8637 (tp) cc_final: 0.8330 (tp) REVERT: I 1032 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8343 (mmmm) REVERT: I 1095 ASP cc_start: 0.8853 (t0) cc_final: 0.8581 (t0) REVERT: J 69 GLU cc_start: 0.7883 (mp0) cc_final: 0.7527 (mp0) REVERT: J 214 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7817 (mtm-85) REVERT: J 235 GLU cc_start: 0.6909 (pm20) cc_final: 0.6634 (pm20) REVERT: J 327 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8192 (mm) REVERT: J 535 ARG cc_start: 0.8037 (ptm-80) cc_final: 0.7793 (ttt-90) REVERT: J 788 LEU cc_start: 0.8304 (mt) cc_final: 0.7629 (tt) REVERT: J 1189 MET cc_start: 0.7621 (tpp) cc_final: 0.7410 (tpp) REVERT: J 1289 ASN cc_start: 0.7055 (p0) cc_final: 0.6445 (m110) REVERT: K 69 ARG cc_start: 0.6853 (ttp80) cc_final: 0.6593 (ttp80) REVERT: K 72 GLN cc_start: 0.8096 (tp40) cc_final: 0.7598 (tp40) REVERT: K 75 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8128 (tm-30) outliers start: 44 outliers final: 41 residues processed: 452 average time/residue: 0.5794 time to fit residues: 424.3313 Evaluate side-chains 436 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 393 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 47 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 chunk 115 optimal weight: 2.9990 chunk 309 optimal weight: 0.5980 chunk 283 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS J 702 GLN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.175235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129459 restraints weight = 33999.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128494 restraints weight = 41101.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.129599 restraints weight = 39201.272| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26542 Z= 0.128 Angle : 0.637 12.177 36103 Z= 0.322 Chirality : 0.042 0.261 4129 Planarity : 0.004 0.062 4519 Dihedral : 13.107 151.841 4202 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.82 % Allowed : 18.10 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3152 helix: 1.37 (0.16), residues: 1078 sheet: -0.93 (0.25), residues: 438 loop : -1.54 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP J1020 HIS 0.006 0.001 HIS J 104 PHE 0.013 0.001 PHE I 405 TYR 0.014 0.001 TYR I1018 ARG 0.010 0.000 ARG I 202 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 1068) hydrogen bonds : angle 4.44053 ( 2966) metal coordination : bond 0.00731 ( 8) metal coordination : angle 3.01499 ( 12) covalent geometry : bond 0.00302 (26534) covalent geometry : angle 0.63430 (36091) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 410 time to evaluate : 3.396 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: G 76 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: G 120 ASP cc_start: 0.8035 (p0) cc_final: 0.7557 (p0) REVERT: G 200 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8360 (ttpt) REVERT: H 18 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7588 (mm-40) REVERT: H 51 MET cc_start: 0.7936 (tpp) cc_final: 0.7629 (ttm) REVERT: I 70 TYR cc_start: 0.8350 (t80) cc_final: 0.7945 (t80) REVERT: I 434 ASP cc_start: 0.8118 (t70) cc_final: 0.7685 (t0) REVERT: I 524 ILE cc_start: 0.8810 (tp) cc_final: 0.8546 (tp) REVERT: I 1032 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8302 (mmmm) REVERT: I 1095 ASP cc_start: 0.8779 (t0) cc_final: 0.8529 (t0) REVERT: J 69 GLU cc_start: 0.7800 (mp0) cc_final: 0.7503 (mp0) REVERT: J 235 GLU cc_start: 0.6847 (pm20) cc_final: 0.6585 (pm20) REVERT: J 327 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8236 (mm) REVERT: J 535 ARG cc_start: 0.8027 (ptm-80) cc_final: 0.7770 (ttt-90) REVERT: J 698 MET cc_start: 0.8679 (tpp) cc_final: 0.8437 (mmm) REVERT: J 788 LEU cc_start: 0.8309 (mt) cc_final: 0.7633 (tt) REVERT: J 1289 ASN cc_start: 0.7051 (p0) cc_final: 0.6550 (m110) REVERT: K 69 ARG cc_start: 0.6784 (ttp80) cc_final: 0.6518 (ttp80) REVERT: K 72 GLN cc_start: 0.7925 (tp40) cc_final: 0.7417 (tp40) REVERT: K 75 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7952 (tm-30) outliers start: 49 outliers final: 40 residues processed: 441 average time/residue: 0.4004 time to fit residues: 278.7300 Evaluate side-chains 438 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 396 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 205 optimal weight: 0.7980 chunk 287 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 313 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 233 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 702 GLN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.174423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126218 restraints weight = 33913.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.123931 restraints weight = 34979.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125063 restraints weight = 34174.878| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26542 Z= 0.150 Angle : 0.651 12.651 36103 Z= 0.330 Chirality : 0.043 0.298 4129 Planarity : 0.004 0.062 4519 Dihedral : 13.110 151.999 4202 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.67 % Allowed : 18.47 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 3152 helix: 1.33 (0.16), residues: 1078 sheet: -0.97 (0.24), residues: 445 loop : -1.50 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP J1020 HIS 0.006 0.001 HIS J 104 PHE 0.013 0.001 PHE I 405 TYR 0.018 0.001 TYR G 185 ARG 0.011 0.000 ARG I 202 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 1068) hydrogen bonds : angle 4.46532 ( 2966) metal coordination : bond 0.00855 ( 8) metal coordination : angle 3.18032 ( 12) covalent geometry : bond 0.00360 (26534) covalent geometry : angle 0.64900 (36091) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 404 time to evaluate : 3.170 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: G 76 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: G 120 ASP cc_start: 0.8052 (p0) cc_final: 0.7570 (p0) REVERT: G 200 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8361 (ttpt) REVERT: H 18 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7605 (mm-40) REVERT: H 51 MET cc_start: 0.7974 (tpp) cc_final: 0.7632 (ttm) REVERT: I 542 ARG cc_start: 0.6817 (ttt180) cc_final: 0.6488 (ttt180) REVERT: I 1032 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8367 (mmmm) REVERT: I 1095 ASP cc_start: 0.8839 (t0) cc_final: 0.8568 (t0) REVERT: J 69 GLU cc_start: 0.7887 (mp0) cc_final: 0.7512 (mp0) REVERT: J 235 GLU cc_start: 0.6884 (pm20) cc_final: 0.6619 (pm20) REVERT: J 281 ARG cc_start: 0.7502 (mmp80) cc_final: 0.7271 (mmp80) REVERT: J 327 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8247 (mm) REVERT: J 462 ASP cc_start: 0.8315 (p0) cc_final: 0.8030 (p0) REVERT: J 535 ARG cc_start: 0.8009 (ptm-80) cc_final: 0.7776 (ttt-90) REVERT: J 698 MET cc_start: 0.8691 (tpp) cc_final: 0.8447 (mmm) REVERT: J 1289 ASN cc_start: 0.7048 (p0) cc_final: 0.6730 (m110) REVERT: K 72 GLN cc_start: 0.8075 (tp40) cc_final: 0.7535 (tp40) REVERT: K 75 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8075 (tm-30) outliers start: 45 outliers final: 42 residues processed: 431 average time/residue: 0.3905 time to fit residues: 266.4783 Evaluate side-chains 435 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 391 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 119 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 302 optimal weight: 0.9990 chunk 283 optimal weight: 50.0000 chunk 114 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 93 optimal weight: 0.0010 chunk 148 optimal weight: 8.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 702 GLN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.175555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126825 restraints weight = 33919.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.124660 restraints weight = 35063.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125907 restraints weight = 33151.313| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26542 Z= 0.129 Angle : 0.651 12.518 36103 Z= 0.328 Chirality : 0.043 0.286 4129 Planarity : 0.004 0.062 4519 Dihedral : 13.090 151.793 4202 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.74 % Allowed : 18.81 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 3152 helix: 1.39 (0.16), residues: 1076 sheet: -0.92 (0.24), residues: 453 loop : -1.47 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP J1193 HIS 0.006 0.001 HIS J 104 PHE 0.013 0.001 PHE I 405 TYR 0.021 0.001 TYR H 177 ARG 0.014 0.001 ARG J 81 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 1068) hydrogen bonds : angle 4.43514 ( 2966) metal coordination : bond 0.00749 ( 8) metal coordination : angle 2.74764 ( 12) covalent geometry : bond 0.00305 (26534) covalent geometry : angle 0.64952 (36091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9081.46 seconds wall clock time: 161 minutes 49.92 seconds (9709.92 seconds total)