Starting phenix.real_space_refine on Fri Aug 9 23:56:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k58_36897/08_2024/8k58_36897.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k58_36897/08_2024/8k58_36897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k58_36897/08_2024/8k58_36897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k58_36897/08_2024/8k58_36897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k58_36897/08_2024/8k58_36897.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k58_36897/08_2024/8k58_36897.cif" } resolution = 3.15 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= 0.001 sd= 0.028 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 57 5.49 5 S 112 5.16 5 C 17026 2.51 5 N 4875 2.21 5 O 5435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 541": "OE1" <-> "OE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C ASP 959": "OD1" <-> "OD2" Residue "C GLU 962": "OE1" <-> "OE2" Residue "C GLU 968": "OE1" <-> "OE2" Residue "C TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1026": "OE1" <-> "OE2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1064": "OD1" <-> "OD2" Residue "C ASP 1088": "OD1" <-> "OD2" Residue "C GLU 1167": "OE1" <-> "OE2" Residue "C GLU 1222": "OE1" <-> "OE2" Residue "C TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1279": "OE1" <-> "OE2" Residue "C GLU 1321": "OE1" <-> "OE2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "C GLU 1338": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 462": "OD1" <-> "OD2" Residue "D ASP 464": "OD1" <-> "OD2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 643": "OD1" <-> "OD2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D ASP 727": "OD1" <-> "OD2" Residue "D ASP 806": "OD1" <-> "OD2" Residue "D ASP 891": "OD1" <-> "OD2" Residue "D TYR 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 925": "OE1" <-> "OE2" Residue "D ASP 1143": "OD1" <-> "OD2" Residue "D GLU 1276": "OE1" <-> "OE2" Residue "D GLU 1278": "OE1" <-> "OE2" Residue "D TYR 1282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1317": "OE1" <-> "OE2" Residue "D GLU 1327": "OE1" <-> "OE2" Residue "D GLU 1349": "OE1" <-> "OE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27505 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain: "D" Number of atoms: 10494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1352, 10494 Classifications: {'peptide': 1352} Modifications used: {'COO': 1} Link IDs: {'CIS': 7, 'PTRANS': 55, 'TRANS': 1289} Chain breaks: 1 Chain: "E" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 606 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "A" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1788 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "G" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "I" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 448 Inner-chain residues flagged as termini: ['pdbres=" DA I 14 "'] Classifications: {'DNA': 22} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 21} Chain: "H" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "J" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 218 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Time building chain proxies: 17.99, per 1000 atoms: 0.65 Number of scatterers: 27505 At special positions: 0 Unit cell: (128.74, 161.54, 164, 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 112 16.00 P 57 15.00 O 5435 8.00 N 4875 7.00 C 17026 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: 16.04 Conformation dependent library (CDL) restraints added in 5.5 seconds 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6204 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 50 sheets defined 40.1% alpha, 18.3% beta 18 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 12.25 Creating SS restraints... Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.786A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.513A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.354A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.836A pdb=" N LEU C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.708A pdb=" N LYS C 295 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.895A pdb=" N SER C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.559A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.695A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.729A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.534A pdb=" N ASP C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 removed outlier: 3.528A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 614' Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.697A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.446A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 864 removed outlier: 3.883A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.513A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 removed outlier: 3.843A pdb=" N LEU C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.869A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.766A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.617A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.516A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.580A pdb=" N GLU D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.809A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.645A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 263 through 285 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.508A pdb=" N MET D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 406 through 418 removed outlier: 3.763A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 490 removed outlier: 4.159A pdb=" N ILE D 490 " --> pdb=" O THR D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.967A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.544A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.699A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.904A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.567A pdb=" N MET D 724 " --> pdb=" O ASN D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 739 removed outlier: 3.583A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.573A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.202A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 removed outlier: 3.520A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 900' Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.545A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1069 through 1074 removed outlier: 4.091A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1223 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.745A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.313A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 4.083A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.815A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.739A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.057A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.573A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.844A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.472A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 15 removed outlier: 3.585A pdb=" N ILE G 15 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 39 removed outlier: 3.564A pdb=" N SER G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 52 removed outlier: 3.846A pdb=" N MET G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 87 Processing helix chain 'G' and resid 107 through 128 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.512A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.774A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 230 removed outlier: 4.670A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.477A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.907A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 11.348A pdb=" N ALA C 94 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N MET C 124 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 96 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL C 122 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL C 98 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLN C 120 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU C 100 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS C 118 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.406A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 154 through 160 Processing sheet with id=AA6, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.746A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.775A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AA9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.904A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB2, first strand: chain 'C' and resid 623 through 624 removed outlier: 3.617A pdb=" N HIS C 628 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.926A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.692A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AB6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AB7, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 4.267A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1066 through 1068 Processing sheet with id=AB9, first strand: chain 'C' and resid 846 through 847 removed outlier: 5.912A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC2, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.867A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.084A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.723A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AC6, first strand: chain 'D' and resid 103 through 111 removed outlier: 6.639A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AC8, first strand: chain 'D' and resid 316 through 317 removed outlier: 4.065A pdb=" N THR D 317 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 320 " --> pdb=" O THR D 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 526 through 528 removed outlier: 7.042A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 707 through 708 removed outlier: 3.817A pdb=" N ILE D 707 " --> pdb=" O GLU D 714 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.110A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD4, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.690A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP D 830 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 949 through 952 removed outlier: 7.394A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 991 through 997 removed outlier: 4.002A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 964 through 968 removed outlier: 4.392A pdb=" N LYS D 964 " --> pdb=" O THR D 976 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 6.261A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU D1121 " --> pdb=" O GLN D1108 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU D1109 " --> pdb=" O SER D1057 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER D1057 " --> pdb=" O LEU D1109 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR D1047 " --> pdb=" O VAL D1060 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id=AE1, first strand: chain 'D' and resid 1156 through 1157 removed outlier: 4.189A pdb=" N ASP D1208 " --> pdb=" O ALA D1157 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id=AE3, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 6.403A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.380A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU A 198 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 190 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.776A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY A 151 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.939A pdb=" N GLY A 151 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AE8, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AE9, first strand: chain 'G' and resid 92 through 94 Processing sheet with id=AF1, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.737A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 98 through 105 removed outlier: 6.592A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AF4, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AF5, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.582A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 1163 hydrogen bonds defined for protein. 3294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 19.70 Time building geometry restraints manager: 16.72 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: 7938 1.33 - 1.45: 4098 1.45 - 1.57: 15696 1.57 - 1.69: 116 1.69 - 1.81: 194 Bond restraints: 28042 Sorted by residual: bond pdb=" CB PRO D 251 " pdb=" CG PRO D 251 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.92e+00 bond pdb=" CB PRO D 498 " pdb=" CG PRO D 498 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.87e+00 bond pdb=" CD GLU C1143 " pdb=" OE1 GLU C1143 " ideal model delta sigma weight residual 1.249 1.219 0.030 1.90e-02 2.77e+03 2.41e+00 bond pdb=" CA GLY D 828 " pdb=" C GLY D 828 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.35e+00 bond pdb=" CB ARG B 44 " pdb=" CG ARG B 44 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.29e+00 ... (remaining 28037 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.72: 818 105.72 - 112.80: 15212 112.80 - 119.88: 9394 119.88 - 126.96: 12368 126.96 - 134.04: 348 Bond angle restraints: 38140 Sorted by residual: angle pdb=" N ILE C 414 " pdb=" CA ILE C 414 " pdb=" C ILE C 414 " ideal model delta sigma weight residual 113.10 107.46 5.64 9.70e-01 1.06e+00 3.39e+01 angle pdb=" N SER C1162 " pdb=" CA SER C1162 " pdb=" C SER C1162 " ideal model delta sigma weight residual 114.31 106.99 7.32 1.29e+00 6.01e-01 3.22e+01 angle pdb=" CA PRO D 251 " pdb=" N PRO D 251 " pdb=" CD PRO D 251 " ideal model delta sigma weight residual 112.00 104.56 7.44 1.40e+00 5.10e-01 2.82e+01 angle pdb=" CA PRO D 498 " pdb=" N PRO D 498 " pdb=" CD PRO D 498 " ideal model delta sigma weight residual 112.00 105.25 6.75 1.40e+00 5.10e-01 2.32e+01 angle pdb=" C ASP C 234 " pdb=" CA ASP C 234 " pdb=" CB ASP C 234 " ideal model delta sigma weight residual 115.79 110.34 5.45 1.19e+00 7.06e-01 2.10e+01 ... (remaining 38135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.19: 16322 30.19 - 60.38: 630 60.38 - 90.57: 178 90.57 - 120.76: 0 120.76 - 150.95: 2 Dihedral angle restraints: 17132 sinusoidal: 7491 harmonic: 9641 Sorted by residual: dihedral pdb=" CA MET D 330 " pdb=" C MET D 330 " pdb=" N ILE D 331 " pdb=" CA ILE D 331 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA GLN E 29 " pdb=" C GLN E 29 " pdb=" N MET E 30 " pdb=" CA MET E 30 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ARG C 827 " pdb=" C ARG C 827 " pdb=" N PHE C 828 " pdb=" CA PHE C 828 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 17129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3409 0.049 - 0.097: 723 0.097 - 0.146: 199 0.146 - 0.195: 16 0.195 - 0.243: 2 Chirality restraints: 4349 Sorted by residual: chirality pdb=" CA GLN E 29 " pdb=" N GLN E 29 " pdb=" C GLN E 29 " pdb=" CB GLN E 29 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL C 690 " pdb=" CA VAL C 690 " pdb=" CG1 VAL C 690 " pdb=" CG2 VAL C 690 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO D 498 " pdb=" N PRO D 498 " pdb=" C PRO D 498 " pdb=" CB PRO D 498 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 4346 not shown) Planarity restraints: 4796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 497 " -0.082 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO D 498 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO D 498 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO D 498 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 250 " -0.077 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO D 251 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO D 251 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO D 251 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 39 " -0.055 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO E 40 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 40 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 40 " -0.045 5.00e-02 4.00e+02 ... (remaining 4793 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 815 2.70 - 3.25: 28559 3.25 - 3.80: 46321 3.80 - 4.35: 60188 4.35 - 4.90: 97542 Nonbonded interactions: 233425 Sorted by model distance: nonbonded pdb=" OG SER D 969 " pdb=" O SER D1117 " model vdw 2.144 3.040 nonbonded pdb=" OG SER D 568 " pdb=" NZ LYS D 570 " model vdw 2.198 3.120 nonbonded pdb=" O VAL C 700 " pdb=" NH1 ARG C1069 " model vdw 2.207 3.120 nonbonded pdb=" OD1 ASP D 134 " pdb=" NH2 ARG D 137 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASP C1240 " pdb=" NZ LYS D 445 " model vdw 2.215 3.120 ... (remaining 233420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 233) selection = (chain 'B' and resid 7 through 233) } 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 individual isotropic 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.210 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 102.120 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.170 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: 0.030 Load rotamer database and sin/cos tables:3.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5693 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 : 0.003 0.111 28042 Z= 0.226 Angle : 0.713 15.961 38140 Z= 0.413 Chirality : 0.044 0.243 4349 Planarity : 0.005 0.120 4796 Dihedral : 17.145 150.954 10928 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.79 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3341 helix: 0.74 (0.15), residues: 1202 sheet: -0.31 (0.25), residues: 381 loop : -1.39 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 115 HIS 0.018 0.001 HIS B 37 PHE 0.024 0.002 PHE C1270 TYR 0.017 0.001 TYR C 555 ARG 0.014 0.001 ARG D 610 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 606 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 LYS cc_start: 0.6065 (mmtp) cc_final: 0.5722 (mmtm) REVERT: C 124 MET cc_start: 0.5699 (pmm) cc_final: 0.5226 (pmm) REVERT: C 130 MET cc_start: 0.6591 (ttm) cc_final: 0.6334 (ttm) REVERT: C 193 ASN cc_start: 0.7276 (m-40) cc_final: 0.6953 (m-40) REVERT: C 205 PRO cc_start: 0.7942 (Cg_exo) cc_final: 0.7606 (Cg_endo) REVERT: C 396 ASP cc_start: 0.7043 (t70) cc_final: 0.6609 (t0) REVERT: C 411 ARG cc_start: 0.5640 (mtt180) cc_final: 0.5397 (mtt180) REVERT: C 422 LYS cc_start: 0.6870 (mttm) cc_final: 0.6289 (pttp) REVERT: C 445 ILE cc_start: 0.7537 (mm) cc_final: 0.7304 (mt) REVERT: C 512 SER cc_start: 0.8595 (t) cc_final: 0.7964 (t) REVERT: C 562 GLU cc_start: 0.6817 (tp30) cc_final: 0.6410 (tt0) REVERT: C 631 GLU cc_start: 0.7688 (mt-10) cc_final: 0.6785 (mp0) REVERT: C 653 MET cc_start: 0.7027 (tmm) cc_final: 0.6668 (tmm) REVERT: C 805 MET cc_start: 0.7523 (ptt) cc_final: 0.7320 (ptt) REVERT: C 842 ASP cc_start: 0.7678 (t0) cc_final: 0.7383 (t0) REVERT: C 876 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6475 (mm-30) REVERT: C 917 SER cc_start: 0.7678 (p) cc_final: 0.6951 (m) REVERT: C 1079 ILE cc_start: 0.6138 (pt) cc_final: 0.5751 (mt) REVERT: C 1119 MET cc_start: 0.6339 (tpt) cc_final: 0.4609 (ttt) REVERT: C 1151 LEU cc_start: 0.5702 (tp) cc_final: 0.5220 (mp) REVERT: C 1170 MET cc_start: 0.6448 (tpp) cc_final: 0.6169 (mmt) REVERT: C 1188 ASP cc_start: 0.6425 (t70) cc_final: 0.6089 (t0) REVERT: C 1209 GLN cc_start: 0.7819 (mt0) cc_final: 0.7407 (mt0) REVERT: C 1231 TYR cc_start: 0.7364 (t80) cc_final: 0.6966 (t80) REVERT: C 1297 ASP cc_start: 0.5112 (t0) cc_final: 0.4868 (t0) REVERT: D 26 SER cc_start: 0.7052 (t) cc_final: 0.6504 (p) REVERT: D 53 ARG cc_start: 0.5671 (mtm180) cc_final: 0.4843 (mpt90) REVERT: D 180 MET cc_start: 0.3074 (mmp) cc_final: 0.2513 (mmt) REVERT: D 278 ARG cc_start: 0.6900 (ttp-170) cc_final: 0.6688 (ttp-170) REVERT: D 283 LEU cc_start: 0.6408 (mm) cc_final: 0.6177 (mt) REVERT: D 298 MET cc_start: 0.4903 (ptm) cc_final: 0.3839 (tpp) REVERT: D 332 LYS cc_start: 0.6680 (ttpt) cc_final: 0.6081 (mtpp) REVERT: D 395 LYS cc_start: 0.7276 (ttpp) cc_final: 0.7035 (tptt) REVERT: D 457 TYR cc_start: 0.6920 (m-80) cc_final: 0.6241 (m-80) REVERT: D 488 ASN cc_start: 0.7496 (m-40) cc_final: 0.7261 (m110) REVERT: D 490 ILE cc_start: 0.8582 (pt) cc_final: 0.8264 (mt) REVERT: D 505 ASP cc_start: 0.7053 (t70) cc_final: 0.6328 (t0) REVERT: D 685 ILE cc_start: 0.7526 (mt) cc_final: 0.7218 (mt) REVERT: D 713 GLU cc_start: 0.6488 (pm20) cc_final: 0.6056 (mt-10) REVERT: D 725 MET cc_start: 0.5405 (tpt) cc_final: 0.5204 (tpp) REVERT: D 743 MET cc_start: 0.6530 (ptm) cc_final: 0.5822 (ptm) REVERT: D 785 ASP cc_start: 0.6956 (t0) cc_final: 0.6713 (t0) REVERT: D 870 ASP cc_start: 0.7116 (m-30) cc_final: 0.6903 (t70) REVERT: D 881 LYS cc_start: 0.7124 (tttt) cc_final: 0.6474 (tttm) REVERT: D 892 PHE cc_start: 0.7574 (m-10) cc_final: 0.6674 (m-80) REVERT: D 1146 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6331 (mm-30) REVERT: D 1151 LYS cc_start: 0.7400 (mppt) cc_final: 0.7071 (mmmt) REVERT: D 1152 GLU cc_start: 0.6551 (mt-10) cc_final: 0.6171 (mt-10) REVERT: D 1156 LEU cc_start: 0.4826 (mt) cc_final: 0.3997 (pp) REVERT: D 1263 LYS cc_start: 0.6920 (mmtt) cc_final: 0.6303 (mtpt) REVERT: D 1279 GLN cc_start: 0.7124 (mm110) cc_final: 0.6660 (mm-40) REVERT: D 1281 GLU cc_start: 0.6605 (mm-30) cc_final: 0.6382 (pt0) REVERT: D 1314 LEU cc_start: 0.6126 (mt) cc_final: 0.5925 (mt) REVERT: D 1369 ARG cc_start: 0.7477 (ttt180) cc_final: 0.6703 (ttp80) REVERT: E 12 LYS cc_start: 0.6023 (mmtm) cc_final: 0.5807 (mmtp) REVERT: E 63 ILE cc_start: 0.7316 (mm) cc_final: 0.6765 (mt) REVERT: E 67 ARG cc_start: 0.7322 (ttm110) cc_final: 0.7087 (mtt-85) REVERT: A 105 SER cc_start: 0.7840 (p) cc_final: 0.7417 (m) REVERT: A 204 GLU cc_start: 0.5017 (pt0) cc_final: 0.4727 (mt-10) REVERT: G 1 MET cc_start: 0.3074 (mmp) cc_final: 0.2031 (tmm) REVERT: B 18 GLN cc_start: 0.6564 (pt0) cc_final: 0.6289 (pt0) REVERT: B 29 GLU cc_start: 0.5142 (pm20) cc_final: 0.4151 (pm20) REVERT: B 33 ARG cc_start: 0.6859 (ttt-90) cc_final: 0.6400 (tmm-80) REVERT: B 99 ILE cc_start: 0.6686 (mm) cc_final: 0.6425 (mt) REVERT: B 101 THR cc_start: 0.5557 (t) cc_final: 0.5284 (t) outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 0.4615 time to fit residues: 414.8995 Evaluate side-chains 375 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 8.9990 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 197 optimal weight: 0.0050 chunk 306 optimal weight: 20.0000 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 752 ASN C 811 ASN C 955 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 206 ASN D 232 ASN D 294 ASN D 320 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 489 ASN D 690 ASN D 739 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 41 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28042 Z= 0.319 Angle : 0.691 9.786 38140 Z= 0.365 Chirality : 0.046 0.222 4349 Planarity : 0.005 0.069 4796 Dihedral : 13.902 150.765 4363 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 1.61 % Allowed : 9.49 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3341 helix: 0.68 (0.15), residues: 1222 sheet: -0.59 (0.25), residues: 398 loop : -1.38 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 115 HIS 0.016 0.002 HIS C 554 PHE 0.020 0.002 PHE C 157 TYR 0.026 0.002 TYR D 772 ARG 0.010 0.001 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 399 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 LYS cc_start: 0.6216 (mmtp) cc_final: 0.5746 (mmtm) REVERT: C 37 LYS cc_start: 0.5225 (tptt) cc_final: 0.4990 (tptt) REVERT: C 205 PRO cc_start: 0.8047 (Cg_exo) cc_final: 0.7760 (Cg_endo) REVERT: C 396 ASP cc_start: 0.7027 (t70) cc_final: 0.6796 (t0) REVERT: C 422 LYS cc_start: 0.6927 (mttm) cc_final: 0.6412 (pttp) REVERT: C 512 SER cc_start: 0.8895 (t) cc_final: 0.8623 (t) REVERT: C 631 GLU cc_start: 0.7950 (mt-10) cc_final: 0.6994 (mp0) REVERT: C 768 MET cc_start: 0.7420 (tpt) cc_final: 0.7043 (tpt) REVERT: C 800 MET cc_start: 0.7618 (mtt) cc_final: 0.6992 (mtt) REVERT: C 811 ASN cc_start: 0.7697 (p0) cc_final: 0.7495 (p0) REVERT: C 851 THR cc_start: 0.8305 (t) cc_final: 0.7884 (p) REVERT: C 876 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6500 (mm-30) REVERT: C 886 LYS cc_start: 0.5509 (ttpp) cc_final: 0.5241 (ttmm) REVERT: C 917 SER cc_start: 0.7783 (p) cc_final: 0.7027 (m) REVERT: C 967 LEU cc_start: 0.7494 (mt) cc_final: 0.7247 (mt) REVERT: C 1143 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.5982 (mp0) REVERT: C 1151 LEU cc_start: 0.5949 (tp) cc_final: 0.5677 (mt) REVERT: C 1170 MET cc_start: 0.6483 (tpp) cc_final: 0.6200 (mmp) REVERT: C 1188 ASP cc_start: 0.7058 (t70) cc_final: 0.6694 (t0) REVERT: C 1209 GLN cc_start: 0.8018 (mt0) cc_final: 0.7730 (mt0) REVERT: C 1231 TYR cc_start: 0.7475 (t80) cc_final: 0.7149 (t80) REVERT: D 26 SER cc_start: 0.7140 (t) cc_final: 0.6608 (p) REVERT: D 53 ARG cc_start: 0.5744 (mtm180) cc_final: 0.5005 (mpt180) REVERT: D 180 MET cc_start: 0.2708 (mmp) cc_final: 0.0161 (pmm) REVERT: D 196 GLN cc_start: 0.6024 (OUTLIER) cc_final: 0.5618 (tp-100) REVERT: D 298 MET cc_start: 0.4979 (ptm) cc_final: 0.3757 (mmt) REVERT: D 332 LYS cc_start: 0.6755 (ttpt) cc_final: 0.6048 (mtpp) REVERT: D 395 LYS cc_start: 0.7134 (ttpp) cc_final: 0.6899 (tptp) REVERT: D 458 ASN cc_start: 0.6789 (t0) cc_final: 0.6572 (t0) REVERT: D 505 ASP cc_start: 0.7259 (t70) cc_final: 0.6718 (t0) REVERT: D 644 MET cc_start: 0.7054 (mtp) cc_final: 0.6721 (mtt) REVERT: D 685 ILE cc_start: 0.7592 (mt) cc_final: 0.7349 (mt) REVERT: D 713 GLU cc_start: 0.6579 (pm20) cc_final: 0.6317 (mt-10) REVERT: D 892 PHE cc_start: 0.7615 (m-10) cc_final: 0.6735 (m-80) REVERT: D 1151 LYS cc_start: 0.7209 (mppt) cc_final: 0.6984 (mmmt) REVERT: D 1156 LEU cc_start: 0.5505 (mt) cc_final: 0.4230 (pp) REVERT: D 1281 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6377 (pt0) REVERT: D 1369 ARG cc_start: 0.7304 (ttt180) cc_final: 0.6838 (ttp-110) REVERT: E 12 LYS cc_start: 0.6053 (mmtm) cc_final: 0.5828 (mmtp) REVERT: E 74 GLU cc_start: 0.5783 (OUTLIER) cc_final: 0.4926 (tt0) REVERT: A 105 SER cc_start: 0.7800 (p) cc_final: 0.7370 (m) REVERT: A 204 GLU cc_start: 0.4941 (pt0) cc_final: 0.4604 (mt-10) REVERT: G 1 MET cc_start: 0.2627 (mmp) cc_final: 0.2079 (tmm) REVERT: B 29 GLU cc_start: 0.5243 (pm20) cc_final: 0.4305 (pm20) REVERT: B 51 MET cc_start: 0.5560 (tpt) cc_final: 0.4857 (tpt) outliers start: 46 outliers final: 28 residues processed: 431 average time/residue: 0.4153 time to fit residues: 278.6802 Evaluate side-chains 370 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 339 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 990 ARG Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1332 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 186 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 255 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 307 optimal weight: 50.0000 chunk 332 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 304 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 28042 Z= 0.300 Angle : 0.655 9.223 38140 Z= 0.344 Chirality : 0.045 0.256 4349 Planarity : 0.005 0.054 4796 Dihedral : 13.816 147.163 4363 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 2.59 % Allowed : 12.96 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3341 helix: 0.58 (0.15), residues: 1227 sheet: -0.62 (0.25), residues: 384 loop : -1.43 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 115 HIS 0.017 0.001 HIS C 554 PHE 0.019 0.002 PHE C 157 TYR 0.039 0.002 TYR G 62 ARG 0.008 0.001 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 367 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 LYS cc_start: 0.6409 (mmtp) cc_final: 0.5786 (mmtm) REVERT: C 205 PRO cc_start: 0.8095 (Cg_exo) cc_final: 0.7805 (Cg_endo) REVERT: C 239 MET cc_start: 0.5628 (mmm) cc_final: 0.5088 (mmt) REVERT: C 347 ILE cc_start: 0.6862 (mm) cc_final: 0.6574 (mm) REVERT: C 396 ASP cc_start: 0.7058 (t70) cc_final: 0.6805 (t0) REVERT: C 422 LYS cc_start: 0.6884 (mttm) cc_final: 0.6398 (pttp) REVERT: C 631 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7027 (mp0) REVERT: C 768 MET cc_start: 0.7323 (tpt) cc_final: 0.6994 (tpt) REVERT: C 811 ASN cc_start: 0.7852 (p0) cc_final: 0.7290 (p0) REVERT: C 830 THR cc_start: 0.6564 (m) cc_final: 0.5911 (p) REVERT: C 851 THR cc_start: 0.8282 (t) cc_final: 0.7863 (p) REVERT: C 876 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6624 (mm-30) REVERT: C 955 GLN cc_start: 0.6934 (tm130) cc_final: 0.6706 (tt0) REVERT: C 1079 ILE cc_start: 0.6005 (pt) cc_final: 0.5660 (mt) REVERT: C 1085 MET cc_start: 0.6154 (mmt) cc_final: 0.5696 (mmt) REVERT: C 1170 MET cc_start: 0.6522 (tpp) cc_final: 0.6225 (mmp) REVERT: C 1188 ASP cc_start: 0.7158 (t70) cc_final: 0.6852 (t0) REVERT: C 1209 GLN cc_start: 0.8119 (mt0) cc_final: 0.7835 (mt0) REVERT: C 1231 TYR cc_start: 0.7524 (t80) cc_final: 0.7208 (t80) REVERT: D 53 ARG cc_start: 0.5817 (mtm180) cc_final: 0.5389 (mmt90) REVERT: D 193 ASP cc_start: 0.4179 (t70) cc_final: 0.3920 (t70) REVERT: D 298 MET cc_start: 0.5195 (ptm) cc_final: 0.4141 (mmt) REVERT: D 332 LYS cc_start: 0.6797 (ttpt) cc_final: 0.6116 (mtpp) REVERT: D 395 LYS cc_start: 0.7205 (ttpp) cc_final: 0.6931 (tptp) REVERT: D 581 MET cc_start: 0.6021 (ptt) cc_final: 0.5742 (ptm) REVERT: D 594 GLN cc_start: 0.5108 (tp-100) cc_final: 0.4419 (pt0) REVERT: D 685 ILE cc_start: 0.7641 (mt) cc_final: 0.7366 (mt) REVERT: D 822 MET cc_start: 0.5982 (mmm) cc_final: 0.5530 (mmm) REVERT: D 892 PHE cc_start: 0.7535 (m-10) cc_final: 0.7301 (m-80) REVERT: D 913 GLU cc_start: 0.7023 (tt0) cc_final: 0.6607 (tt0) REVERT: D 1156 LEU cc_start: 0.5340 (mt) cc_final: 0.4054 (pp) REVERT: D 1250 ASP cc_start: 0.6190 (m-30) cc_final: 0.5970 (t0) REVERT: D 1263 LYS cc_start: 0.6880 (mmtt) cc_final: 0.6499 (mtpt) REVERT: D 1367 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6773 (mm110) REVERT: D 1369 ARG cc_start: 0.7401 (ttt180) cc_final: 0.6834 (ttp-110) REVERT: E 12 LYS cc_start: 0.6089 (mmtm) cc_final: 0.5851 (mmtp) REVERT: E 74 GLU cc_start: 0.5749 (OUTLIER) cc_final: 0.4872 (tt0) REVERT: A 105 SER cc_start: 0.7672 (p) cc_final: 0.7259 (m) REVERT: A 204 GLU cc_start: 0.4897 (pt0) cc_final: 0.4557 (mt-10) REVERT: G 1 MET cc_start: 0.2696 (mmp) cc_final: 0.2109 (tmm) REVERT: G 29 GLN cc_start: 0.4756 (mm-40) cc_final: 0.4402 (tp40) REVERT: G 75 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7666 (tp30) REVERT: G 77 MET cc_start: 0.5738 (mpp) cc_final: 0.5465 (mpp) REVERT: B 29 GLU cc_start: 0.5340 (pm20) cc_final: 0.4328 (pm20) REVERT: B 35 PHE cc_start: 0.5655 (OUTLIER) cc_final: 0.5274 (t80) REVERT: B 51 MET cc_start: 0.5715 (tpt) cc_final: 0.4989 (tpt) REVERT: B 127 GLN cc_start: 0.6454 (mt0) cc_final: 0.6032 (mm110) REVERT: B 152 TYR cc_start: 0.8427 (t80) cc_final: 0.8225 (t80) REVERT: B 182 ARG cc_start: 0.4821 (ttm110) cc_final: 0.4082 (ttm-80) REVERT: B 217 ILE cc_start: 0.4252 (OUTLIER) cc_final: 0.3601 (mt) outliers start: 74 outliers final: 49 residues processed: 424 average time/residue: 0.4043 time to fit residues: 270.9542 Evaluate side-chains 383 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 330 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 615 LYS Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 990 ARG Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1332 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 217 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 30.0000 chunk 231 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 308 optimal weight: 4.9990 chunk 326 optimal weight: 30.0000 chunk 161 optimal weight: 20.0000 chunk 292 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 673 HIS ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 GLN D 94 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS D 875 ASN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 194 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 28042 Z= 0.450 Angle : 0.747 8.368 38140 Z= 0.392 Chirality : 0.048 0.326 4349 Planarity : 0.006 0.062 4796 Dihedral : 13.973 146.134 4363 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.86 % Rotamer: Outliers : 3.85 % Allowed : 14.85 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3341 helix: 0.33 (0.15), residues: 1203 sheet: -0.76 (0.26), residues: 368 loop : -1.53 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 115 HIS 0.020 0.002 HIS C 554 PHE 0.025 0.002 PHE C 157 TYR 0.028 0.002 TYR D 772 ARG 0.009 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 354 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 ILE cc_start: 0.6247 (OUTLIER) cc_final: 0.5856 (tt) REVERT: C 347 ILE cc_start: 0.7001 (mm) cc_final: 0.6791 (mm) REVERT: C 396 ASP cc_start: 0.7163 (t70) cc_final: 0.6883 (t0) REVERT: C 422 LYS cc_start: 0.6838 (mttm) cc_final: 0.6339 (pttp) REVERT: C 447 HIS cc_start: 0.6431 (OUTLIER) cc_final: 0.5989 (t-170) REVERT: C 631 GLU cc_start: 0.7974 (mt-10) cc_final: 0.6942 (mp0) REVERT: C 637 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.5371 (ptm-80) REVERT: C 768 MET cc_start: 0.7565 (tpt) cc_final: 0.7272 (tpt) REVERT: C 805 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7082 (ptt) REVERT: C 811 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7606 (p0) REVERT: C 876 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6660 (mm-30) REVERT: C 1078 LYS cc_start: 0.6202 (pttt) cc_final: 0.5850 (ptpt) REVERT: C 1085 MET cc_start: 0.6724 (mmt) cc_final: 0.6494 (mmt) REVERT: C 1174 GLU cc_start: 0.7219 (mm-30) cc_final: 0.7016 (mm-30) REVERT: C 1188 ASP cc_start: 0.7464 (t70) cc_final: 0.7222 (t0) REVERT: C 1209 GLN cc_start: 0.8104 (mt0) cc_final: 0.7384 (mt0) REVERT: C 1231 TYR cc_start: 0.7695 (t80) cc_final: 0.7231 (t80) REVERT: C 1290 MET cc_start: 0.7591 (ttm) cc_final: 0.7299 (ttm) REVERT: D 53 ARG cc_start: 0.5792 (mtm180) cc_final: 0.5452 (mmt90) REVERT: D 92 VAL cc_start: 0.5783 (OUTLIER) cc_final: 0.5558 (t) REVERT: D 193 ASP cc_start: 0.4146 (t70) cc_final: 0.3933 (t0) REVERT: D 283 LEU cc_start: 0.5810 (mt) cc_final: 0.5502 (tt) REVERT: D 298 MET cc_start: 0.5065 (ptm) cc_final: 0.4080 (mmt) REVERT: D 395 LYS cc_start: 0.7422 (ttpp) cc_final: 0.7129 (tptp) REVERT: D 504 GLN cc_start: 0.6547 (pt0) cc_final: 0.6041 (pt0) REVERT: D 511 TYR cc_start: 0.6215 (t80) cc_final: 0.5990 (t80) REVERT: D 660 GLU cc_start: 0.6332 (mm-30) cc_final: 0.5364 (tp30) REVERT: D 685 ILE cc_start: 0.7651 (mt) cc_final: 0.7418 (mt) REVERT: D 822 MET cc_start: 0.5966 (mmm) cc_final: 0.5404 (mmm) REVERT: D 838 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7287 (mtp85) REVERT: D 846 GLU cc_start: 0.5725 (pt0) cc_final: 0.5086 (pm20) REVERT: D 870 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7125 (t70) REVERT: D 889 ASP cc_start: 0.6618 (m-30) cc_final: 0.6359 (t0) REVERT: D 913 GLU cc_start: 0.7109 (tt0) cc_final: 0.6886 (tt0) REVERT: D 1040 MET cc_start: 0.2524 (tpt) cc_final: 0.2096 (ttp) REVERT: D 1095 MET cc_start: 0.2173 (tpt) cc_final: -0.0513 (ptt) REVERT: D 1156 LEU cc_start: 0.5519 (mt) cc_final: 0.4129 (pp) REVERT: D 1189 MET cc_start: 0.8071 (mmp) cc_final: 0.6425 (tmm) REVERT: D 1367 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6741 (mm-40) REVERT: D 1369 ARG cc_start: 0.7462 (ttt180) cc_final: 0.6841 (ttp-110) REVERT: E 12 LYS cc_start: 0.6134 (mmtm) cc_final: 0.5883 (mmtp) REVERT: E 73 GLN cc_start: 0.5603 (OUTLIER) cc_final: 0.5008 (mm-40) REVERT: E 74 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.4878 (tt0) REVERT: A 105 SER cc_start: 0.7633 (p) cc_final: 0.7201 (m) REVERT: A 204 GLU cc_start: 0.4780 (pt0) cc_final: 0.4483 (mt-10) REVERT: G 29 GLN cc_start: 0.4947 (mm-40) cc_final: 0.4528 (tp40) REVERT: B 29 GLU cc_start: 0.5472 (pm20) cc_final: 0.4233 (pm20) REVERT: B 51 MET cc_start: 0.5793 (tpt) cc_final: 0.5108 (tpt) REVERT: B 182 ARG cc_start: 0.5023 (ttm110) cc_final: 0.4510 (ttm-80) outliers start: 110 outliers final: 69 residues processed: 437 average time/residue: 0.3962 time to fit residues: 274.2725 Evaluate side-chains 389 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 309 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 615 LYS Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 838 ARG Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 243 optimal weight: 30.0000 chunk 134 optimal weight: 0.8980 chunk 278 optimal weight: 0.8980 chunk 225 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 293 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN D 875 ASN D1279 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28042 Z= 0.216 Angle : 0.613 9.060 38140 Z= 0.323 Chirality : 0.043 0.210 4349 Planarity : 0.005 0.055 4796 Dihedral : 13.810 146.012 4363 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 3.12 % Allowed : 16.78 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3341 helix: 0.53 (0.15), residues: 1216 sheet: -0.75 (0.26), residues: 391 loop : -1.49 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 36 HIS 0.017 0.001 HIS C 554 PHE 0.024 0.001 PHE D 17 TYR 0.043 0.001 TYR G 62 ARG 0.009 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 344 time to evaluate : 2.925 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: C 8 LYS cc_start: 0.6680 (mmtp) cc_final: 0.5947 (mppt) REVERT: C 39 ILE cc_start: 0.6178 (OUTLIER) cc_final: 0.5697 (tt) REVERT: C 176 ILE cc_start: 0.6694 (mm) cc_final: 0.6484 (mm) REVERT: C 183 TRP cc_start: 0.6472 (m-10) cc_final: 0.6138 (m-10) REVERT: C 239 MET cc_start: 0.4050 (mmm) cc_final: 0.3789 (mmm) REVERT: C 347 ILE cc_start: 0.6880 (mm) cc_final: 0.6610 (mm) REVERT: C 396 ASP cc_start: 0.7028 (t70) cc_final: 0.6754 (t0) REVERT: C 407 ARG cc_start: 0.8122 (tpp80) cc_final: 0.7641 (tpp80) REVERT: C 422 LYS cc_start: 0.6777 (mttm) cc_final: 0.6321 (pttp) REVERT: C 447 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.6029 (t-170) REVERT: C 631 GLU cc_start: 0.7953 (mt-10) cc_final: 0.6913 (mp0) REVERT: C 768 MET cc_start: 0.7323 (tpt) cc_final: 0.7011 (tpt) REVERT: C 805 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7036 (ptt) REVERT: C 811 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.6958 (p0) REVERT: C 851 THR cc_start: 0.8254 (t) cc_final: 0.7863 (p) REVERT: C 876 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6608 (mm-30) REVERT: C 964 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6714 (tt) REVERT: C 1188 ASP cc_start: 0.7062 (t70) cc_final: 0.6831 (t0) REVERT: C 1209 GLN cc_start: 0.8098 (mt0) cc_final: 0.7378 (mt0) REVERT: C 1315 MET cc_start: 0.6978 (ttp) cc_final: 0.6265 (ttp) REVERT: D 53 ARG cc_start: 0.5752 (mtm180) cc_final: 0.5430 (mmt90) REVERT: D 278 ARG cc_start: 0.6972 (mtp180) cc_final: 0.6755 (ttm170) REVERT: D 283 LEU cc_start: 0.5630 (mt) cc_final: 0.5295 (tt) REVERT: D 298 MET cc_start: 0.5158 (ptm) cc_final: 0.3968 (mmt) REVERT: D 330 MET cc_start: 0.6494 (ppp) cc_final: 0.5778 (ppp) REVERT: D 395 LYS cc_start: 0.7419 (ttpp) cc_final: 0.7124 (tptp) REVERT: D 537 TYR cc_start: 0.6432 (t80) cc_final: 0.5648 (t80) REVERT: D 660 GLU cc_start: 0.6278 (mm-30) cc_final: 0.5373 (tp30) REVERT: D 685 ILE cc_start: 0.7703 (mt) cc_final: 0.7432 (mt) REVERT: D 822 MET cc_start: 0.6458 (mmm) cc_final: 0.5769 (mmm) REVERT: D 838 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6877 (mtp85) REVERT: D 846 GLU cc_start: 0.5580 (pt0) cc_final: 0.5020 (pm20) REVERT: D 870 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.7065 (t70) REVERT: D 913 GLU cc_start: 0.7117 (tt0) cc_final: 0.6854 (tt0) REVERT: D 1040 MET cc_start: 0.2576 (tpt) cc_final: 0.2196 (ttp) REVERT: D 1156 LEU cc_start: 0.5416 (mt) cc_final: 0.4026 (pp) REVERT: D 1189 MET cc_start: 0.7940 (mmp) cc_final: 0.6442 (tmm) REVERT: D 1243 LEU cc_start: 0.7822 (tp) cc_final: 0.7573 (tt) REVERT: D 1369 ARG cc_start: 0.7378 (ttt180) cc_final: 0.6700 (ttp-110) REVERT: E 12 LYS cc_start: 0.6139 (mmtm) cc_final: 0.5893 (mmtp) REVERT: E 73 GLN cc_start: 0.5628 (OUTLIER) cc_final: 0.5038 (mm-40) REVERT: E 74 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.4858 (tt0) REVERT: A 105 SER cc_start: 0.7778 (p) cc_final: 0.7372 (m) REVERT: A 204 GLU cc_start: 0.4803 (pt0) cc_final: 0.4356 (mt-10) REVERT: G 1 MET cc_start: 0.3856 (mmm) cc_final: 0.1235 (tmm) REVERT: G 73 TRP cc_start: 0.7217 (t60) cc_final: 0.6484 (t60) REVERT: B 29 GLU cc_start: 0.5400 (pm20) cc_final: 0.4344 (pm20) REVERT: B 51 MET cc_start: 0.5724 (tpt) cc_final: 0.5062 (tpt) REVERT: B 127 GLN cc_start: 0.6756 (mt0) cc_final: 0.6293 (mm110) REVERT: B 227 GLN cc_start: 0.5480 (OUTLIER) cc_final: 0.5191 (mt0) outliers start: 89 outliers final: 46 residues processed: 411 average time/residue: 0.4002 time to fit residues: 260.3675 Evaluate side-chains 369 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 313 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 838 ARG Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 0.7980 chunk 294 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 chunk 191 optimal weight: 0.0060 chunk 80 optimal weight: 0.9990 chunk 327 optimal weight: 30.0000 chunk 271 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 458 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 ASN D 875 ASN A 75 GLN G 29 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28042 Z= 0.198 Angle : 0.594 8.810 38140 Z= 0.314 Chirality : 0.043 0.209 4349 Planarity : 0.004 0.057 4796 Dihedral : 13.719 145.727 4363 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 3.22 % Allowed : 17.23 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3341 helix: 0.67 (0.15), residues: 1217 sheet: -0.70 (0.25), residues: 396 loop : -1.43 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 73 HIS 0.014 0.001 HIS C 554 PHE 0.022 0.001 PHE D 17 TYR 0.017 0.001 TYR C 555 ARG 0.010 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 333 time to evaluate : 2.723 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: C 8 LYS cc_start: 0.6694 (mmtp) cc_final: 0.5787 (mmtm) REVERT: C 39 ILE cc_start: 0.6327 (OUTLIER) cc_final: 0.5855 (tt) REVERT: C 183 TRP cc_start: 0.6331 (m-10) cc_final: 0.6079 (m-10) REVERT: C 239 MET cc_start: 0.4076 (mmm) cc_final: 0.3743 (mmm) REVERT: C 396 ASP cc_start: 0.7030 (t70) cc_final: 0.6776 (t0) REVERT: C 407 ARG cc_start: 0.8096 (tpp80) cc_final: 0.7727 (tpp80) REVERT: C 422 LYS cc_start: 0.6709 (mttm) cc_final: 0.6310 (pttp) REVERT: C 447 HIS cc_start: 0.6506 (OUTLIER) cc_final: 0.6120 (t-170) REVERT: C 631 GLU cc_start: 0.7929 (mt-10) cc_final: 0.6890 (mp0) REVERT: C 768 MET cc_start: 0.7271 (tpt) cc_final: 0.6728 (mmm) REVERT: C 805 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7126 (ptt) REVERT: C 811 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.6951 (p0) REVERT: C 851 THR cc_start: 0.8240 (t) cc_final: 0.7829 (p) REVERT: C 876 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6636 (mm-30) REVERT: C 964 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6726 (tt) REVERT: C 1079 ILE cc_start: 0.5561 (pt) cc_final: 0.5343 (mt) REVERT: C 1119 MET cc_start: 0.5564 (tpt) cc_final: 0.5117 (tpt) REVERT: C 1188 ASP cc_start: 0.6976 (t70) cc_final: 0.6764 (t0) REVERT: C 1209 GLN cc_start: 0.8087 (mt0) cc_final: 0.7371 (mt0) REVERT: C 1315 MET cc_start: 0.7035 (ttp) cc_final: 0.6378 (ttt) REVERT: D 53 ARG cc_start: 0.5777 (mtm180) cc_final: 0.5439 (mmt90) REVERT: D 180 MET cc_start: 0.2588 (mmp) cc_final: -0.0549 (pmm) REVERT: D 278 ARG cc_start: 0.7013 (mtp180) cc_final: 0.6754 (ttm170) REVERT: D 283 LEU cc_start: 0.5663 (mt) cc_final: 0.5315 (tt) REVERT: D 298 MET cc_start: 0.5386 (ptm) cc_final: 0.4570 (mmt) REVERT: D 332 LYS cc_start: 0.6729 (ttpt) cc_final: 0.6076 (mtpp) REVERT: D 395 LYS cc_start: 0.7432 (ttpp) cc_final: 0.7143 (tptp) REVERT: D 466 MET cc_start: 0.7266 (ttm) cc_final: 0.7018 (ttm) REVERT: D 537 TYR cc_start: 0.6356 (t80) cc_final: 0.5745 (t80) REVERT: D 651 HIS cc_start: 0.7018 (m-70) cc_final: 0.6781 (t-170) REVERT: D 685 ILE cc_start: 0.7680 (mt) cc_final: 0.7411 (mt) REVERT: D 822 MET cc_start: 0.6430 (mmm) cc_final: 0.5378 (mmm) REVERT: D 846 GLU cc_start: 0.5505 (pt0) cc_final: 0.5027 (pm20) REVERT: D 864 LEU cc_start: 0.5561 (mp) cc_final: 0.5269 (tt) REVERT: D 870 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7064 (t70) REVERT: D 913 GLU cc_start: 0.7141 (tt0) cc_final: 0.6923 (tt0) REVERT: D 1040 MET cc_start: 0.2432 (tpt) cc_final: 0.2107 (ttp) REVERT: D 1095 MET cc_start: 0.2605 (tpt) cc_final: -0.0219 (ptt) REVERT: D 1152 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6385 (mp0) REVERT: D 1156 LEU cc_start: 0.5500 (mt) cc_final: 0.4166 (pp) REVERT: D 1189 MET cc_start: 0.7909 (mmp) cc_final: 0.6473 (tmm) REVERT: D 1243 LEU cc_start: 0.7807 (tp) cc_final: 0.7560 (tt) REVERT: D 1263 LYS cc_start: 0.6796 (mmtt) cc_final: 0.6293 (mtpt) REVERT: D 1369 ARG cc_start: 0.7372 (ttt180) cc_final: 0.6696 (ttp-110) REVERT: E 12 LYS cc_start: 0.6197 (mmtm) cc_final: 0.5938 (mmtp) REVERT: E 73 GLN cc_start: 0.5586 (OUTLIER) cc_final: 0.5013 (mm-40) REVERT: E 74 GLU cc_start: 0.5659 (OUTLIER) cc_final: 0.4904 (tt0) REVERT: A 75 GLN cc_start: 0.4848 (tt0) cc_final: 0.4575 (tt0) REVERT: A 105 SER cc_start: 0.7732 (p) cc_final: 0.7331 (m) REVERT: A 204 GLU cc_start: 0.4876 (pt0) cc_final: 0.4589 (mt-10) REVERT: G 1 MET cc_start: 0.3900 (mmm) cc_final: 0.1304 (tmm) REVERT: G 29 GLN cc_start: 0.5680 (OUTLIER) cc_final: 0.5420 (tp40) REVERT: G 73 TRP cc_start: 0.7104 (t60) cc_final: 0.6587 (t60) REVERT: B 29 GLU cc_start: 0.5351 (pm20) cc_final: 0.4391 (pm20) REVERT: B 51 MET cc_start: 0.5635 (tpt) cc_final: 0.4913 (tpt) REVERT: B 127 GLN cc_start: 0.6796 (mt0) cc_final: 0.6313 (mm110) REVERT: B 227 GLN cc_start: 0.5448 (OUTLIER) cc_final: 0.5160 (mt0) outliers start: 92 outliers final: 53 residues processed: 406 average time/residue: 0.3885 time to fit residues: 251.8903 Evaluate side-chains 383 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 320 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 238 optimal weight: 40.0000 chunk 185 optimal weight: 7.9990 chunk 275 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 chunk 325 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 HIS ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN D 875 ASN A 23 HIS G 29 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 28042 Z= 0.369 Angle : 0.691 10.890 38140 Z= 0.362 Chirality : 0.046 0.279 4349 Planarity : 0.005 0.057 4796 Dihedral : 13.854 145.967 4363 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 3.54 % Allowed : 17.86 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3341 helix: 0.44 (0.15), residues: 1216 sheet: -0.81 (0.25), residues: 399 loop : -1.48 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 36 HIS 0.023 0.002 HIS C 554 PHE 0.021 0.002 PHE C1270 TYR 0.045 0.002 TYR G 62 ARG 0.018 0.001 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 325 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.5876 (tt) REVERT: C 175 ARG cc_start: 0.6619 (ttm110) cc_final: 0.6356 (ttm110) REVERT: C 239 MET cc_start: 0.4424 (mmm) cc_final: 0.3883 (mmm) REVERT: C 396 ASP cc_start: 0.7008 (t70) cc_final: 0.6782 (t0) REVERT: C 407 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7698 (tpp80) REVERT: C 422 LYS cc_start: 0.6809 (mttm) cc_final: 0.6382 (pttp) REVERT: C 631 GLU cc_start: 0.7986 (mt-10) cc_final: 0.6935 (mp0) REVERT: C 768 MET cc_start: 0.7450 (tpt) cc_final: 0.6916 (mmm) REVERT: C 805 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7072 (ptt) REVERT: C 811 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7429 (p0) REVERT: C 876 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6767 (mm-30) REVERT: C 1085 MET cc_start: 0.6612 (mmt) cc_final: 0.6299 (mmt) REVERT: C 1107 MET cc_start: 0.6673 (mtp) cc_final: 0.6453 (mtp) REVERT: C 1188 ASP cc_start: 0.7369 (t70) cc_final: 0.7062 (t0) REVERT: C 1209 GLN cc_start: 0.8118 (mt0) cc_final: 0.7418 (mt0) REVERT: C 1315 MET cc_start: 0.7191 (ttp) cc_final: 0.6822 (ttt) REVERT: D 53 ARG cc_start: 0.5802 (mtm180) cc_final: 0.5536 (mmt90) REVERT: D 278 ARG cc_start: 0.6984 (mtp180) cc_final: 0.6764 (ttm170) REVERT: D 283 LEU cc_start: 0.5673 (mt) cc_final: 0.5326 (tt) REVERT: D 298 MET cc_start: 0.5373 (ptm) cc_final: 0.4503 (mmt) REVERT: D 395 LYS cc_start: 0.7495 (ttpp) cc_final: 0.7214 (tptp) REVERT: D 413 ASP cc_start: 0.5188 (m-30) cc_final: 0.4850 (m-30) REVERT: D 651 HIS cc_start: 0.6994 (m-70) cc_final: 0.6737 (t-170) REVERT: D 725 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.5727 (mmt) REVERT: D 846 GLU cc_start: 0.5635 (pt0) cc_final: 0.5135 (pm20) REVERT: D 870 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7135 (t70) REVERT: D 913 GLU cc_start: 0.7247 (tt0) cc_final: 0.7022 (tt0) REVERT: D 1040 MET cc_start: 0.2418 (tpt) cc_final: 0.2150 (ttp) REVERT: D 1095 MET cc_start: 0.2092 (tpt) cc_final: -0.0421 (ptt) REVERT: D 1152 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6284 (mp0) REVERT: D 1156 LEU cc_start: 0.5469 (mt) cc_final: 0.4033 (pp) REVERT: D 1189 MET cc_start: 0.7880 (mmp) cc_final: 0.6513 (tmm) REVERT: D 1243 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7585 (tt) REVERT: D 1369 ARG cc_start: 0.7418 (ttt180) cc_final: 0.6752 (ttp-110) REVERT: E 12 LYS cc_start: 0.6300 (mmtm) cc_final: 0.6035 (mmtp) REVERT: E 73 GLN cc_start: 0.5577 (OUTLIER) cc_final: 0.4992 (mm-40) REVERT: E 74 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.4883 (tt0) REVERT: A 105 SER cc_start: 0.7689 (p) cc_final: 0.7277 (m) REVERT: A 204 GLU cc_start: 0.4847 (pt0) cc_final: 0.4525 (mt-10) REVERT: G 1 MET cc_start: 0.3975 (mmm) cc_final: 0.1126 (tmm) REVERT: G 29 GLN cc_start: 0.6036 (OUTLIER) cc_final: 0.5612 (tp40) REVERT: G 73 TRP cc_start: 0.7016 (t60) cc_final: 0.6603 (t60) REVERT: B 29 GLU cc_start: 0.5584 (pm20) cc_final: 0.4565 (pm20) REVERT: B 51 MET cc_start: 0.5676 (tpt) cc_final: 0.4974 (tpt) REVERT: B 227 GLN cc_start: 0.5525 (OUTLIER) cc_final: 0.5215 (mt0) outliers start: 101 outliers final: 69 residues processed: 401 average time/residue: 0.3934 time to fit residues: 253.2613 Evaluate side-chains 388 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 309 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1177 ARG Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 653 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 221 optimal weight: 0.0020 chunk 161 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 256 optimal weight: 0.4980 overall best weight: 2.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN A 75 GLN G 29 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 28042 Z= 0.397 Angle : 0.713 11.662 38140 Z= 0.374 Chirality : 0.047 0.292 4349 Planarity : 0.005 0.057 4796 Dihedral : 13.944 144.858 4363 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.87 % Favored : 94.04 % Rotamer: Outliers : 3.43 % Allowed : 18.32 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.14 (0.14), residues: 3341 helix: 0.35 (0.15), residues: 1205 sheet: -0.99 (0.25), residues: 407 loop : -1.51 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 183 HIS 0.037 0.002 HIS C 554 PHE 0.038 0.002 PHE C1270 TYR 0.027 0.002 TYR C1231 ARG 0.010 0.001 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 321 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 ILE cc_start: 0.6269 (OUTLIER) cc_final: 0.5903 (tt) REVERT: C 183 TRP cc_start: 0.6523 (m-10) cc_final: 0.5720 (m-10) REVERT: C 239 MET cc_start: 0.4682 (mmm) cc_final: 0.4069 (mmm) REVERT: C 396 ASP cc_start: 0.7057 (t70) cc_final: 0.6847 (t0) REVERT: C 407 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7733 (tpp80) REVERT: C 422 LYS cc_start: 0.6761 (mttm) cc_final: 0.6314 (pttp) REVERT: C 562 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6152 (tt0) REVERT: C 631 GLU cc_start: 0.8033 (mt-10) cc_final: 0.6940 (mp0) REVERT: C 632 ASP cc_start: 0.6041 (t0) cc_final: 0.5610 (m-30) REVERT: C 768 MET cc_start: 0.7460 (tpt) cc_final: 0.7197 (mmm) REVERT: C 805 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7039 (ptt) REVERT: C 811 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7379 (p0) REVERT: C 876 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6775 (mm-30) REVERT: C 1078 LYS cc_start: 0.6413 (pttt) cc_final: 0.5415 (ptpt) REVERT: C 1085 MET cc_start: 0.6750 (mmt) cc_final: 0.6358 (mmt) REVERT: C 1188 ASP cc_start: 0.7378 (t70) cc_final: 0.7096 (t0) REVERT: C 1209 GLN cc_start: 0.8146 (mt0) cc_final: 0.7420 (mt0) REVERT: C 1315 MET cc_start: 0.7066 (ttp) cc_final: 0.6812 (ttt) REVERT: D 53 ARG cc_start: 0.5784 (mtm180) cc_final: 0.5547 (mmt90) REVERT: D 97 VAL cc_start: 0.7205 (m) cc_final: 0.7002 (p) REVERT: D 278 ARG cc_start: 0.6969 (mtp180) cc_final: 0.6765 (ttm170) REVERT: D 283 LEU cc_start: 0.5548 (mt) cc_final: 0.5211 (tt) REVERT: D 298 MET cc_start: 0.5360 (ptm) cc_final: 0.4484 (mmt) REVERT: D 375 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6623 (mm-30) REVERT: D 395 LYS cc_start: 0.7522 (ttpp) cc_final: 0.7237 (tptp) REVERT: D 413 ASP cc_start: 0.5279 (m-30) cc_final: 0.4926 (m-30) REVERT: D 725 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.5754 (mmt) REVERT: D 846 GLU cc_start: 0.5653 (pt0) cc_final: 0.5121 (pm20) REVERT: D 870 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7177 (t70) REVERT: D 913 GLU cc_start: 0.7283 (tt0) cc_final: 0.7054 (tt0) REVERT: D 1152 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6257 (mp0) REVERT: D 1189 MET cc_start: 0.7763 (mmp) cc_final: 0.6474 (tmm) REVERT: D 1243 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7575 (tt) REVERT: D 1250 ASP cc_start: 0.6288 (m-30) cc_final: 0.5748 (t0) REVERT: D 1369 ARG cc_start: 0.7436 (ttt180) cc_final: 0.6762 (ttp-110) REVERT: E 12 LYS cc_start: 0.6272 (mmtm) cc_final: 0.6007 (mmtp) REVERT: E 73 GLN cc_start: 0.5589 (OUTLIER) cc_final: 0.5018 (mm-40) REVERT: E 74 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5022 (tt0) REVERT: A 105 SER cc_start: 0.7696 (p) cc_final: 0.7289 (m) REVERT: A 204 GLU cc_start: 0.4842 (pt0) cc_final: 0.4483 (mt-10) REVERT: G 1 MET cc_start: 0.4044 (mmm) cc_final: 0.1131 (tmm) REVERT: G 29 GLN cc_start: 0.5866 (OUTLIER) cc_final: 0.5350 (tp40) REVERT: G 75 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7501 (mt-10) REVERT: B 29 GLU cc_start: 0.5645 (pm20) cc_final: 0.4575 (pm20) REVERT: B 51 MET cc_start: 0.5648 (tpt) cc_final: 0.4939 (tpt) REVERT: B 227 GLN cc_start: 0.5532 (OUTLIER) cc_final: 0.5216 (mt0) outliers start: 98 outliers final: 70 residues processed: 394 average time/residue: 0.3855 time to fit residues: 245.8953 Evaluate side-chains 391 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 309 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1177 ARG Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 653 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 0.4980 chunk 312 optimal weight: 20.0000 chunk 284 optimal weight: 0.4980 chunk 303 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 238 optimal weight: 50.0000 chunk 93 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 chunk 287 optimal weight: 0.0030 chunk 302 optimal weight: 8.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 808 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN A 75 GLN ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28042 Z= 0.192 Angle : 0.613 13.555 38140 Z= 0.321 Chirality : 0.043 0.230 4349 Planarity : 0.004 0.056 4796 Dihedral : 13.770 144.865 4363 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 2.31 % Allowed : 19.54 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % 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: -0.90 (0.14), residues: 3341 helix: 0.66 (0.15), residues: 1220 sheet: -0.80 (0.25), residues: 401 loop : -1.49 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 183 HIS 0.014 0.001 HIS C 554 PHE 0.018 0.001 PHE D 17 TYR 0.025 0.001 TYR G 61 ARG 0.012 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 339 time to evaluate : 2.856 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: C 183 TRP cc_start: 0.6465 (m-10) cc_final: 0.5642 (m-10) REVERT: C 239 MET cc_start: 0.4506 (mmm) cc_final: 0.3538 (mmp) REVERT: C 396 ASP cc_start: 0.6988 (t70) cc_final: 0.6727 (t0) REVERT: C 407 ARG cc_start: 0.8112 (tpp80) cc_final: 0.7741 (tpp80) REVERT: C 422 LYS cc_start: 0.6733 (mttm) cc_final: 0.6331 (pttp) REVERT: C 631 GLU cc_start: 0.8034 (mt-10) cc_final: 0.6944 (mp0) REVERT: C 768 MET cc_start: 0.7082 (tpt) cc_final: 0.5889 (mmm) REVERT: C 785 ASP cc_start: 0.7167 (m-30) cc_final: 0.6880 (p0) REVERT: C 805 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7042 (ptt) REVERT: C 811 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.7206 (p0) REVERT: C 851 THR cc_start: 0.8256 (t) cc_final: 0.7829 (p) REVERT: C 876 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6764 (mm-30) REVERT: C 1079 ILE cc_start: 0.5665 (pt) cc_final: 0.5346 (mt) REVERT: C 1085 MET cc_start: 0.6377 (mmt) cc_final: 0.6124 (mmt) REVERT: C 1143 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6230 (mp0) REVERT: C 1188 ASP cc_start: 0.6886 (t70) cc_final: 0.6659 (t0) REVERT: C 1209 GLN cc_start: 0.8099 (mt0) cc_final: 0.7398 (mt0) REVERT: D 53 ARG cc_start: 0.5791 (mtm180) cc_final: 0.5488 (mmt90) REVERT: D 97 VAL cc_start: 0.7233 (m) cc_final: 0.7032 (p) REVERT: D 137 ARG cc_start: 0.5324 (mmm-85) cc_final: 0.4486 (mmm160) REVERT: D 278 ARG cc_start: 0.6944 (mtp180) cc_final: 0.6702 (ttm170) REVERT: D 283 LEU cc_start: 0.5505 (mt) cc_final: 0.5180 (tt) REVERT: D 298 MET cc_start: 0.5426 (ptm) cc_final: 0.4596 (mmt) REVERT: D 329 ASP cc_start: 0.6261 (m-30) cc_final: 0.5953 (m-30) REVERT: D 395 LYS cc_start: 0.7492 (ttpp) cc_final: 0.7195 (tptp) REVERT: D 413 ASP cc_start: 0.4929 (m-30) cc_final: 0.4621 (m-30) REVERT: D 466 MET cc_start: 0.7264 (ttm) cc_final: 0.6986 (ttm) REVERT: D 581 MET cc_start: 0.6631 (ttm) cc_final: 0.6424 (ttm) REVERT: D 725 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.5548 (mmt) REVERT: D 846 GLU cc_start: 0.5573 (pt0) cc_final: 0.5021 (pm20) REVERT: D 870 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7037 (t70) REVERT: D 1095 MET cc_start: 0.2197 (tpt) cc_final: -0.0162 (mmm) REVERT: D 1152 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6322 (mp0) REVERT: D 1189 MET cc_start: 0.7719 (mmp) cc_final: 0.6254 (tmm) REVERT: D 1191 PRO cc_start: 0.7305 (Cg_exo) cc_final: 0.6866 (Cg_endo) REVERT: D 1243 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7661 (tt) REVERT: D 1250 ASP cc_start: 0.5859 (m-30) cc_final: 0.5520 (t0) REVERT: D 1263 LYS cc_start: 0.6717 (mmtt) cc_final: 0.6356 (mtpt) REVERT: D 1369 ARG cc_start: 0.7368 (ttt180) cc_final: 0.6663 (ttp-110) REVERT: E 12 LYS cc_start: 0.6271 (mmtm) cc_final: 0.6012 (mmtp) REVERT: E 67 ARG cc_start: 0.7292 (ttm110) cc_final: 0.7083 (mtt-85) REVERT: E 73 GLN cc_start: 0.5607 (OUTLIER) cc_final: 0.5061 (mm-40) REVERT: E 74 GLU cc_start: 0.5845 (OUTLIER) cc_final: 0.5072 (tt0) REVERT: A 33 ARG cc_start: 0.7805 (tmm-80) cc_final: 0.6945 (tpp80) REVERT: A 105 SER cc_start: 0.7693 (p) cc_final: 0.7331 (m) REVERT: A 204 GLU cc_start: 0.4878 (pt0) cc_final: 0.4585 (mt-10) REVERT: G 1 MET cc_start: 0.3989 (mmm) cc_final: 0.1202 (tmm) REVERT: G 29 GLN cc_start: 0.5718 (OUTLIER) cc_final: 0.5496 (tp-100) REVERT: G 73 TRP cc_start: 0.6994 (t60) cc_final: 0.6730 (t60) REVERT: B 29 GLU cc_start: 0.5450 (pm20) cc_final: 0.4605 (pm20) REVERT: B 51 MET cc_start: 0.5605 (tpt) cc_final: 0.4867 (tpt) REVERT: B 227 GLN cc_start: 0.5451 (OUTLIER) cc_final: 0.5156 (mt0) outliers start: 66 outliers final: 49 residues processed: 390 average time/residue: 0.4084 time to fit residues: 256.2509 Evaluate side-chains 367 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 308 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 10.0000 chunk 321 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 223 optimal weight: 0.9990 chunk 336 optimal weight: 6.9990 chunk 309 optimal weight: 40.0000 chunk 268 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 164 optimal weight: 0.0060 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1259 GLN A 75 GLN G 29 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28042 Z= 0.309 Angle : 0.666 12.990 38140 Z= 0.347 Chirality : 0.045 0.241 4349 Planarity : 0.005 0.056 4796 Dihedral : 13.791 145.203 4363 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.51 % Favored : 94.40 % Rotamer: Outliers : 2.38 % Allowed : 19.79 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 3341 helix: 0.51 (0.15), residues: 1222 sheet: -0.96 (0.25), residues: 412 loop : -1.48 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 36 HIS 0.027 0.001 HIS C 554 PHE 0.022 0.002 PHE C1270 TYR 0.027 0.002 TYR G 61 ARG 0.013 0.001 ARG C 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 315 time to evaluate : 3.021 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: C 183 TRP cc_start: 0.6544 (m-10) cc_final: 0.5727 (m-10) REVERT: C 239 MET cc_start: 0.4583 (mmm) cc_final: 0.3924 (mmm) REVERT: C 396 ASP cc_start: 0.7005 (t70) cc_final: 0.6756 (t0) REVERT: C 422 LYS cc_start: 0.6801 (mttm) cc_final: 0.6355 (pttp) REVERT: C 631 GLU cc_start: 0.8036 (mt-10) cc_final: 0.6935 (mp0) REVERT: C 637 ARG cc_start: 0.5700 (OUTLIER) cc_final: 0.5371 (ptm-80) REVERT: C 768 MET cc_start: 0.7223 (tpt) cc_final: 0.6818 (mmm) REVERT: C 805 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7221 (ptt) REVERT: C 811 ASN cc_start: 0.7625 (OUTLIER) cc_final: 0.7003 (p0) REVERT: C 851 THR cc_start: 0.8261 (t) cc_final: 0.7834 (p) REVERT: C 876 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6788 (mm-30) REVERT: C 1085 MET cc_start: 0.6591 (mmt) cc_final: 0.6252 (mmt) REVERT: C 1143 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6275 (mp0) REVERT: C 1188 ASP cc_start: 0.7161 (t70) cc_final: 0.6821 (t0) REVERT: C 1209 GLN cc_start: 0.8113 (mt0) cc_final: 0.7412 (mt0) REVERT: C 1230 MET cc_start: 0.7732 (ttp) cc_final: 0.7516 (ttp) REVERT: C 1289 GLU cc_start: 0.6056 (mp0) cc_final: 0.5584 (mp0) REVERT: D 53 ARG cc_start: 0.5906 (mtm180) cc_final: 0.5587 (mmt90) REVERT: D 97 VAL cc_start: 0.7251 (m) cc_final: 0.7043 (p) REVERT: D 137 ARG cc_start: 0.5294 (mmm-85) cc_final: 0.4457 (mmm160) REVERT: D 278 ARG cc_start: 0.6994 (mtp180) cc_final: 0.6756 (ttm170) REVERT: D 283 LEU cc_start: 0.5518 (mt) cc_final: 0.5187 (tt) REVERT: D 298 MET cc_start: 0.5392 (ptm) cc_final: 0.4549 (mmt) REVERT: D 329 ASP cc_start: 0.6442 (m-30) cc_final: 0.6147 (m-30) REVERT: D 395 LYS cc_start: 0.7593 (ttpp) cc_final: 0.7298 (tptp) REVERT: D 413 ASP cc_start: 0.5246 (m-30) cc_final: 0.4897 (m-30) REVERT: D 725 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.5682 (mmt) REVERT: D 846 GLU cc_start: 0.5620 (pt0) cc_final: 0.5092 (pm20) REVERT: D 870 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7068 (t70) REVERT: D 913 GLU cc_start: 0.7040 (tt0) cc_final: 0.6244 (mt-10) REVERT: D 1152 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6317 (mp0) REVERT: D 1189 MET cc_start: 0.7614 (mmp) cc_final: 0.6166 (tmm) REVERT: D 1243 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7543 (tt) REVERT: D 1250 ASP cc_start: 0.6054 (m-30) cc_final: 0.5733 (t0) REVERT: D 1263 LYS cc_start: 0.6832 (mmtt) cc_final: 0.6392 (mtpt) REVERT: D 1369 ARG cc_start: 0.7396 (ttt180) cc_final: 0.6674 (ttp-110) REVERT: E 12 LYS cc_start: 0.6293 (mmtm) cc_final: 0.6030 (mmtp) REVERT: E 73 GLN cc_start: 0.5621 (OUTLIER) cc_final: 0.5071 (mm-40) REVERT: E 74 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.5026 (tt0) REVERT: A 105 SER cc_start: 0.7694 (p) cc_final: 0.7298 (m) REVERT: A 204 GLU cc_start: 0.4906 (pt0) cc_final: 0.4529 (mt-10) REVERT: G 1 MET cc_start: 0.3958 (mmm) cc_final: 0.1178 (tmm) REVERT: B 12 ARG cc_start: 0.2031 (mtm180) cc_final: 0.1736 (mtm180) REVERT: B 29 GLU cc_start: 0.5713 (pm20) cc_final: 0.4756 (pm20) REVERT: B 51 MET cc_start: 0.5667 (tpt) cc_final: 0.4887 (tpt) REVERT: B 227 GLN cc_start: 0.5496 (OUTLIER) cc_final: 0.5168 (mt0) outliers start: 68 outliers final: 49 residues processed: 367 average time/residue: 0.4085 time to fit residues: 239.0572 Evaluate side-chains 363 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 304 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 212 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 247 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 0.0980 chunk 268 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 275 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 HIS ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN A 75 GLN G 29 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.238092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.194273 restraints weight = 34301.198| |-----------------------------------------------------------------------------| r_work (start): 0.4509 rms_B_bonded: 2.38 r_work: 0.4223 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28042 Z= 0.189 Angle : 0.614 13.168 38140 Z= 0.319 Chirality : 0.043 0.225 4349 Planarity : 0.004 0.055 4796 Dihedral : 13.656 144.093 4363 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 2.24 % Allowed : 20.07 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3341 helix: 0.68 (0.15), residues: 1225 sheet: -0.71 (0.26), residues: 383 loop : -1.41 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 183 HIS 0.015 0.001 HIS C 554 PHE 0.018 0.001 PHE D 17 TYR 0.029 0.001 TYR G 61 ARG 0.013 0.000 ARG C 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6740.57 seconds wall clock time: 121 minutes 2.98 seconds (7262.98 seconds total)