Starting phenix.real_space_refine on Fri Sep 19 13:51:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xug_33468/09_2025/7xug_33468.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xug_33468/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xug_33468/09_2025/7xug_33468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xug_33468/09_2025/7xug_33468.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xug_33468/09_2025/7xug_33468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xug_33468/09_2025/7xug_33468.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 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: 5.74, per 1000 atoms: 0.22 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: 2.39 Conformation dependent library (CDL) restraints added in 997.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.95 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: 6.38 Time building geometry restraints manager: 3.15 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 29.660 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.420 ------------------------------------------------------------------------------- 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 : 6.60 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.023 0.001 ARG I1033 TYR 0.040 0.003 TYR I1018 PHE 0.027 0.003 PHE J 17 TRP 0.015 0.002 TRP J1193 HIS 0.009 0.002 HIS J 80 Details of bonding type rmsd covalent geometry : bond 0.00883 (26534) covalent geometry : angle 0.86931 (36091) hydrogen bonds : bond 0.15059 ( 1068) hydrogen bonds : angle 6.44076 ( 2966) metal coordination : bond 0.01755 ( 8) metal coordination : angle 5.29015 ( 12) *********************** 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 : 0.956 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: 0.1947 time to fit residues: 140.5941 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 : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.0670 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.0050 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 0.5532 ------------------------------------------------------------------------------- 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** I1268 GLN J 232 ASN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.172242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123908 restraints weight = 33915.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121329 restraints weight = 36457.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122676 restraints weight = 32223.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123632 restraints weight = 22371.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124047 restraints weight = 20129.158| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26542 Z= 0.139 Angle : 0.661 9.986 36103 Z= 0.344 Chirality : 0.044 0.217 4129 Planarity : 0.005 0.069 4519 Dihedral : 13.384 151.495 4202 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 1.04 % Allowed : 8.09 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.15), residues: 3152 helix: 0.75 (0.16), residues: 1073 sheet: -1.41 (0.25), residues: 402 loop : -2.00 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 170 TYR 0.025 0.001 TYR I1018 PHE 0.019 0.001 PHE I 337 TRP 0.034 0.002 TRP J1020 HIS 0.006 0.001 HIS G 23 Details of bonding type rmsd covalent geometry : bond 0.00308 (26534) covalent geometry : angle 0.65881 (36091) hydrogen bonds : bond 0.04681 ( 1068) hydrogen bonds : angle 5.04463 ( 2966) metal coordination : bond 0.00910 ( 8) metal coordination : angle 3.08295 ( 12) *********************** 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 501 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 473 time to evaluate : 1.101 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: H 51 MET cc_start: 0.7969 (tpp) cc_final: 0.7686 (ttm) REVERT: H 75 GLN cc_start: 0.7753 (tt0) cc_final: 0.7462 (tt0) REVERT: I 14 ASP cc_start: 0.8526 (t0) cc_final: 0.8310 (t0) REVERT: I 239 MET cc_start: 0.6675 (tmm) cc_final: 0.6393 (tmm) REVERT: I 299 LYS cc_start: 0.7320 (tptp) cc_final: 0.7051 (tptp) REVERT: I 369 MET cc_start: 0.8028 (tmm) cc_final: 0.7769 (tmm) REVERT: I 628 HIS cc_start: 0.7052 (m-70) cc_final: 0.6760 (m-70) REVERT: I 1211 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7464 (ttm110) REVERT: J 140 TYR cc_start: 0.7710 (m-80) cc_final: 0.6592 (m-80) REVERT: J 141 PHE cc_start: 0.8058 (m-80) cc_final: 0.7479 (m-80) REVERT: J 602 SER cc_start: 0.8720 (t) cc_final: 0.8314 (p) REVERT: J 625 MET cc_start: 0.8234 (ttp) cc_final: 0.8017 (ttp) REVERT: J 788 LEU cc_start: 0.8583 (mt) cc_final: 0.7904 (tt) REVERT: J 811 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7146 (mt-10) REVERT: J 918 ILE cc_start: 0.8760 (pt) cc_final: 0.8418 (mt) REVERT: K 11 GLU cc_start: 0.7634 (pp20) cc_final: 0.7427 (pp20) REVERT: K 61 ASN cc_start: 0.7550 (t0) cc_final: 0.7126 (t0) outliers start: 28 outliers final: 19 residues processed: 481 average time/residue: 0.2000 time to fit residues: 148.4377 Evaluate side-chains 418 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 399 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 SER 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 301 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 318 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 6 optimal weight: 0.0020 chunk 314 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 overall best weight: 2.0172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I 955 GLN J 489 ASN 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 = 0.3908 r_free = 0.3908 target = 0.167896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120231 restraints weight = 34441.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117385 restraints weight = 41756.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.118528 restraints weight = 40241.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119270 restraints weight = 26753.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121819 restraints weight = 22151.570| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26542 Z= 0.223 Angle : 0.671 10.889 36103 Z= 0.346 Chirality : 0.045 0.190 4129 Planarity : 0.005 0.054 4519 Dihedral : 13.368 151.562 4202 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.50 % Favored : 93.46 % Rotamer: Outliers : 2.04 % Allowed : 11.98 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.15), residues: 3152 helix: 0.84 (0.16), residues: 1075 sheet: -1.40 (0.24), residues: 434 loop : -1.98 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 170 TYR 0.025 0.001 TYR I1018 PHE 0.020 0.002 PHE I 337 TRP 0.021 0.002 TRP J1020 HIS 0.006 0.001 HIS I 628 Details of bonding type rmsd covalent geometry : bond 0.00534 (26534) covalent geometry : angle 0.66640 (36091) hydrogen bonds : bond 0.04881 ( 1068) hydrogen bonds : angle 4.90598 ( 2966) metal coordination : bond 0.01627 ( 8) metal coordination : angle 4.47984 ( 12) *********************** 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 461 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 406 time to evaluate : 1.067 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 77 ASP cc_start: 0.7801 (m-30) cc_final: 0.7561 (m-30) REVERT: H 51 MET cc_start: 0.8042 (tpp) cc_final: 0.7748 (ttm) REVERT: I 369 MET cc_start: 0.8023 (tmm) cc_final: 0.7751 (tmm) REVERT: I 370 MET cc_start: 0.7914 (mmm) cc_final: 0.7569 (mmm) REVERT: I 628 HIS cc_start: 0.7050 (m-70) cc_final: 0.6693 (m-70) REVERT: I 1188 ASP cc_start: 0.8748 (p0) cc_final: 0.8539 (p0) REVERT: J 37 GLU cc_start: 0.6709 (tt0) cc_final: 0.6503 (tt0) REVERT: J 140 TYR cc_start: 0.7339 (m-80) cc_final: 0.7047 (m-80) REVERT: J 788 LEU cc_start: 0.8511 (mt) cc_final: 0.7910 (tt) REVERT: J 1104 LYS cc_start: 0.8579 (tmtt) cc_final: 0.8370 (tptp) REVERT: K 72 GLN cc_start: 0.8041 (tp40) cc_final: 0.7766 (tp40) outliers start: 55 outliers final: 38 residues processed: 438 average time/residue: 0.1842 time to fit residues: 125.6179 Evaluate side-chains 416 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 378 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 101 THR 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 115 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 223 LEU 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 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 777 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 119 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 619 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 1219 ASP 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 158 optimal weight: 0.7980 chunk 216 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.0970 chunk 246 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 702 GLN ** 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 = 0.3939 r_free = 0.3939 target = 0.170924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122491 restraints weight = 34084.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120139 restraints weight = 35616.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121127 restraints weight = 36014.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121890 restraints weight = 22726.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124116 restraints weight = 18888.037| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26542 Z= 0.126 Angle : 0.609 9.225 36103 Z= 0.314 Chirality : 0.043 0.315 4129 Planarity : 0.004 0.063 4519 Dihedral : 13.275 151.279 4202 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.17 % Favored : 94.80 % Rotamer: Outliers : 2.00 % Allowed : 14.06 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.15), residues: 3152 helix: 1.12 (0.16), residues: 1077 sheet: -1.12 (0.25), residues: 412 loop : -1.84 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 67 TYR 0.013 0.001 TYR I1018 PHE 0.015 0.001 PHE I 337 TRP 0.024 0.002 TRP J1020 HIS 0.006 0.001 HIS I 628 Details of bonding type rmsd covalent geometry : bond 0.00291 (26534) covalent geometry : angle 0.60537 (36091) hydrogen bonds : bond 0.04022 ( 1068) hydrogen bonds : angle 4.67686 ( 2966) metal coordination : bond 0.00856 ( 8) metal coordination : angle 3.87295 ( 12) *********************** 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 479 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 425 time to evaluate : 0.896 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: H 51 MET cc_start: 0.8018 (tpp) cc_final: 0.7783 (ttm) REVERT: H 104 LYS cc_start: 0.8395 (tptp) cc_final: 0.8006 (tptm) REVERT: H 226 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7324 (tm-30) REVERT: I 202 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7296 (ttp-110) REVERT: I 524 ILE cc_start: 0.8695 (tp) cc_final: 0.8444 (tp) REVERT: I 1042 LEU cc_start: 0.8045 (mt) cc_final: 0.7775 (mt) REVERT: J 136 GLU cc_start: 0.7900 (pp20) cc_final: 0.7683 (pp20) REVERT: J 602 SER cc_start: 0.8717 (t) cc_final: 0.8277 (p) REVERT: J 788 LEU cc_start: 0.8355 (mt) cc_final: 0.7792 (tt) REVERT: J 918 ILE cc_start: 0.8815 (pt) cc_final: 0.8347 (mt) REVERT: K 72 GLN cc_start: 0.8168 (tp40) cc_final: 0.7829 (tp40) REVERT: K 75 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8211 (tm-30) outliers start: 54 outliers final: 36 residues processed: 453 average time/residue: 0.1745 time to fit residues: 123.4264 Evaluate side-chains 430 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 394 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 ILE 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 90 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 347 ILE Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 514 PHE 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 777 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 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 807 LEU 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 317 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 304 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** 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 = 0.3953 r_free = 0.3953 target = 0.171792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124002 restraints weight = 33854.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121650 restraints weight = 35861.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122850 restraints weight = 37034.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123443 restraints weight = 23827.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125341 restraints weight = 20414.568| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26542 Z= 0.203 Angle : 0.653 9.144 36103 Z= 0.334 Chirality : 0.044 0.205 4129 Planarity : 0.005 0.066 4519 Dihedral : 13.305 151.737 4202 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.41 % Favored : 93.56 % Rotamer: Outliers : 2.67 % Allowed : 15.39 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.15), residues: 3152 helix: 1.10 (0.16), residues: 1078 sheet: -1.12 (0.25), residues: 431 loop : -1.86 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 67 TYR 0.024 0.001 TYR I1018 PHE 0.015 0.001 PHE I 405 TRP 0.024 0.002 TRP J1020 HIS 0.007 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00487 (26534) covalent geometry : angle 0.64995 (36091) hydrogen bonds : bond 0.04428 ( 1068) hydrogen bonds : angle 4.67912 ( 2966) metal coordination : bond 0.01171 ( 8) metal coordination : angle 3.77553 ( 12) *********************** 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 480 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 408 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: H 18 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7498 (mm-40) REVERT: H 51 MET cc_start: 0.8010 (tpp) cc_final: 0.7742 (ttm) REVERT: H 226 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7351 (tm-30) REVERT: I 424 ASP cc_start: 0.7627 (m-30) cc_final: 0.7400 (m-30) REVERT: I 1042 LEU cc_start: 0.8079 (mt) cc_final: 0.7854 (mt) REVERT: J 698 MET cc_start: 0.8711 (tpp) cc_final: 0.8482 (mmm) REVERT: J 788 LEU cc_start: 0.8430 (mt) cc_final: 0.7799 (tt) outliers start: 72 outliers final: 59 residues processed: 452 average time/residue: 0.1822 time to fit residues: 128.4504 Evaluate side-chains 438 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 378 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 157 THR 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 G residue 211 ILE 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 90 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 230 PHE 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 514 PHE Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 561 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 777 VAL Chi-restraints excluded: chain I residue 1056 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 I residue 1293 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 357 VAL Chi-restraints excluded: chain J residue 411 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 807 LEU 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 J residue 1219 ASP 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 26 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 202 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 14 optimal weight: 0.0670 chunk 319 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 313 optimal weight: 0.7980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 139 ASN ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.174377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.125724 restraints weight = 33850.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123436 restraints weight = 34734.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124804 restraints weight = 33438.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125431 restraints weight = 21855.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126802 restraints weight = 18464.922| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2337 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 : 0.612 10.050 36103 Z= 0.311 Chirality : 0.042 0.205 4129 Planarity : 0.004 0.066 4519 Dihedral : 13.219 151.422 4202 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.92 % Rotamer: Outliers : 2.08 % Allowed : 16.80 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.15), residues: 3152 helix: 1.26 (0.16), residues: 1076 sheet: -0.98 (0.25), residues: 424 loop : -1.74 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 175 TYR 0.027 0.001 TYR I 70 PHE 0.015 0.001 PHE I 80 TRP 0.020 0.001 TRP J1193 HIS 0.005 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00289 (26534) covalent geometry : angle 0.60819 (36091) hydrogen bonds : bond 0.03774 ( 1068) hydrogen bonds : angle 4.55707 ( 2966) metal coordination : bond 0.00856 ( 8) metal coordination : angle 3.75830 ( 12) *********************** 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 483 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 427 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: G 200 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8291 (ttpt) REVERT: H 18 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7486 (mm-40) REVERT: I 524 ILE cc_start: 0.8709 (tp) cc_final: 0.8433 (tp) REVERT: I 1042 LEU cc_start: 0.8035 (mt) cc_final: 0.7805 (mt) REVERT: J 172 PHE cc_start: 0.6469 (m-80) cc_final: 0.5639 (m-80) REVERT: J 235 GLU cc_start: 0.6899 (pm20) cc_final: 0.6628 (pm20) REVERT: J 327 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8176 (mm) REVERT: J 602 SER cc_start: 0.8756 (t) cc_final: 0.8279 (p) REVERT: J 698 MET cc_start: 0.8700 (tpp) cc_final: 0.8488 (mmm) REVERT: J 788 LEU cc_start: 0.8312 (mt) cc_final: 0.7716 (tt) REVERT: J 821 MET cc_start: 0.7026 (tpp) cc_final: 0.6807 (tpt) REVERT: J 1104 LYS cc_start: 0.8666 (tmtt) cc_final: 0.8453 (tttm) REVERT: J 1289 ASN cc_start: 0.7076 (p0) cc_final: 0.6358 (m110) REVERT: K 62 GLN cc_start: 0.7850 (tp40) cc_final: 0.7511 (mm-40) REVERT: K 65 ASP cc_start: 0.6842 (p0) cc_final: 0.6596 (p0) REVERT: K 75 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8044 (tm-30) outliers start: 56 outliers final: 46 residues processed: 460 average time/residue: 0.1813 time to fit residues: 130.1809 Evaluate side-chains 437 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 389 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 110 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 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 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 514 PHE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 777 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 252 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 583 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 807 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 316 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 296 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 297 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3989 r_free = 0.3989 target = 0.175117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126451 restraints weight = 33828.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.124289 restraints weight = 35371.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.125599 restraints weight = 33155.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126022 restraints weight = 22999.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127788 restraints weight = 19593.826| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26542 Z= 0.121 Angle : 0.611 10.452 36103 Z= 0.311 Chirality : 0.042 0.168 4129 Planarity : 0.004 0.066 4519 Dihedral : 13.160 151.650 4202 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.61 % Rotamer: Outliers : 1.97 % Allowed : 17.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.15), residues: 3152 helix: 1.34 (0.16), residues: 1079 sheet: -0.98 (0.25), residues: 419 loop : -1.65 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 214 TYR 0.018 0.001 TYR H 177 PHE 0.013 0.001 PHE I 405 TRP 0.019 0.001 TRP J1193 HIS 0.005 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00280 (26534) covalent geometry : angle 0.60783 (36091) hydrogen bonds : bond 0.03598 ( 1068) hydrogen bonds : angle 4.46252 ( 2966) metal coordination : bond 0.00728 ( 8) metal coordination : angle 3.44507 ( 12) *********************** 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: 53 poor density : 418 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8920 (mppt) cc_final: 0.8634 (mmmm) REVERT: G 76 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: G 200 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8271 (ttpt) REVERT: H 18 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7518 (mm-40) REVERT: I 14 ASP cc_start: 0.8469 (t0) cc_final: 0.8219 (t0) REVERT: I 70 TYR cc_start: 0.8260 (t80) cc_final: 0.8008 (t80) REVERT: I 424 ASP cc_start: 0.7667 (m-30) cc_final: 0.7431 (m-30) REVERT: I 524 ILE cc_start: 0.8684 (tp) cc_final: 0.8407 (tp) REVERT: I 953 LEU cc_start: 0.8427 (tp) cc_final: 0.8133 (tt) REVERT: J 69 GLU cc_start: 0.7834 (mp0) cc_final: 0.7499 (mp0) REVERT: J 235 GLU cc_start: 0.6823 (pm20) cc_final: 0.6558 (pm20) REVERT: J 327 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8192 (mm) REVERT: J 535 ARG cc_start: 0.8013 (ptm-80) cc_final: 0.7734 (ttp80) REVERT: J 602 SER cc_start: 0.8800 (t) cc_final: 0.8301 (p) REVERT: J 698 MET cc_start: 0.8683 (tpp) cc_final: 0.8482 (mmm) REVERT: J 788 LEU cc_start: 0.8393 (mt) cc_final: 0.7715 (tt) REVERT: J 821 MET cc_start: 0.7099 (tpp) cc_final: 0.6868 (tpt) REVERT: J 1289 ASN cc_start: 0.7023 (p0) cc_final: 0.6479 (m110) REVERT: K 62 GLN cc_start: 0.7846 (tp40) cc_final: 0.7501 (mm-40) REVERT: K 65 ASP cc_start: 0.6773 (p0) cc_final: 0.6532 (p0) REVERT: K 69 ARG cc_start: 0.6804 (ttp80) cc_final: 0.6534 (ttp80) REVERT: K 75 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7959 (tm-30) outliers start: 53 outliers final: 42 residues processed: 451 average time/residue: 0.1808 time to fit residues: 127.3308 Evaluate side-chains 447 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 403 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 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 90 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 347 ILE 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 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 252 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 661 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 173 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 301 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.173197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124704 restraints weight = 33802.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122653 restraints weight = 35744.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123901 restraints weight = 34168.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124330 restraints weight = 23172.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126522 restraints weight = 19509.568| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26542 Z= 0.172 Angle : 0.643 11.435 36103 Z= 0.326 Chirality : 0.043 0.209 4129 Planarity : 0.004 0.062 4519 Dihedral : 13.177 151.992 4202 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.00 % Rotamer: Outliers : 2.37 % Allowed : 18.36 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.15), residues: 3152 helix: 1.28 (0.16), residues: 1080 sheet: -1.04 (0.25), residues: 425 loop : -1.65 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 175 TYR 0.015 0.001 TYR H 152 PHE 0.014 0.001 PHE I 405 TRP 0.028 0.002 TRP J1193 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00414 (26534) covalent geometry : angle 0.64084 (36091) hydrogen bonds : bond 0.03979 ( 1068) hydrogen bonds : angle 4.47734 ( 2966) metal coordination : bond 0.00948 ( 8) metal coordination : angle 3.03558 ( 12) *********************** 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 468 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 404 time to evaluate : 1.034 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 76 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: G 200 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8298 (ttpt) REVERT: H 18 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7599 (mm-40) REVERT: I 14 ASP cc_start: 0.8551 (t0) cc_final: 0.8322 (t0) REVERT: I 70 TYR cc_start: 0.8278 (t80) cc_final: 0.7982 (t80) REVERT: I 202 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7406 (ttp80) REVERT: I 369 MET cc_start: 0.7942 (tpt) cc_final: 0.7733 (tpt) REVERT: I 370 MET cc_start: 0.7565 (mmp) cc_final: 0.7245 (mmm) REVERT: I 371 ARG cc_start: 0.7510 (mtm-85) cc_final: 0.7277 (mtm-85) REVERT: I 378 ARG cc_start: 0.7622 (ptm-80) cc_final: 0.7335 (ttp80) REVERT: I 1032 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8336 (mmmm) REVERT: J 69 GLU cc_start: 0.7777 (mp0) cc_final: 0.7472 (mp0) REVERT: J 235 GLU cc_start: 0.6867 (pm20) cc_final: 0.6589 (pm20) REVERT: J 327 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8242 (mm) REVERT: J 788 LEU cc_start: 0.8440 (mt) cc_final: 0.7786 (tt) REVERT: J 821 MET cc_start: 0.7120 (tpp) cc_final: 0.6827 (tpp) REVERT: J 1289 ASN cc_start: 0.7126 (p0) cc_final: 0.6566 (m110) REVERT: J 1290 ARG cc_start: 0.7283 (ttp-110) cc_final: 0.7039 (ptt180) REVERT: K 62 GLN cc_start: 0.7806 (tp40) cc_final: 0.7501 (mm-40) outliers start: 64 outliers final: 55 residues processed: 444 average time/residue: 0.1931 time to fit residues: 134.2009 Evaluate side-chains 439 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 382 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 198 LEU 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 90 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 347 ILE Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 561 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 252 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 619 ILE Chi-restraints excluded: chain J residue 661 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 294 optimal weight: 0.0020 chunk 91 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 313 optimal weight: 4.9990 chunk 269 optimal weight: 0.4980 chunk 259 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 105 optimal weight: 0.0010 chunk 37 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 314 ASN J 489 ASN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129338 restraints weight = 33828.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126643 restraints weight = 35692.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127788 restraints weight = 38278.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128938 restraints weight = 22056.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134465 restraints weight = 18291.666| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26542 Z= 0.119 Angle : 0.647 22.715 36103 Z= 0.325 Chirality : 0.042 0.238 4129 Planarity : 0.004 0.063 4519 Dihedral : 13.112 151.603 4202 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.85 % Allowed : 19.03 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.15), residues: 3152 helix: 1.42 (0.16), residues: 1076 sheet: -0.92 (0.25), residues: 431 loop : -1.57 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 473 TYR 0.015 0.001 TYR H 152 PHE 0.013 0.001 PHE I 405 TRP 0.031 0.002 TRP J1193 HIS 0.005 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00270 (26534) covalent geometry : angle 0.64520 (36091) hydrogen bonds : bond 0.03489 ( 1068) hydrogen bonds : angle 4.40634 ( 2966) metal coordination : bond 0.00591 ( 8) metal coordination : angle 2.87338 ( 12) *********************** 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 471 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 421 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8887 (mppt) cc_final: 0.8609 (mmmt) REVERT: G 76 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: G 200 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8228 (ttpt) REVERT: H 18 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7664 (mm-40) REVERT: H 194 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6643 (mm-40) REVERT: H 226 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7273 (tm-30) REVERT: I 70 TYR cc_start: 0.8266 (t80) cc_final: 0.7964 (t80) REVERT: I 202 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7264 (ttp80) REVERT: I 370 MET cc_start: 0.7682 (mmp) cc_final: 0.7352 (mmm) REVERT: I 378 ARG cc_start: 0.7736 (ptm-80) cc_final: 0.7350 (ttp80) REVERT: I 524 ILE cc_start: 0.8588 (tp) cc_final: 0.8290 (tp) REVERT: I 542 ARG cc_start: 0.6936 (ttt180) cc_final: 0.6696 (ttt180) REVERT: I 696 ASP cc_start: 0.7333 (t70) cc_final: 0.7107 (t70) REVERT: I 1032 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8528 (mmmm) REVERT: J 69 GLU cc_start: 0.7848 (mp0) cc_final: 0.7476 (mp0) REVERT: J 235 GLU cc_start: 0.6943 (pm20) cc_final: 0.6648 (pm20) REVERT: J 281 ARG cc_start: 0.7700 (mmp80) cc_final: 0.7391 (mmp80) REVERT: J 327 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8197 (mm) REVERT: J 535 ARG cc_start: 0.8134 (ptm-80) cc_final: 0.7777 (ttp80) REVERT: J 788 LEU cc_start: 0.8277 (mt) cc_final: 0.7629 (tt) REVERT: J 821 MET cc_start: 0.7311 (tpp) cc_final: 0.7043 (tpp) REVERT: J 1289 ASN cc_start: 0.6742 (p0) cc_final: 0.6424 (m110) REVERT: K 69 ARG cc_start: 0.6959 (ttp80) cc_final: 0.6699 (ttp80) outliers start: 50 outliers final: 40 residues processed: 453 average time/residue: 0.1864 time to fit residues: 133.5782 Evaluate side-chains 446 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 403 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 110 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 347 ILE 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 514 PHE 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 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 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 661 VAL 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 287 optimal weight: 10.0000 chunk 212 optimal weight: 0.6980 chunk 166 optimal weight: 0.0050 chunk 61 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 chunk 291 optimal weight: 0.9980 chunk 284 optimal weight: 0.3980 chunk 300 optimal weight: 0.8980 chunk 279 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN ** 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 = 0.4001 r_free = 0.4001 target = 0.176381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129155 restraints weight = 33789.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126316 restraints weight = 35471.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127547 restraints weight = 38350.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128719 restraints weight = 22670.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134202 restraints weight = 18977.095| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26542 Z= 0.118 Angle : 0.651 18.177 36103 Z= 0.326 Chirality : 0.043 0.281 4129 Planarity : 0.004 0.065 4519 Dihedral : 13.061 151.838 4202 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.71 % Allowed : 19.47 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 3152 helix: 1.43 (0.16), residues: 1079 sheet: -0.85 (0.24), residues: 443 loop : -1.53 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 473 TYR 0.027 0.001 TYR J 144 PHE 0.019 0.001 PHE J 141 TRP 0.034 0.002 TRP J1020 HIS 0.005 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00275 (26534) covalent geometry : angle 0.64885 (36091) hydrogen bonds : bond 0.03426 ( 1068) hydrogen bonds : angle 4.37850 ( 2966) metal coordination : bond 0.00605 ( 8) metal coordination : angle 2.94582 ( 12) ********************** 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 470 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 424 time to evaluate : 1.000 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 10 LYS cc_start: 0.8841 (mppt) cc_final: 0.8515 (mmmm) REVERT: G 76 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: G 200 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8239 (ttpt) REVERT: H 18 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7626 (mm-40) REVERT: H 208 ASN cc_start: 0.8583 (p0) cc_final: 0.8264 (p0) REVERT: I 70 TYR cc_start: 0.8268 (t80) cc_final: 0.7954 (t80) REVERT: I 202 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7531 (ttp80) REVERT: I 378 ARG cc_start: 0.7719 (ptm-80) cc_final: 0.7402 (ttp80) REVERT: I 524 ILE cc_start: 0.8604 (tp) cc_final: 0.8344 (tp) REVERT: I 542 ARG cc_start: 0.6841 (ttt180) cc_final: 0.6621 (ttt180) REVERT: I 696 ASP cc_start: 0.7349 (t70) cc_final: 0.7130 (t70) REVERT: I 1032 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8544 (mmmm) REVERT: J 69 GLU cc_start: 0.7861 (mp0) cc_final: 0.7449 (mp0) REVERT: J 141 PHE cc_start: 0.8131 (m-80) cc_final: 0.7853 (m-80) REVERT: J 144 TYR cc_start: 0.7296 (m-10) cc_final: 0.6751 (m-10) REVERT: J 235 GLU cc_start: 0.6864 (pm20) cc_final: 0.6556 (pm20) REVERT: J 274 ASN cc_start: 0.8170 (m-40) cc_final: 0.7957 (m110) REVERT: J 327 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8187 (mm) REVERT: J 535 ARG cc_start: 0.8099 (ptm-80) cc_final: 0.7743 (ttp80) REVERT: J 698 MET cc_start: 0.8700 (tpp) cc_final: 0.8454 (mmm) REVERT: J 788 LEU cc_start: 0.8261 (mt) cc_final: 0.7613 (tt) REVERT: J 821 MET cc_start: 0.7230 (tpp) cc_final: 0.6961 (tpp) REVERT: K 41 GLU cc_start: 0.6688 (tm-30) cc_final: 0.6484 (tm-30) REVERT: K 69 ARG cc_start: 0.6960 (ttp80) cc_final: 0.6741 (ttp80) outliers start: 46 outliers final: 40 residues processed: 452 average time/residue: 0.1893 time to fit residues: 134.2571 Evaluate side-chains 441 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 399 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 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 110 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL 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 514 PHE 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 661 VAL Chi-restraints excluded: chain J residue 697 MET 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 J residue 1209 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 86 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 271 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 258 optimal weight: 1.9990 chunk 270 optimal weight: 0.5980 chunk 204 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1289 ASN ** K 75 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 = 0.3985 r_free = 0.3985 target = 0.174785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127073 restraints weight = 33704.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125227 restraints weight = 34380.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126131 restraints weight = 35824.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127257 restraints weight = 22976.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128066 restraints weight = 19470.190| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26542 Z= 0.149 Angle : 0.672 18.374 36103 Z= 0.338 Chirality : 0.043 0.294 4129 Planarity : 0.004 0.063 4519 Dihedral : 13.078 152.042 4202 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.78 % Allowed : 19.51 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.15), residues: 3152 helix: 1.36 (0.16), residues: 1084 sheet: -0.86 (0.24), residues: 448 loop : -1.49 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J1290 TYR 0.022 0.001 TYR J 144 PHE 0.013 0.001 PHE I 405 TRP 0.035 0.002 TRP J1020 HIS 0.005 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00357 (26534) covalent geometry : angle 0.66977 (36091) hydrogen bonds : bond 0.03700 ( 1068) hydrogen bonds : angle 4.42869 ( 2966) metal coordination : bond 0.00788 ( 8) metal coordination : angle 2.73070 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4338.81 seconds wall clock time: 75 minutes 45.30 seconds (4545.30 seconds total)