Starting phenix.real_space_refine on Thu Mar 21 03:47:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k19_22622/03_2024/7k19_22622.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k19_22622/03_2024/7k19_22622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k19_22622/03_2024/7k19_22622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k19_22622/03_2024/7k19_22622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k19_22622/03_2024/7k19_22622.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k19_22622/03_2024/7k19_22622.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 185 5.16 5 C 18559 2.51 5 N 4956 2.21 5 O 5412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A GLU 767": "OE1" <-> "OE2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A GLU 932": "OE1" <-> "OE2" Residue "A TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A ARG 1152": "NH1" <-> "NH2" Residue "A ARG 1155": "NH1" <-> "NH2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A ARG 1420": "NH1" <-> "NH2" Residue "A GLU 1526": "OE1" <-> "OE2" Residue "A GLU 1570": "OE1" <-> "OE2" Residue "A GLU 1640": "OE1" <-> "OE2" Residue "A GLU 1709": "OE1" <-> "OE2" Residue "A ARG 1712": "NH1" <-> "NH2" Residue "A ARG 1727": "NH1" <-> "NH2" Residue "A ARG 1768": "NH1" <-> "NH2" Residue "A ARG 1787": "NH1" <-> "NH2" Residue "A ARG 1788": "NH1" <-> "NH2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1822": "NH1" <-> "NH2" Residue "A ARG 1883": "NH1" <-> "NH2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A GLU 2039": "OE1" <-> "OE2" Residue "A ARG 2143": "NH1" <-> "NH2" Residue "A ARG 2158": "NH1" <-> "NH2" Residue "A ARG 2214": "NH1" <-> "NH2" Residue "A ARG 2228": "NH1" <-> "NH2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A ARG 2311": "NH1" <-> "NH2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A GLU 2343": "OE1" <-> "OE2" Residue "A ARG 2404": "NH1" <-> "NH2" Residue "A ARG 2427": "NH1" <-> "NH2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A ARG 2452": "NH1" <-> "NH2" Residue "A GLU 2460": "OE1" <-> "OE2" Residue "A ARG 2530": "NH1" <-> "NH2" Residue "A ARG 2800": "NH1" <-> "NH2" Residue "A ARG 2940": "NH1" <-> "NH2" Residue "A GLU 2985": "OE1" <-> "OE2" Residue "A ARG 3125": "NH1" <-> "NH2" Residue "A GLU 3194": "OE1" <-> "OE2" Residue "A ARG 3232": "NH1" <-> "NH2" Residue "A ARG 3247": "NH1" <-> "NH2" Residue "A ARG 3287": "NH1" <-> "NH2" Residue "A ARG 3289": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3427": "OE1" <-> "OE2" Residue "A ARG 3467": "NH1" <-> "NH2" Residue "A ARG 3474": "NH1" <-> "NH2" Residue "A GLU 3595": "OE1" <-> "OE2" Residue "A ARG 3629": "NH1" <-> "NH2" Residue "A ARG 3630": "NH1" <-> "NH2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A GLU 3698": "OE1" <-> "OE2" Residue "A ARG 3708": "NH1" <-> "NH2" Residue "A ARG 3733": "NH1" <-> "NH2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A ARG 3763": "NH1" <-> "NH2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A ARG 3864": "NH1" <-> "NH2" Residue "A ARG 3889": "NH1" <-> "NH2" Residue "A PHE 3897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3923": "NH1" <-> "NH2" Residue "A ARG 3962": "NH1" <-> "NH2" Residue "A ARG 4041": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29158 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 28180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3569, 28180 Classifications: {'peptide': 3569} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PCIS': 1, 'PTRANS': 147, 'TRANS': 3420} Chain breaks: 20 Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 561 Unresolved non-hydrogen dihedrals: 407 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 3, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 39, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 315 Chain: "D" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "G" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Time building chain proxies: 15.26, per 1000 atoms: 0.52 Number of scatterers: 29158 At special positions: 0 Unit cell: (129.92, 148.48, 186.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 185 16.00 P 46 15.00 O 5412 8.00 N 4956 7.00 C 18559 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 - 3.50 Amino acid : False - 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: 12.01 Conformation dependent library (CDL) restraints added in 5.7 seconds 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6850 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 5 sheets defined 66.5% alpha, 0.8% beta 22 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 12.11 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 4.127A pdb=" N SER A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 40 removed outlier: 3.611A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 59 Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 78 through 96 removed outlier: 3.724A pdb=" N ARG A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 Processing helix chain 'A' and resid 124 through 138 removed outlier: 4.072A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.906A pdb=" N TYR A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 removed outlier: 3.534A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 232 removed outlier: 4.074A pdb=" N LEU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 307 through 330 removed outlier: 3.859A pdb=" N LYS A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.741A pdb=" N ARG A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.860A pdb=" N GLN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 removed outlier: 3.798A pdb=" N PHE A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.827A pdb=" N HIS A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 477 through 491 removed outlier: 4.118A pdb=" N VAL A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 488 " --> pdb=" O HIS A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 removed outlier: 4.240A pdb=" N SER A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 576 removed outlier: 4.041A pdb=" N VAL A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 632 removed outlier: 3.994A pdb=" N LEU A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 628 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 660 removed outlier: 3.795A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 680 Processing helix chain 'A' and resid 701 through 718 removed outlier: 4.088A pdb=" N LYS A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 734 Processing helix chain 'A' and resid 744 through 747 Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.532A pdb=" N LEU A 752 " --> pdb=" O TYR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 780 removed outlier: 4.427A pdb=" N LEU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 799 removed outlier: 4.082A pdb=" N CYS A 795 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 798 " --> pdb=" O CYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 878 through 883 Processing helix chain 'A' and resid 910 through 918 removed outlier: 4.469A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 946 removed outlier: 4.104A pdb=" N VAL A 928 " --> pdb=" O ARG A 924 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 4.102A pdb=" N LYS A 963 " --> pdb=" O TYR A 959 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 4.775A pdb=" N ARG A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1003 through 1018 removed outlier: 3.788A pdb=" N VAL A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1044 removed outlier: 3.672A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE A1044 " --> pdb=" O SER A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1073 through 1084 removed outlier: 3.947A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1114 Processing helix chain 'A' and resid 1123 through 1142 removed outlier: 3.952A pdb=" N ASP A1129 " --> pdb=" O GLN A1125 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A1136 " --> pdb=" O ASP A1132 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS A1141 " --> pdb=" O ILE A1137 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A1142 " --> pdb=" O ILE A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'A' and resid 1165 through 1175 Processing helix chain 'A' and resid 1176 through 1178 No H-bonds generated for 'chain 'A' and resid 1176 through 1178' Processing helix chain 'A' and resid 1180 through 1195 removed outlier: 4.535A pdb=" N HIS A1185 " --> pdb=" O THR A1181 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1216 removed outlier: 3.826A pdb=" N LEU A1208 " --> pdb=" O PRO A1204 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1226 removed outlier: 4.049A pdb=" N GLY A1226 " --> pdb=" O ASN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1245 removed outlier: 3.577A pdb=" N ARG A1245 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1266 removed outlier: 3.504A pdb=" N LEU A1254 " --> pdb=" O LEU A1250 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS A1255 " --> pdb=" O GLN A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1273 Processing helix chain 'A' and resid 1278 through 1283 removed outlier: 4.025A pdb=" N LEU A1282 " --> pdb=" O ALA A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1300 Processing helix chain 'A' and resid 1326 through 1350 removed outlier: 4.001A pdb=" N TYR A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A1338 " --> pdb=" O LYS A1334 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1353 No H-bonds generated for 'chain 'A' and resid 1351 through 1353' Processing helix chain 'A' and resid 1354 through 1359 Processing helix chain 'A' and resid 1367 through 1377 removed outlier: 4.828A pdb=" N VAL A1373 " --> pdb=" O MET A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1406 Proline residue: A1396 - end of helix removed outlier: 4.292A pdb=" N VAL A1400 " --> pdb=" O PRO A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1420 Processing helix chain 'A' and resid 1424 through 1431 Processing helix chain 'A' and resid 1444 through 1461 Processing helix chain 'A' and resid 1477 through 1492 removed outlier: 3.849A pdb=" N ILE A1491 " --> pdb=" O VAL A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1519 removed outlier: 3.901A pdb=" N ALA A1511 " --> pdb=" O CYS A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1533 removed outlier: 4.071A pdb=" N LEU A1533 " --> pdb=" O VAL A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1564 removed outlier: 4.275A pdb=" N SER A1561 " --> pdb=" O GLU A1557 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1562 " --> pdb=" O TYR A1558 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A1564 " --> pdb=" O TYR A1560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1557 through 1564' Processing helix chain 'A' and resid 1565 through 1574 removed outlier: 3.597A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1584 Processing helix chain 'A' and resid 1589 through 1607 removed outlier: 3.510A pdb=" N VAL A1593 " --> pdb=" O ASN A1589 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN A1603 " --> pdb=" O GLY A1599 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1624 removed outlier: 3.650A pdb=" N GLN A1624 " --> pdb=" O THR A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1630 removed outlier: 3.626A pdb=" N LYS A1628 " --> pdb=" O HIS A1625 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP A1630 " --> pdb=" O LYS A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1655 removed outlier: 3.622A pdb=" N ALA A1644 " --> pdb=" O GLU A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1679 removed outlier: 4.316A pdb=" N LEU A1679 " --> pdb=" O TYR A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1688 No H-bonds generated for 'chain 'A' and resid 1686 through 1688' Processing helix chain 'A' and resid 1689 through 1694 Processing helix chain 'A' and resid 1695 through 1700 removed outlier: 3.871A pdb=" N PHE A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1705 through 1722 Processing helix chain 'A' and resid 1733 through 1751 Processing helix chain 'A' and resid 1757 through 1767 removed outlier: 4.068A pdb=" N VAL A1765 " --> pdb=" O LEU A1761 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A1767 " --> pdb=" O THR A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1786 Processing helix chain 'A' and resid 1790 through 1807 Processing helix chain 'A' and resid 1812 through 1823 removed outlier: 3.585A pdb=" N ARG A1816 " --> pdb=" O LEU A1812 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1830 Processing helix chain 'A' and resid 1837 through 1843 Processing helix chain 'A' and resid 1843 through 1852 removed outlier: 6.412A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1882 removed outlier: 4.191A pdb=" N THR A1865 " --> pdb=" O SER A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1891 Processing helix chain 'A' and resid 1895 through 1900 Processing helix chain 'A' and resid 1910 through 1922 removed outlier: 3.536A pdb=" N THR A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1955 removed outlier: 3.649A pdb=" N LEU A1939 " --> pdb=" O GLU A1935 " (cutoff:3.500A) Processing helix chain 'A' and resid 1970 through 1974 removed outlier: 3.722A pdb=" N LYS A1973 " --> pdb=" O LYS A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1982 removed outlier: 3.510A pdb=" N LEU A1981 " --> pdb=" O ILE A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2035 through 2045 removed outlier: 3.980A pdb=" N PHE A2043 " --> pdb=" O GLU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2087 through 2091 Processing helix chain 'A' and resid 2093 through 2107 removed outlier: 3.642A pdb=" N LEU A2097 " --> pdb=" O CYS A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2126 through 2135 Processing helix chain 'A' and resid 2139 through 2151 removed outlier: 4.141A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A2148 " --> pdb=" O LEU A2144 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A2149 " --> pdb=" O PHE A2145 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A2150 " --> pdb=" O LEU A2146 " (cutoff:3.500A) Processing helix chain 'A' and resid 2157 through 2161 removed outlier: 4.251A pdb=" N ALA A2161 " --> pdb=" O ARG A2158 " (cutoff:3.500A) Processing helix chain 'A' and resid 2162 through 2164 No H-bonds generated for 'chain 'A' and resid 2162 through 2164' Processing helix chain 'A' and resid 2165 through 2174 removed outlier: 3.926A pdb=" N SER A2174 " --> pdb=" O GLN A2170 " (cutoff:3.500A) Processing helix chain 'A' and resid 2182 through 2196 removed outlier: 3.602A pdb=" N TRP A2196 " --> pdb=" O THR A2192 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2222 Processing helix chain 'A' and resid 2227 through 2246 removed outlier: 3.558A pdb=" N PHE A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS A2246 " --> pdb=" O VAL A2242 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2270 through 2282 Processing helix chain 'A' and resid 2295 through 2309 Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 4.030A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2338 through 2354 removed outlier: 3.942A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2371 Processing helix chain 'A' and resid 2378 through 2385 Processing helix chain 'A' and resid 2391 through 2402 removed outlier: 4.046A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2419 through 2425 removed outlier: 3.587A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2419 through 2425' Processing helix chain 'A' and resid 2428 through 2442 removed outlier: 3.687A pdb=" N LEU A2436 " --> pdb=" O GLN A2432 " (cutoff:3.500A) Processing helix chain 'A' and resid 2443 through 2446 Processing helix chain 'A' and resid 2447 through 2459 removed outlier: 3.819A pdb=" N ARG A2452 " --> pdb=" O PRO A2448 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2466 through 2481 removed outlier: 3.628A pdb=" N ARG A2470 " --> pdb=" O SER A2466 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A2477 " --> pdb=" O MET A2473 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A2478 " --> pdb=" O TYR A2474 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP A2479 " --> pdb=" O ASN A2475 " (cutoff:3.500A) Processing helix chain 'A' and resid 2497 through 2509 removed outlier: 4.093A pdb=" N VAL A2505 " --> pdb=" O LEU A2501 " (cutoff:3.500A) Processing helix chain 'A' and resid 2516 through 2526 Processing helix chain 'A' and resid 2536 through 2545 removed outlier: 3.832A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A2545 " --> pdb=" O ALA A2541 " (cutoff:3.500A) Processing helix chain 'A' and resid 2553 through 2565 removed outlier: 4.344A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) Processing helix chain 'A' and resid 2790 through 2799 removed outlier: 3.929A pdb=" N GLN A2799 " --> pdb=" O GLN A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2819 removed outlier: 3.730A pdb=" N SER A2814 " --> pdb=" O SER A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 Processing helix chain 'A' and resid 2851 through 2862 Processing helix chain 'A' and resid 2863 through 2865 No H-bonds generated for 'chain 'A' and resid 2863 through 2865' Processing helix chain 'A' and resid 2875 through 2883 removed outlier: 4.228A pdb=" N ALA A2882 " --> pdb=" O ALA A2878 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2898 removed outlier: 4.014A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG A2891 " --> pdb=" O PRO A2887 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2931 Processing helix chain 'A' and resid 2935 through 2941 Processing helix chain 'A' and resid 2952 through 2958 Processing helix chain 'A' and resid 2966 through 2977 removed outlier: 3.628A pdb=" N TYR A2972 " --> pdb=" O ALA A2968 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP A2973 " --> pdb=" O ALA A2969 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU A2974 " --> pdb=" O LYS A2970 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A2975 " --> pdb=" O GLN A2971 " (cutoff:3.500A) Processing helix chain 'A' and resid 2990 through 3004 removed outlier: 3.746A pdb=" N GLU A2995 " --> pdb=" O LYS A2991 " (cutoff:3.500A) Processing helix chain 'A' and resid 3011 through 3017 Processing helix chain 'A' and resid 3027 through 3032 removed outlier: 3.650A pdb=" N TRP A3031 " --> pdb=" O LEU A3027 " (cutoff:3.500A) Processing helix chain 'A' and resid 3034 through 3039 removed outlier: 3.605A pdb=" N THR A3039 " --> pdb=" O PHE A3035 " (cutoff:3.500A) Processing helix chain 'A' and resid 3039 through 3053 removed outlier: 4.031A pdb=" N TYR A3043 " --> pdb=" O THR A3039 " (cutoff:3.500A) Processing helix chain 'A' and resid 3060 through 3069 Processing helix chain 'A' and resid 3083 through 3093 Processing helix chain 'A' and resid 3095 through 3117 removed outlier: 4.261A pdb=" N SER A3116 " --> pdb=" O GLN A3112 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A3117 " --> pdb=" O ASN A3113 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3146 Processing helix chain 'A' and resid 3154 through 3167 Processing helix chain 'A' and resid 3175 through 3197 Processing helix chain 'A' and resid 3227 through 3249 Processing helix chain 'A' and resid 3251 through 3262 Processing helix chain 'A' and resid 3264 through 3268 removed outlier: 3.600A pdb=" N THR A3268 " --> pdb=" O GLU A3265 " (cutoff:3.500A) Processing helix chain 'A' and resid 3270 through 3290 removed outlier: 3.849A pdb=" N SER A3290 " --> pdb=" O CYS A3286 " (cutoff:3.500A) Processing helix chain 'A' and resid 3294 through 3309 removed outlier: 3.921A pdb=" N LEU A3298 " --> pdb=" O SER A3294 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A3302 " --> pdb=" O LEU A3298 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR A3303 " --> pdb=" O THR A3299 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3341 removed outlier: 3.738A pdb=" N PHE A3323 " --> pdb=" O ASN A3319 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A3341 " --> pdb=" O ILE A3337 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3360 Processing helix chain 'A' and resid 3373 through 3391 removed outlier: 4.417A pdb=" N ALA A3388 " --> pdb=" O HIS A3384 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A3389 " --> pdb=" O LEU A3385 " (cutoff:3.500A) Processing helix chain 'A' and resid 3409 through 3428 removed outlier: 3.671A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.879A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3461 through 3464 Processing helix chain 'A' and resid 3465 through 3475 removed outlier: 3.741A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3479 through 3488 removed outlier: 4.019A pdb=" N MET A3483 " --> pdb=" O THR A3479 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A3484 " --> pdb=" O LEU A3480 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3497 No H-bonds generated for 'chain 'A' and resid 3495 through 3497' Processing helix chain 'A' and resid 3498 through 3504 removed outlier: 3.715A pdb=" N MET A3502 " --> pdb=" O TRP A3498 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A3504 " --> pdb=" O SER A3500 " (cutoff:3.500A) Processing helix chain 'A' and resid 3515 through 3525 Processing helix chain 'A' and resid 3526 through 3528 No H-bonds generated for 'chain 'A' and resid 3526 through 3528' Processing helix chain 'A' and resid 3529 through 3537 removed outlier: 3.633A pdb=" N PHE A3533 " --> pdb=" O ILE A3529 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3562 removed outlier: 4.417A pdb=" N LYS A3550 " --> pdb=" O SER A3546 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A3551 " --> pdb=" O THR A3547 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A3552 " --> pdb=" O GLY A3548 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3577 Processing helix chain 'A' and resid 3580 through 3597 removed outlier: 3.662A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU A3595 " --> pdb=" O ASP A3591 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A3597 " --> pdb=" O ARG A3593 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3616 removed outlier: 3.633A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) Processing helix chain 'A' and resid 3621 through 3627 Processing helix chain 'A' and resid 3632 through 3640 removed outlier: 4.292A pdb=" N LYS A3638 " --> pdb=" O GLN A3634 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3651 removed outlier: 4.014A pdb=" N LYS A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A3647 " --> pdb=" O HIS A3643 " (cutoff:3.500A) Processing helix chain 'A' and resid 3660 through 3671 Processing helix chain 'A' and resid 3686 through 3690 removed outlier: 3.950A pdb=" N ASP A3689 " --> pdb=" O TRP A3686 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A3690 " --> pdb=" O MET A3687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3686 through 3690' Processing helix chain 'A' and resid 3760 through 3775 Processing helix chain 'A' and resid 3779 through 3785 removed outlier: 4.286A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 3.975A pdb=" N MET A3820 " --> pdb=" O LEU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 removed outlier: 3.538A pdb=" N LYS A3825 " --> pdb=" O SER A3821 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A3826 " --> pdb=" O GLN A3822 " (cutoff:3.500A) Processing helix chain 'A' and resid 3836 through 3846 Processing helix chain 'A' and resid 3853 through 3859 removed outlier: 4.189A pdb=" N TYR A3859 " --> pdb=" O TYR A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 removed outlier: 3.981A pdb=" N THR A3867 " --> pdb=" O ASN A3863 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A3874 " --> pdb=" O SER A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3891 removed outlier: 3.939A pdb=" N MET A3890 " --> pdb=" O ALA A3886 " (cutoff:3.500A) Processing helix chain 'A' and resid 3895 through 3915 removed outlier: 4.527A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS A3903 " --> pdb=" O ALA A3899 " (cutoff:3.500A) Processing helix chain 'A' and resid 3924 through 3927 Processing helix chain 'A' and resid 3964 through 3971 removed outlier: 4.086A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3979 through 3992 Processing helix chain 'A' and resid 3996 through 4007 Processing helix chain 'A' and resid 4013 through 4023 removed outlier: 3.873A pdb=" N LYS A4023 " --> pdb=" O LYS A4019 " (cutoff:3.500A) Processing helix chain 'A' and resid 4040 through 4052 Processing helix chain 'A' and resid 4055 through 4066 removed outlier: 3.871A pdb=" N THR A4060 " --> pdb=" O PRO A4056 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4081 Processing helix chain 'A' and resid 4099 through 4112 removed outlier: 3.721A pdb=" N THR A4112 " --> pdb=" O MET A4108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 3719 through 3721 removed outlier: 4.308A pdb=" N GLY A3721 " --> pdb=" O ARG A3741 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3727 through 3728 removed outlier: 3.802A pdb=" N LYS A3753 " --> pdb=" O GLY A3801 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A3802 " --> pdb=" O PRO A3795 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU A3804 " --> pdb=" O VAL A3793 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A3793 " --> pdb=" O GLU A3804 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 3809 through 3811 1427 hydrogen bonds defined for protein. 4212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 18.26 Time building geometry restraints manager: 13.05 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: 8109 1.33 - 1.46: 6601 1.46 - 1.58: 14750 1.58 - 1.70: 91 1.70 - 1.83: 286 Bond restraints: 29837 Sorted by residual: bond pdb=" C LEU A 911 " pdb=" N PRO A 912 " ideal model delta sigma weight residual 1.334 1.364 -0.030 8.40e-03 1.42e+04 1.30e+01 bond pdb=" N VAL A1021 " pdb=" CA VAL A1021 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.19e-02 7.06e+03 8.97e+00 bond pdb=" N VAL A1992 " pdb=" CA VAL A1992 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.08e+00 bond pdb=" N THR A 398 " pdb=" CA THR A 398 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.44e+00 bond pdb=" C ASP A2289 " pdb=" N PRO A2290 " ideal model delta sigma weight residual 1.339 1.429 -0.090 3.40e-02 8.65e+02 7.03e+00 ... (remaining 29832 not shown) Histogram of bond angle deviations from ideal: 82.19 - 92.93: 2 92.93 - 103.66: 528 103.66 - 114.40: 18131 114.40 - 125.13: 21232 125.13 - 135.87: 675 Bond angle restraints: 40568 Sorted by residual: angle pdb=" N ASN A3311 " pdb=" CA ASN A3311 " pdb=" C ASN A3311 " ideal model delta sigma weight residual 112.03 82.19 29.84 1.31e+00 5.83e-01 5.19e+02 angle pdb=" N PRO A1469 " pdb=" CA PRO A1469 " pdb=" C PRO A1469 " ideal model delta sigma weight residual 112.47 88.12 24.35 2.06e+00 2.36e-01 1.40e+02 angle pdb=" N VAL A4033 " pdb=" CA VAL A4033 " pdb=" C VAL A4033 " ideal model delta sigma weight residual 113.20 105.88 7.32 9.60e-01 1.09e+00 5.81e+01 angle pdb=" C ASP A1019 " pdb=" N PRO A1020 " pdb=" CA PRO A1020 " ideal model delta sigma weight residual 119.84 129.10 -9.26 1.25e+00 6.40e-01 5.48e+01 angle pdb=" C LEU A1468 " pdb=" N PRO A1469 " pdb=" CA PRO A1469 " ideal model delta sigma weight residual 119.84 128.53 -8.69 1.25e+00 6.40e-01 4.84e+01 ... (remaining 40563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 15246 17.69 - 35.37: 2112 35.37 - 53.05: 520 53.05 - 70.74: 123 70.74 - 88.42: 32 Dihedral angle restraints: 18033 sinusoidal: 7530 harmonic: 10503 Sorted by residual: dihedral pdb=" N ASN A3311 " pdb=" C ASN A3311 " pdb=" CA ASN A3311 " pdb=" CB ASN A3311 " ideal model delta harmonic sigma weight residual 122.80 106.80 16.00 0 2.50e+00 1.60e-01 4.10e+01 dihedral pdb=" CA VAL A3692 " pdb=" C VAL A3692 " pdb=" N GLU A3693 " pdb=" CA GLU A3693 " ideal model delta harmonic sigma weight residual -180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA PRO A2548 " pdb=" C PRO A2548 " pdb=" N LYS A2549 " pdb=" CA LYS A2549 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 18030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 4462 0.121 - 0.241: 193 0.241 - 0.362: 8 0.362 - 0.483: 1 0.483 - 0.603: 1 Chirality restraints: 4665 Sorted by residual: chirality pdb=" CA ASN A3311 " pdb=" N ASN A3311 " pdb=" C ASN A3311 " pdb=" CB ASN A3311 " both_signs ideal model delta sigma weight residual False 2.51 3.11 -0.60 2.00e-01 2.50e+01 9.10e+00 chirality pdb=" CA PRO A1469 " pdb=" N PRO A1469 " pdb=" C PRO A1469 " pdb=" CB PRO A1469 " both_signs ideal model delta sigma weight residual False 2.72 3.09 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE A 740 " pdb=" CA ILE A 740 " pdb=" CG1 ILE A 740 " pdb=" CG2 ILE A 740 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 4662 not shown) Planarity restraints: 4970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A1991 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C PRO A1991 " -0.085 2.00e-02 2.50e+03 pdb=" O PRO A1991 " 0.033 2.00e-02 2.50e+03 pdb=" N VAL A1992 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1686 " 0.023 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" C LEU A1686 " -0.083 2.00e-02 2.50e+03 pdb=" O LEU A1686 " 0.033 2.00e-02 2.50e+03 pdb=" N HIS A1687 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A2182 " -0.022 2.00e-02 2.50e+03 4.54e-02 2.07e+01 pdb=" C ILE A2182 " 0.079 2.00e-02 2.50e+03 pdb=" O ILE A2182 " -0.031 2.00e-02 2.50e+03 pdb=" N HIS A2183 " -0.026 2.00e-02 2.50e+03 ... (remaining 4967 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 405 2.61 - 3.18: 25069 3.18 - 3.76: 47217 3.76 - 4.33: 59365 4.33 - 4.90: 92489 Nonbonded interactions: 224545 Sorted by model distance: nonbonded pdb=" N ASN A3311 " pdb=" N VAL A3312 " model vdw 2.038 2.560 nonbonded pdb=" O ASN A1055 " pdb=" OG SER A1058 " model vdw 2.242 2.440 nonbonded pdb=" O LYS A 205 " pdb=" OG1 THR A 209 " model vdw 2.242 2.440 nonbonded pdb=" O TYR A1560 " pdb=" OG SER A1564 " model vdw 2.251 2.440 nonbonded pdb=" O SER A 72 " pdb=" OG SER A 72 " model vdw 2.258 2.440 ... (remaining 224540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.930 Check model and map are aligned: 0.480 Set scattering table: 0.250 Process input model: 94.090 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.006 0.090 29837 Z= 0.389 Angle : 1.100 29.841 40568 Z= 0.599 Chirality : 0.058 0.603 4665 Planarity : 0.008 0.090 4970 Dihedral : 17.644 88.425 11183 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.73 % Favored : 86.96 % Rotamer: Outliers : 0.65 % Allowed : 12.15 % Favored : 87.20 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.11), residues: 3527 helix: -2.62 (0.08), residues: 2189 sheet: -1.86 (0.82), residues: 39 loop : -4.32 (0.14), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A3916 HIS 0.008 0.002 HIS A 533 PHE 0.039 0.002 PHE A2260 TYR 0.026 0.002 TYR A3610 ARG 0.006 0.001 ARG A1340 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 396 time to evaluate : 3.389 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: A 59 PHE cc_start: 0.4739 (m-80) cc_final: 0.4433 (m-10) REVERT: A 189 MET cc_start: 0.5052 (mpp) cc_final: 0.4776 (mpp) REVERT: A 264 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7879 (mmm160) REVERT: A 749 VAL cc_start: 0.9148 (m) cc_final: 0.8940 (t) REVERT: A 785 MET cc_start: 0.7112 (mmm) cc_final: 0.6833 (mmt) REVERT: A 1015 ASP cc_start: 0.7326 (p0) cc_final: 0.6559 (p0) REVERT: A 1392 MET cc_start: 0.7139 (tmm) cc_final: 0.6895 (tmm) REVERT: A 1804 MET cc_start: 0.9117 (ptm) cc_final: 0.8840 (tmm) REVERT: A 1860 GLU cc_start: 0.9280 (pm20) cc_final: 0.8804 (mm-30) REVERT: A 1871 MET cc_start: 0.9255 (ttm) cc_final: 0.9040 (ttm) REVERT: A 2038 GLU cc_start: 0.7336 (mp0) cc_final: 0.6994 (mp0) REVERT: A 2126 MET cc_start: 0.7480 (ttm) cc_final: 0.7109 (ttm) REVERT: A 2222 HIS cc_start: 0.8158 (m-70) cc_final: 0.7631 (m90) REVERT: A 2408 MET cc_start: 0.6941 (ttm) cc_final: 0.6517 (tpt) REVERT: A 2442 MET cc_start: 0.8980 (ptm) cc_final: 0.8696 (ptt) REVERT: A 2473 MET cc_start: 0.7543 (ttp) cc_final: 0.7188 (ttp) REVERT: A 2545 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8344 (pp) REVERT: A 3046 ARG cc_start: 0.8343 (ttt90) cc_final: 0.8068 (ptm160) REVERT: A 3256 MET cc_start: 0.7925 (tpp) cc_final: 0.7664 (tpp) REVERT: A 3523 ASP cc_start: 0.7295 (m-30) cc_final: 0.6882 (m-30) REVERT: A 3687 MET cc_start: 0.8040 (ptp) cc_final: 0.6837 (ptp) REVERT: A 3850 HIS cc_start: 0.7377 (t-170) cc_final: 0.7114 (m90) REVERT: A 3869 THR cc_start: 0.8627 (m) cc_final: 0.8349 (t) outliers start: 20 outliers final: 10 residues processed: 414 average time/residue: 0.4234 time to fit residues: 276.6311 Evaluate side-chains 283 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 271 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 0.0670 chunk 272 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 92 optimal weight: 0.0020 chunk 183 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 281 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 326 optimal weight: 4.9990 overall best weight: 1.0130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 233 ASN A 339 GLN A 377 ASN A 533 HIS A 739 ASN A1049 GLN ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 HIS A1418 HIS A1568 ASN A1598 ASN A1665 HIS ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1830 HIS A1859 ASN A1897 ASN A1898 GLN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2270 ASN A2432 GLN A2481 HIS A2534 ASN A2553 HIS A2830 ASN A2859 GLN A2885 GLN ** A2977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3028 ASN A3037 GLN ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3113 ASN A3148 GLN A3150 ASN A3154 GLN A3319 ASN A3383 GLN A3423 GLN A3457 ASN A3510 GLN A3527 GLN A3551 ASN A3569 GLN A3577 GLN A3679 ASN A3697 ASN A3787 GLN A3863 ASN A4000 ASN A4088 ASN ** A4092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29837 Z= 0.175 Angle : 0.700 14.271 40568 Z= 0.361 Chirality : 0.041 0.188 4665 Planarity : 0.005 0.081 4970 Dihedral : 13.244 88.188 4337 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.28 % Favored : 88.66 % Rotamer: Outliers : 0.10 % Allowed : 5.27 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.13), residues: 3527 helix: -1.31 (0.10), residues: 2234 sheet: -2.35 (0.70), residues: 51 loop : -3.96 (0.15), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3686 HIS 0.008 0.001 HIS A 32 PHE 0.029 0.002 PHE A2851 TYR 0.022 0.001 TYR A3168 ARG 0.005 0.000 ARG A2377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 383 time to evaluate : 3.458 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: A 59 PHE cc_start: 0.4944 (m-80) cc_final: 0.4472 (m-10) REVERT: A 785 MET cc_start: 0.7027 (mmm) cc_final: 0.6737 (mmt) REVERT: A 880 MET cc_start: 0.8177 (mmm) cc_final: 0.7896 (mmm) REVERT: A 1015 ASP cc_start: 0.7676 (p0) cc_final: 0.7072 (p0) REVERT: A 1348 LEU cc_start: 0.9122 (tt) cc_final: 0.8882 (mm) REVERT: A 1392 MET cc_start: 0.7069 (tmm) cc_final: 0.6832 (tmm) REVERT: A 1871 MET cc_start: 0.9220 (ttm) cc_final: 0.9017 (ttm) REVERT: A 2038 GLU cc_start: 0.7412 (mp0) cc_final: 0.7015 (mp0) REVERT: A 2126 MET cc_start: 0.7538 (ttm) cc_final: 0.7003 (ttm) REVERT: A 2379 MET cc_start: 0.8662 (mmt) cc_final: 0.8229 (mmm) REVERT: A 2442 MET cc_start: 0.8863 (ptm) cc_final: 0.8619 (ptt) REVERT: A 2445 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7284 (mmtm) REVERT: A 3061 LEU cc_start: 0.8664 (tp) cc_final: 0.8411 (tp) REVERT: A 3610 TYR cc_start: 0.7104 (t80) cc_final: 0.6697 (t80) REVERT: A 3746 ARG cc_start: 0.7884 (mpp80) cc_final: 0.7443 (mpp80) REVERT: A 3850 HIS cc_start: 0.7224 (t-170) cc_final: 0.6963 (m90) outliers start: 3 outliers final: 1 residues processed: 386 average time/residue: 0.4000 time to fit residues: 250.4471 Evaluate side-chains 267 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 181 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 271 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 323 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 262 optimal weight: 0.0370 overall best weight: 1.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS A1126 GLN A1146 ASN A1598 ASN A1603 GLN A1665 HIS ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2514 ASN A2518 GLN ** A2977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3524 ASN A3527 GLN A3679 ASN A3787 GLN ** A4015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29837 Z= 0.200 Angle : 0.679 13.549 40568 Z= 0.351 Chirality : 0.041 0.170 4665 Planarity : 0.004 0.080 4970 Dihedral : 13.016 84.166 4337 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.68 % Favored : 88.26 % Rotamer: Outliers : 0.10 % Allowed : 5.46 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.13), residues: 3527 helix: -0.76 (0.10), residues: 2250 sheet: -2.27 (0.72), residues: 45 loop : -3.74 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A3842 HIS 0.012 0.001 HIS A2183 PHE 0.016 0.001 PHE A1990 TYR 0.018 0.001 TYR A 366 ARG 0.005 0.000 ARG A1178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 361 time to evaluate : 3.554 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: A 59 PHE cc_start: 0.5043 (m-80) cc_final: 0.4565 (m-10) REVERT: A 144 MET cc_start: 0.7124 (tpp) cc_final: 0.6726 (tmm) REVERT: A 272 LEU cc_start: 0.8076 (mp) cc_final: 0.7843 (mp) REVERT: A 529 ASP cc_start: 0.7969 (p0) cc_final: 0.7298 (t70) REVERT: A 880 MET cc_start: 0.8115 (mmm) cc_final: 0.7760 (mmm) REVERT: A 940 PHE cc_start: 0.7369 (t80) cc_final: 0.6949 (t80) REVERT: A 970 LEU cc_start: 0.8567 (pt) cc_final: 0.7564 (mt) REVERT: A 1015 ASP cc_start: 0.7696 (p0) cc_final: 0.7177 (p0) REVERT: A 1107 TYR cc_start: 0.7481 (m-10) cc_final: 0.7134 (m-80) REVERT: A 1392 MET cc_start: 0.7051 (tmm) cc_final: 0.6789 (tmm) REVERT: A 1871 MET cc_start: 0.9217 (ttm) cc_final: 0.9005 (ttm) REVERT: A 2038 GLU cc_start: 0.7407 (mp0) cc_final: 0.6991 (mp0) REVERT: A 2126 MET cc_start: 0.7611 (ttm) cc_final: 0.7308 (ttm) REVERT: A 2243 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: A 2379 MET cc_start: 0.8765 (mmt) cc_final: 0.8237 (mmm) REVERT: A 2445 LYS cc_start: 0.7750 (mmtt) cc_final: 0.7156 (mmtm) REVERT: A 3046 ARG cc_start: 0.8360 (ptm160) cc_final: 0.8147 (ptm160) REVERT: A 3061 LEU cc_start: 0.8579 (tp) cc_final: 0.8302 (tp) REVERT: A 3450 MET cc_start: 0.4376 (ttt) cc_final: 0.4071 (ttt) REVERT: A 3519 GLU cc_start: 0.8923 (tp30) cc_final: 0.8373 (tp30) REVERT: A 3523 ASP cc_start: 0.7620 (m-30) cc_final: 0.6599 (m-30) REVERT: A 3572 ILE cc_start: 0.9267 (mm) cc_final: 0.8723 (mm) REVERT: A 3668 LEU cc_start: 0.8877 (pp) cc_final: 0.8629 (mt) REVERT: A 3850 HIS cc_start: 0.7446 (t-170) cc_final: 0.7166 (m90) outliers start: 3 outliers final: 1 residues processed: 363 average time/residue: 0.3961 time to fit residues: 235.4102 Evaluate side-chains 275 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 273 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 322 optimal weight: 5.9990 chunk 245 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 219 optimal weight: 0.6980 chunk 327 optimal weight: 0.9990 chunk 347 optimal weight: 0.6980 chunk 171 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 334 HIS A 485 GLN A1598 ASN ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3166 ASN ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3679 ASN ** A4015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29837 Z= 0.161 Angle : 0.655 13.882 40568 Z= 0.331 Chirality : 0.040 0.197 4665 Planarity : 0.004 0.076 4970 Dihedral : 12.862 82.307 4337 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.92 % Favored : 89.03 % Rotamer: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.14), residues: 3527 helix: -0.37 (0.11), residues: 2256 sheet: -1.85 (0.77), residues: 45 loop : -3.65 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1829 HIS 0.009 0.001 HIS A 484 PHE 0.026 0.001 PHE A2851 TYR 0.016 0.001 TYR A 959 ARG 0.006 0.000 ARG A1937 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 3.619 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: A 59 PHE cc_start: 0.5004 (m-80) cc_final: 0.4557 (m-10) REVERT: A 144 MET cc_start: 0.6984 (tpp) cc_final: 0.6572 (tmm) REVERT: A 529 ASP cc_start: 0.7910 (p0) cc_final: 0.7379 (t70) REVERT: A 654 ILE cc_start: 0.9052 (mt) cc_final: 0.8775 (tt) REVERT: A 880 MET cc_start: 0.8025 (mmm) cc_final: 0.7722 (mmm) REVERT: A 933 LEU cc_start: 0.8304 (pp) cc_final: 0.7757 (tp) REVERT: A 940 PHE cc_start: 0.7317 (t80) cc_final: 0.6755 (t80) REVERT: A 962 TYR cc_start: 0.7661 (m-80) cc_final: 0.7345 (m-80) REVERT: A 970 LEU cc_start: 0.8548 (pt) cc_final: 0.7598 (mt) REVERT: A 1107 TYR cc_start: 0.7469 (m-10) cc_final: 0.7190 (m-80) REVERT: A 1392 MET cc_start: 0.6948 (tmm) cc_final: 0.6736 (tmm) REVERT: A 1694 THR cc_start: 0.8951 (p) cc_final: 0.8733 (p) REVERT: A 1743 MET cc_start: 0.8382 (mmp) cc_final: 0.7950 (mmm) REVERT: A 1871 MET cc_start: 0.9223 (ttm) cc_final: 0.8989 (ttm) REVERT: A 2038 GLU cc_start: 0.7321 (mp0) cc_final: 0.6948 (mp0) REVERT: A 2126 MET cc_start: 0.7786 (ttm) cc_final: 0.7516 (mtp) REVERT: A 2379 MET cc_start: 0.8756 (mmt) cc_final: 0.8210 (mmm) REVERT: A 2445 LYS cc_start: 0.7751 (mmtt) cc_final: 0.7140 (mmtm) REVERT: A 3046 ARG cc_start: 0.8323 (ptm160) cc_final: 0.8109 (ptm160) REVERT: A 3450 MET cc_start: 0.3875 (ttt) cc_final: 0.3522 (ttt) REVERT: A 3519 GLU cc_start: 0.8891 (tp30) cc_final: 0.8248 (tp30) REVERT: A 3523 ASP cc_start: 0.7555 (m-30) cc_final: 0.6472 (m-30) REVERT: A 3668 LEU cc_start: 0.8860 (pp) cc_final: 0.8602 (mt) REVERT: A 3710 LYS cc_start: 0.8542 (mppt) cc_final: 0.8147 (tppt) REVERT: A 3850 HIS cc_start: 0.7430 (t-170) cc_final: 0.7218 (m90) outliers start: 1 outliers final: 1 residues processed: 378 average time/residue: 0.3982 time to fit residues: 246.4872 Evaluate side-chains 269 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 289 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 258 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 296 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 311 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN ** A1175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN A1737 ASN ** A1817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2103 HIS A2170 GLN A2234 ASN ** A2475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2483 ASN A2977 ASN ** A3093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3133 GLN ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3516 HIS A3660 ASN A3671 ASN A3679 ASN ** A3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3808 ASN ** A3908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 GLN ** A4015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 29837 Z= 0.399 Angle : 0.845 15.094 40568 Z= 0.439 Chirality : 0.047 0.185 4665 Planarity : 0.006 0.079 4970 Dihedral : 13.208 83.647 4337 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.67 % Favored : 86.28 % Rotamer: Outliers : 0.06 % Allowed : 4.95 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.13), residues: 3527 helix: -0.85 (0.10), residues: 2266 sheet: -1.25 (1.37), residues: 16 loop : -3.65 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A2981 HIS 0.011 0.002 HIS A 32 PHE 0.037 0.003 PHE A3887 TYR 0.034 0.002 TYR A 762 ARG 0.008 0.001 ARG A3125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 321 time to evaluate : 3.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.5563 (m-80) cc_final: 0.4708 (m-10) REVERT: A 144 MET cc_start: 0.7077 (tpp) cc_final: 0.6695 (tmm) REVERT: A 272 LEU cc_start: 0.8085 (mp) cc_final: 0.7785 (mp) REVERT: A 880 MET cc_start: 0.8137 (mmm) cc_final: 0.7715 (mmm) REVERT: A 1109 GLU cc_start: 0.7995 (pt0) cc_final: 0.7732 (pt0) REVERT: A 1155 ARG cc_start: 0.7631 (tmt170) cc_final: 0.7225 (tmm160) REVERT: A 1392 MET cc_start: 0.7147 (tmm) cc_final: 0.6937 (tmm) REVERT: A 1570 GLU cc_start: 0.7970 (tp30) cc_final: 0.7565 (tt0) REVERT: A 1743 MET cc_start: 0.8239 (mmp) cc_final: 0.7959 (mmm) REVERT: A 1871 MET cc_start: 0.9225 (ttm) cc_final: 0.9005 (ttm) REVERT: A 2038 GLU cc_start: 0.7503 (mp0) cc_final: 0.7154 (mp0) REVERT: A 2126 MET cc_start: 0.8087 (ttm) cc_final: 0.7747 (ttm) REVERT: A 2307 MET cc_start: 0.8316 (tpp) cc_final: 0.8087 (tpp) REVERT: A 2379 MET cc_start: 0.8856 (mmt) cc_final: 0.8293 (mmm) REVERT: A 2445 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7103 (mmtm) REVERT: A 3450 MET cc_start: 0.4335 (ttt) cc_final: 0.3936 (ttt) REVERT: A 3519 GLU cc_start: 0.8859 (tp30) cc_final: 0.8276 (tp30) REVERT: A 3523 ASP cc_start: 0.7477 (m-30) cc_final: 0.6896 (m-30) REVERT: A 3610 TYR cc_start: 0.6564 (t80) cc_final: 0.5665 (t80) REVERT: A 3710 LYS cc_start: 0.8758 (mppt) cc_final: 0.8484 (mppt) REVERT: A 3746 ARG cc_start: 0.7835 (mpp80) cc_final: 0.7486 (mpp80) REVERT: A 3850 HIS cc_start: 0.7486 (t-170) cc_final: 0.7088 (m90) REVERT: A 3971 MET cc_start: 0.7953 (mmm) cc_final: 0.7716 (mmm) outliers start: 2 outliers final: 0 residues processed: 323 average time/residue: 0.4335 time to fit residues: 231.7237 Evaluate side-chains 247 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 116 optimal weight: 10.0000 chunk 312 optimal weight: 0.0570 chunk 68 optimal weight: 0.9990 chunk 203 optimal weight: 0.0570 chunk 85 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 288 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1175 HIS ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN A1721 HIS ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2475 ASN ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN A3679 ASN A3808 ASN A3908 HIS ** A3926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29837 Z= 0.182 Angle : 0.688 14.480 40568 Z= 0.349 Chirality : 0.042 0.186 4665 Planarity : 0.004 0.079 4970 Dihedral : 13.009 86.001 4337 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.26 % Favored : 88.72 % Rotamer: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 3527 helix: -0.39 (0.11), residues: 2265 sheet: -1.97 (1.00), residues: 28 loop : -3.49 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A2981 HIS 0.005 0.001 HIS A 484 PHE 0.025 0.001 PHE A2851 TYR 0.028 0.001 TYR A 762 ARG 0.004 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 361 time to evaluate : 3.345 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: A 59 PHE cc_start: 0.5417 (m-80) cc_final: 0.4734 (m-10) REVERT: A 144 MET cc_start: 0.7029 (tpp) cc_final: 0.6660 (tmm) REVERT: A 251 PHE cc_start: 0.8527 (m-80) cc_final: 0.8307 (m-80) REVERT: A 529 ASP cc_start: 0.7954 (p0) cc_final: 0.7518 (t70) REVERT: A 540 MET cc_start: 0.6758 (ppp) cc_final: 0.6479 (ppp) REVERT: A 754 MET cc_start: 0.7394 (mtt) cc_final: 0.7132 (mtt) REVERT: A 785 MET cc_start: 0.7154 (mmt) cc_final: 0.6853 (mmt) REVERT: A 858 MET cc_start: 0.7775 (ttt) cc_final: 0.7535 (ttm) REVERT: A 880 MET cc_start: 0.8085 (mmm) cc_final: 0.7757 (mmm) REVERT: A 1107 TYR cc_start: 0.7541 (m-10) cc_final: 0.7305 (m-80) REVERT: A 1392 MET cc_start: 0.7054 (tmm) cc_final: 0.6807 (tmm) REVERT: A 1570 GLU cc_start: 0.7890 (tp30) cc_final: 0.7591 (tt0) REVERT: A 1743 MET cc_start: 0.8202 (mmp) cc_final: 0.7800 (mmm) REVERT: A 1927 MET cc_start: 0.7640 (mmp) cc_final: 0.7400 (mmp) REVERT: A 2038 GLU cc_start: 0.7530 (mp0) cc_final: 0.7125 (mp0) REVERT: A 2126 MET cc_start: 0.7731 (ttm) cc_final: 0.7428 (ttm) REVERT: A 2379 MET cc_start: 0.8776 (mmt) cc_final: 0.8153 (mmm) REVERT: A 2445 LYS cc_start: 0.7584 (mmtt) cc_final: 0.7043 (mmtm) REVERT: A 3450 MET cc_start: 0.3768 (ttt) cc_final: 0.3406 (ttt) REVERT: A 3519 GLU cc_start: 0.8662 (tp30) cc_final: 0.8260 (tp30) REVERT: A 3523 ASP cc_start: 0.7335 (m-30) cc_final: 0.6885 (m-30) REVERT: A 3634 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7433 (pp30) REVERT: A 3710 LYS cc_start: 0.8803 (mppt) cc_final: 0.8596 (mppt) REVERT: A 3746 ARG cc_start: 0.7813 (mpp80) cc_final: 0.7498 (mpp80) REVERT: A 3846 MET cc_start: 0.8851 (tpp) cc_final: 0.8605 (tpp) REVERT: A 3850 HIS cc_start: 0.7093 (t-170) cc_final: 0.6779 (m90) REVERT: A 3858 MET cc_start: 0.5703 (mtt) cc_final: 0.5489 (mtt) outliers start: 2 outliers final: 0 residues processed: 363 average time/residue: 0.3917 time to fit residues: 234.0907 Evaluate side-chains 266 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 334 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 197 optimal weight: 0.8980 chunk 253 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 292 optimal weight: 6.9990 chunk 193 optimal weight: 0.0370 chunk 346 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 GLN A1146 ASN ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN A1830 HIS A1957 ASN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN A3679 ASN A3808 ASN ** A3926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29837 Z= 0.181 Angle : 0.682 14.231 40568 Z= 0.344 Chirality : 0.041 0.178 4665 Planarity : 0.004 0.078 4970 Dihedral : 12.900 85.489 4337 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.88 % Favored : 88.09 % Rotamer: Outliers : 0.06 % Allowed : 1.71 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.14), residues: 3527 helix: -0.20 (0.11), residues: 2275 sheet: -0.60 (1.46), residues: 16 loop : -3.36 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A2981 HIS 0.004 0.001 HIS A 783 PHE 0.044 0.001 PHE A3189 TYR 0.030 0.001 TYR A 385 ARG 0.005 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 360 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.5422 (m-80) cc_final: 0.4790 (m-10) REVERT: A 144 MET cc_start: 0.6916 (tpp) cc_final: 0.6504 (tmm) REVERT: A 251 PHE cc_start: 0.8519 (m-80) cc_final: 0.8249 (m-80) REVERT: A 754 MET cc_start: 0.7365 (mtt) cc_final: 0.7131 (mtt) REVERT: A 880 MET cc_start: 0.8125 (mmm) cc_final: 0.7763 (mmm) REVERT: A 933 LEU cc_start: 0.8444 (pp) cc_final: 0.7999 (tp) REVERT: A 940 PHE cc_start: 0.7282 (t80) cc_final: 0.6764 (t80) REVERT: A 1107 TYR cc_start: 0.7623 (m-10) cc_final: 0.7207 (m-80) REVERT: A 1392 MET cc_start: 0.7025 (tmm) cc_final: 0.6786 (tmm) REVERT: A 1570 GLU cc_start: 0.7869 (tp30) cc_final: 0.7615 (tt0) REVERT: A 1743 MET cc_start: 0.8209 (mmp) cc_final: 0.7838 (mmm) REVERT: A 1871 MET cc_start: 0.9144 (ttm) cc_final: 0.8890 (ttm) REVERT: A 1927 MET cc_start: 0.7276 (mmp) cc_final: 0.6996 (mmp) REVERT: A 2038 GLU cc_start: 0.7521 (mp0) cc_final: 0.7112 (mp0) REVERT: A 2126 MET cc_start: 0.7907 (ttm) cc_final: 0.7617 (ttm) REVERT: A 2185 MET cc_start: 0.7877 (mtt) cc_final: 0.7665 (mmm) REVERT: A 2307 MET cc_start: 0.8395 (tpp) cc_final: 0.7913 (tpp) REVERT: A 2379 MET cc_start: 0.8764 (mmt) cc_final: 0.8159 (mmm) REVERT: A 2445 LYS cc_start: 0.7609 (mmtt) cc_final: 0.7125 (mmtm) REVERT: A 3046 ARG cc_start: 0.8362 (ptm160) cc_final: 0.8136 (ptm160) REVERT: A 3450 MET cc_start: 0.3768 (ttt) cc_final: 0.3462 (ttt) REVERT: A 3519 GLU cc_start: 0.8682 (tp30) cc_final: 0.8272 (tp30) REVERT: A 3523 ASP cc_start: 0.7391 (m-30) cc_final: 0.6940 (m-30) REVERT: A 3634 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7333 (pp30) REVERT: A 3746 ARG cc_start: 0.7870 (mpp80) cc_final: 0.7601 (mpp80) REVERT: A 3850 HIS cc_start: 0.7285 (t-170) cc_final: 0.6972 (m90) REVERT: A 3910 LEU cc_start: 0.8491 (tp) cc_final: 0.8171 (tp) outliers start: 2 outliers final: 0 residues processed: 362 average time/residue: 0.3955 time to fit residues: 237.3173 Evaluate side-chains 268 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 214 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 314 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS A 625 ASN ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN ** A2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN A3679 ASN A3808 ASN ** A3926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29837 Z= 0.230 Angle : 0.708 14.688 40568 Z= 0.360 Chirality : 0.042 0.189 4665 Planarity : 0.004 0.076 4970 Dihedral : 12.952 85.523 4337 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.22 % Favored : 87.75 % Rotamer: Outliers : 0.03 % Allowed : 1.45 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 3527 helix: -0.20 (0.11), residues: 2263 sheet: -0.37 (1.53), residues: 16 loop : -3.40 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A2981 HIS 0.012 0.001 HIS A 484 PHE 0.029 0.002 PHE A3189 TYR 0.026 0.001 TYR A 762 ARG 0.003 0.000 ARG A1340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 348 time to evaluate : 3.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.5473 (m-80) cc_final: 0.4891 (m-10) REVERT: A 144 MET cc_start: 0.6964 (tpp) cc_final: 0.6587 (tmm) REVERT: A 251 PHE cc_start: 0.8520 (m-80) cc_final: 0.8243 (m-80) REVERT: A 413 PHE cc_start: 0.8730 (m-80) cc_final: 0.8518 (m-10) REVERT: A 880 MET cc_start: 0.8175 (mmm) cc_final: 0.7693 (mmm) REVERT: A 892 LEU cc_start: 0.7765 (mm) cc_final: 0.7538 (mm) REVERT: A 933 LEU cc_start: 0.8495 (pp) cc_final: 0.8018 (tp) REVERT: A 940 PHE cc_start: 0.7340 (t80) cc_final: 0.6703 (t80) REVERT: A 1155 ARG cc_start: 0.7477 (tmt170) cc_final: 0.7234 (tmm160) REVERT: A 1342 MET cc_start: 0.7844 (mpp) cc_final: 0.6972 (mpp) REVERT: A 1369 MET cc_start: 0.8085 (mpp) cc_final: 0.7780 (mpp) REVERT: A 1392 MET cc_start: 0.7093 (tmm) cc_final: 0.6842 (tmm) REVERT: A 1570 GLU cc_start: 0.7909 (tp30) cc_final: 0.7623 (tt0) REVERT: A 1743 MET cc_start: 0.8261 (mmp) cc_final: 0.7820 (mmm) REVERT: A 1871 MET cc_start: 0.9182 (ttm) cc_final: 0.8918 (ttm) REVERT: A 2038 GLU cc_start: 0.7444 (mp0) cc_final: 0.6997 (mp0) REVERT: A 2126 MET cc_start: 0.7971 (ttm) cc_final: 0.7657 (ttm) REVERT: A 2185 MET cc_start: 0.8020 (mtt) cc_final: 0.7777 (mmm) REVERT: A 2307 MET cc_start: 0.8424 (tpp) cc_final: 0.7919 (tpp) REVERT: A 2379 MET cc_start: 0.8802 (mmt) cc_final: 0.8190 (mmm) REVERT: A 2445 LYS cc_start: 0.7638 (mmtt) cc_final: 0.7151 (mmtm) REVERT: A 3046 ARG cc_start: 0.8374 (ptm160) cc_final: 0.8138 (ptm160) REVERT: A 3450 MET cc_start: 0.3839 (ttt) cc_final: 0.3519 (ttt) REVERT: A 3519 GLU cc_start: 0.8700 (tp30) cc_final: 0.8303 (tp30) REVERT: A 3523 ASP cc_start: 0.7344 (m-30) cc_final: 0.6914 (m-30) REVERT: A 3746 ARG cc_start: 0.7864 (mpp80) cc_final: 0.7470 (mpp80) REVERT: A 3850 HIS cc_start: 0.7280 (t-170) cc_final: 0.6959 (m90) REVERT: A 3910 LEU cc_start: 0.8581 (tp) cc_final: 0.8282 (tp) outliers start: 1 outliers final: 0 residues processed: 349 average time/residue: 0.4115 time to fit residues: 238.1041 Evaluate side-chains 260 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 331 optimal weight: 1.9990 chunk 302 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 253 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 291 optimal weight: 5.9990 chunk 304 optimal weight: 1.9990 chunk 321 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS A 613 HIS A1598 ASN A1613 HIS ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3808 ASN ** A3926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29837 Z= 0.177 Angle : 0.688 14.124 40568 Z= 0.343 Chirality : 0.042 0.186 4665 Planarity : 0.004 0.077 4970 Dihedral : 12.877 85.552 4337 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.28 % Favored : 88.69 % Rotamer: Outliers : 0.06 % Allowed : 0.65 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3527 helix: -0.04 (0.11), residues: 2278 sheet: -0.12 (1.60), residues: 16 loop : -3.40 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A2981 HIS 0.012 0.001 HIS A 484 PHE 0.028 0.001 PHE A3189 TYR 0.021 0.001 TYR A 762 ARG 0.003 0.000 ARG A 746 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 357 time to evaluate : 3.604 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: A 59 PHE cc_start: 0.5332 (m-80) cc_final: 0.4775 (m-10) REVERT: A 144 MET cc_start: 0.6935 (tpp) cc_final: 0.6524 (tmm) REVERT: A 251 PHE cc_start: 0.8405 (m-80) cc_final: 0.8130 (m-80) REVERT: A 487 LEU cc_start: 0.9564 (mm) cc_final: 0.9016 (mm) REVERT: A 754 MET cc_start: 0.7306 (mtt) cc_final: 0.7092 (mtt) REVERT: A 880 MET cc_start: 0.8103 (mmm) cc_final: 0.7718 (mmm) REVERT: A 933 LEU cc_start: 0.8403 (pp) cc_final: 0.7921 (tp) REVERT: A 940 PHE cc_start: 0.7275 (t80) cc_final: 0.6800 (t80) REVERT: A 1107 TYR cc_start: 0.7625 (m-10) cc_final: 0.7233 (m-80) REVERT: A 1342 MET cc_start: 0.7849 (mpp) cc_final: 0.6959 (mpp) REVERT: A 1348 LEU cc_start: 0.9235 (pp) cc_final: 0.8622 (mp) REVERT: A 1392 MET cc_start: 0.7019 (tmm) cc_final: 0.6760 (tmm) REVERT: A 1570 GLU cc_start: 0.7879 (tp30) cc_final: 0.7664 (tt0) REVERT: A 1743 MET cc_start: 0.8267 (mmp) cc_final: 0.7769 (mmm) REVERT: A 1774 MET cc_start: 0.7773 (mtm) cc_final: 0.7259 (mmm) REVERT: A 1871 MET cc_start: 0.9081 (ttm) cc_final: 0.8793 (ttm) REVERT: A 2037 SER cc_start: 0.8212 (p) cc_final: 0.7926 (p) REVERT: A 2038 GLU cc_start: 0.7388 (mp0) cc_final: 0.6972 (mp0) REVERT: A 2126 MET cc_start: 0.7618 (ttm) cc_final: 0.7348 (ttm) REVERT: A 2307 MET cc_start: 0.8374 (tpp) cc_final: 0.7893 (tpp) REVERT: A 2379 MET cc_start: 0.8736 (mmt) cc_final: 0.8151 (mmm) REVERT: A 2445 LYS cc_start: 0.7609 (mmtt) cc_final: 0.7095 (mmtm) REVERT: A 3046 ARG cc_start: 0.8342 (ptm160) cc_final: 0.8112 (ptm160) REVERT: A 3129 LEU cc_start: 0.8847 (tt) cc_final: 0.8631 (tt) REVERT: A 3132 VAL cc_start: 0.8885 (m) cc_final: 0.8575 (t) REVERT: A 3519 GLU cc_start: 0.8633 (tp30) cc_final: 0.8168 (tp30) REVERT: A 3523 ASP cc_start: 0.7283 (m-30) cc_final: 0.6766 (m-30) REVERT: A 3665 MET cc_start: 0.7034 (mtt) cc_final: 0.6630 (mtt) REVERT: A 3668 LEU cc_start: 0.8846 (pp) cc_final: 0.8566 (mt) REVERT: A 3746 ARG cc_start: 0.7817 (mpp80) cc_final: 0.7512 (mpp80) REVERT: A 3850 HIS cc_start: 0.7200 (t-170) cc_final: 0.6760 (m90) REVERT: A 3910 LEU cc_start: 0.8398 (tp) cc_final: 0.8146 (tp) REVERT: A 3974 MET cc_start: 0.8791 (mmm) cc_final: 0.8587 (mmm) outliers start: 2 outliers final: 0 residues processed: 357 average time/residue: 0.3757 time to fit residues: 223.2867 Evaluate side-chains 277 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 340 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 237 optimal weight: 0.9990 chunk 357 optimal weight: 10.0000 chunk 329 optimal weight: 4.9990 chunk 284 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 219 optimal weight: 0.0170 chunk 174 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS A 753 GLN A1598 ASN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3808 ASN ** A3926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29837 Z= 0.172 Angle : 0.674 13.955 40568 Z= 0.336 Chirality : 0.041 0.203 4665 Planarity : 0.004 0.077 4970 Dihedral : 12.787 84.265 4337 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.45 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3527 helix: 0.08 (0.11), residues: 2276 sheet: 1.17 (1.83), residues: 13 loop : -3.36 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A2981 HIS 0.009 0.001 HIS A 484 PHE 0.026 0.001 PHE A3189 TYR 0.021 0.001 TYR A 762 ARG 0.004 0.000 ARG A 746 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 3.318 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: A 59 PHE cc_start: 0.5337 (m-80) cc_final: 0.4810 (m-10) REVERT: A 144 MET cc_start: 0.6794 (tpp) cc_final: 0.6378 (tmm) REVERT: A 487 LEU cc_start: 0.9580 (mm) cc_final: 0.9029 (mm) REVERT: A 725 LEU cc_start: 0.7912 (tp) cc_final: 0.7690 (tp) REVERT: A 754 MET cc_start: 0.7378 (mtt) cc_final: 0.7174 (mtt) REVERT: A 880 MET cc_start: 0.8091 (mmm) cc_final: 0.7638 (mmm) REVERT: A 933 LEU cc_start: 0.8415 (pp) cc_final: 0.7940 (tp) REVERT: A 940 PHE cc_start: 0.7245 (t80) cc_final: 0.6783 (t80) REVERT: A 1342 MET cc_start: 0.7920 (mpp) cc_final: 0.6974 (mpp) REVERT: A 1348 LEU cc_start: 0.9187 (pp) cc_final: 0.8494 (mp) REVERT: A 1392 MET cc_start: 0.6977 (tmm) cc_final: 0.6723 (tmm) REVERT: A 1743 MET cc_start: 0.8309 (mmp) cc_final: 0.7748 (mmm) REVERT: A 1774 MET cc_start: 0.7665 (mtm) cc_final: 0.7258 (mmm) REVERT: A 1871 MET cc_start: 0.9085 (ttm) cc_final: 0.8782 (ttm) REVERT: A 2037 SER cc_start: 0.8177 (p) cc_final: 0.7876 (p) REVERT: A 2038 GLU cc_start: 0.7318 (mp0) cc_final: 0.6858 (mp0) REVERT: A 2126 MET cc_start: 0.7886 (ttm) cc_final: 0.7583 (ttm) REVERT: A 2307 MET cc_start: 0.8362 (tpp) cc_final: 0.7881 (tpp) REVERT: A 2379 MET cc_start: 0.8744 (mmt) cc_final: 0.8162 (mmm) REVERT: A 2445 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7059 (mmtm) REVERT: A 3028 ASN cc_start: 0.8352 (t0) cc_final: 0.8034 (t0) REVERT: A 3132 VAL cc_start: 0.8847 (m) cc_final: 0.8610 (t) REVERT: A 3238 MET cc_start: 0.8181 (mtm) cc_final: 0.7551 (mtt) REVERT: A 3519 GLU cc_start: 0.8709 (tp30) cc_final: 0.8250 (tp30) REVERT: A 3523 ASP cc_start: 0.7279 (m-30) cc_final: 0.6765 (m-30) REVERT: A 3665 MET cc_start: 0.6920 (mtt) cc_final: 0.6572 (mtt) REVERT: A 3668 LEU cc_start: 0.8866 (pp) cc_final: 0.8608 (mt) REVERT: A 3850 HIS cc_start: 0.6966 (t-170) cc_final: 0.6550 (m90) REVERT: A 3910 LEU cc_start: 0.8399 (tp) cc_final: 0.8134 (tp) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.3847 time to fit residues: 234.2669 Evaluate side-chains 278 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 262 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 292 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 250 optimal weight: 0.0270 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS A1598 ASN ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3327 ASN ** A3926 ASN ** 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 = 0.3770 r_free = 0.3770 target = 0.089242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.072972 restraints weight = 149308.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074320 restraints weight = 96846.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075299 restraints weight = 70724.348| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29837 Z= 0.160 Angle : 0.674 14.524 40568 Z= 0.331 Chirality : 0.041 0.200 4665 Planarity : 0.004 0.078 4970 Dihedral : 12.692 84.271 4337 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.83 % Favored : 89.14 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 3527 helix: 0.22 (0.11), residues: 2281 sheet: 1.15 (1.78), residues: 13 loop : -3.36 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A2981 HIS 0.008 0.001 HIS A 484 PHE 0.026 0.001 PHE A3189 TYR 0.022 0.001 TYR A 651 ARG 0.004 0.000 ARG A 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5579.11 seconds wall clock time: 102 minutes 20.27 seconds (6140.27 seconds total)