Starting phenix.real_space_refine on Thu Jul 25 04:47:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phk_17668/07_2024/8phk_17668_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phk_17668/07_2024/8phk_17668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phk_17668/07_2024/8phk_17668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phk_17668/07_2024/8phk_17668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phk_17668/07_2024/8phk_17668_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phk_17668/07_2024/8phk_17668_neut.cif" } resolution = 3.1 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= 0.009 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 87 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 17421 2.51 5 N 4998 2.21 5 O 5604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 103": "OD1" <-> "OD2" Residue "I PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 441": "OE1" <-> "OE2" Residue "I GLU 504": "OE1" <-> "OE2" Residue "I GLU 813": "OE1" <-> "OE2" Residue "I GLU 867": "OE1" <-> "OE2" Residue "I GLU 876": "OE1" <-> "OE2" Residue "I ASP 937": "OD1" <-> "OD2" Residue "I ASP 995": "OD1" <-> "OD2" Residue "I GLU 1197": "OE1" <-> "OE2" Residue "I ASP 1241": "OD1" <-> "OD2" Residue "I GLU 1279": "OE1" <-> "OE2" Residue "I GLU 1329": "OE1" <-> "OE2" Residue "J ASP 289": "OD1" <-> "OD2" Residue "J ASP 902": "OD1" <-> "OD2" Residue "J GLU 925": "OE1" <-> "OE2" Residue "J PHE 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1158": "OE1" <-> "OE2" Residue "J PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 8": "OD1" <-> "OD2" Residue "K ASP 44": "OD1" <-> "OD2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 28225 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1294 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 150} Chain: "I" Number of atoms: 10431 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 bond proxies already assigned to first conformer: 10580 Chain: "J" Number of atoms: 10440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1342, 10440 Classifications: {'peptide': 1342} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1286} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "G" Number of atoms: 1807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Conformer: "B" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} bond proxies already assigned to first conformer: 1812 Chain: "H" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 784 Classifications: {'DNA': 38} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 37} Chain: "R" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12174 SG CYS J 70 24.393 69.954 83.528 1.00119.04 S ATOM 12188 SG CYS J 72 23.310 66.311 83.232 1.00118.34 S ATOM 12296 SG CYS J 85 21.845 68.517 85.926 1.00117.72 S ATOM 12320 SG CYS J 88 25.534 67.472 86.117 1.00115.59 S ATOM 18008 SG CYS J 814 56.521 126.276 92.019 1.00108.47 S ATOM 18573 SG CYS J 888 58.636 123.461 91.132 1.00106.90 S ATOM 18624 SG CYS J 895 57.608 126.109 88.414 1.00 98.23 S ATOM 18645 SG CYS J 898 60.284 126.828 90.894 1.00 99.88 S Time building chain proxies: 20.50, per 1000 atoms: 0.73 Number of scatterers: 28225 At special positions: 0 Unit cell: (139.776, 169.728, 158.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 112 16.00 P 87 15.00 Mg 1 11.99 O 5604 8.00 N 4998 7.00 C 17421 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: 10.62 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " Number of angles added : 12 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6238 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 51 sheets defined 38.5% alpha, 18.6% beta 38 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 9.21 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 38 through 42 Processing helix chain 'P' and resid 65 through 71 removed outlier: 3.620A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 98 removed outlier: 3.525A pdb=" N ILE P 93 " --> pdb=" O PRO P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 124 removed outlier: 3.967A pdb=" N PHE P 123 " --> pdb=" O GLU P 120 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU P 124 " --> pdb=" O GLY P 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 120 through 124' Processing helix chain 'P' and resid 155 through 157 No H-bonds generated for 'chain 'P' and resid 155 through 157' Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.646A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.648A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.093A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 3.829A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS I 295 " --> pdb=" O TYR I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 295' Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.557A pdb=" N GLY I 329 " --> pdb=" O LEU I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.704A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 410 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 482 Processing helix chain 'I' and resid 488 through 493 removed outlier: 4.179A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 488 through 493' Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.818A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 544 through 549 removed outlier: 4.058A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP I 549 " --> pdb=" O PHE I 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 544 through 549' Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.529A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.840A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 614' Processing helix chain 'I' and resid 624 through 628 removed outlier: 4.289A pdb=" N HIS I 628 " --> pdb=" O GLU I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.000A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.660A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 983 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.573A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 997 removed outlier: 4.027A pdb=" N ARG I 996 " --> pdb=" O PRO I 993 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.127A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 3.808A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.754A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.518A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 removed outlier: 3.646A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.812A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.656A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.664A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.757A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.855A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.566A pdb=" N VAL J 618 " --> pdb=" O LEU J 614 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.096A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.115A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.828A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 removed outlier: 3.688A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.587A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.326A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1296 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.714A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN J1326 " --> pdb=" O ALA J1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.648A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1360 through 1373 removed outlier: 3.768A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 34 removed outlier: 3.661A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY K 34 " --> pdb=" O MET K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.748A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 removed outlier: 4.360A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.631A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 162 removed outlier: 3.788A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.212A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 154 through 160 removed outlier: 3.616A pdb=" N ARG H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.772A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 232 removed outlier: 3.565A pdb=" N VAL H 232 " --> pdb=" O GLU H 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 229 through 232' Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 37 Processing sheet with id=AA3, first strand: chain 'P' and resid 149 through 153 removed outlier: 7.490A pdb=" N MET P 140 " --> pdb=" O THR P 131 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE P 129 " --> pdb=" O LEU P 142 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN P 144 " --> pdb=" O GLN P 127 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN P 127 " --> pdb=" O ASN P 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.586A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.030A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA7, first strand: chain 'I' and resid 148 through 151 Processing sheet with id=AA8, first strand: chain 'I' and resid 154 through 159 removed outlier: 4.872A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 226 through 231 removed outlier: 4.790A pdb=" N GLU I 226 " --> pdb=" O PHE I 337 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB2, first strand: chain 'I' and resid 296 through 297 removed outlier: 4.090A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.613A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 529 through 531 Processing sheet with id=AB5, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.681A pdb=" N LYS I 593 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB7, first strand: chain 'I' and resid 716 through 717 removed outlier: 4.122A pdb=" N ALA I 784 " --> pdb=" O ALA I 716 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.123A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC1, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC2, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.524A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.724A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.551A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 882 through 884 removed outlier: 3.972A pdb=" N VAL I 884 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC7, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC8, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC9, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AD1, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.029A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.816A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.682A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 253 through 254 removed outlier: 4.081A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD5, first strand: chain 'J' and resid 705 through 709 removed outlier: 3.687A pdb=" N THR J 705 " --> pdb=" O GLN J 716 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD7, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD8, first strand: chain 'J' and resid 825 through 827 removed outlier: 3.911A pdb=" N GLU J 833 " --> pdb=" O VAL J 825 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 842 through 843 removed outlier: 4.096A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.396A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.635A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.265A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 6.379A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE6, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.512A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.474A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.001A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.571A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AF2, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.948A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AF4, first strand: chain 'H' and resid 15 through 20 removed outlier: 6.732A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 97 through 105 removed outlier: 7.938A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.592A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) 1143 hydrogen bonds defined for protein. 3212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 13.78 Time building geometry restraints manager: 11.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9269 1.34 - 1.46: 4631 1.46 - 1.58: 14577 1.58 - 1.70: 172 1.70 - 1.82: 194 Bond restraints: 28843 Sorted by residual: bond pdb=" CB GLU J 925 " pdb=" CG GLU J 925 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.99e+00 bond pdb=" CB ASP I1126 " pdb=" CG ASP I1126 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.39e+00 bond pdb=" CB LYS J 599 " pdb=" CG LYS J 599 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CB GLN K 75 " pdb=" CG GLN K 75 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CB ASP J 751 " pdb=" CG ASP J 751 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.23e+00 ... (remaining 28838 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.40: 869 105.40 - 112.55: 15159 112.55 - 119.69: 9647 119.69 - 126.83: 13200 126.83 - 133.98: 480 Bond angle restraints: 39355 Sorted by residual: angle pdb=" CB MET I 488 " pdb=" CG MET I 488 " pdb=" SD MET I 488 " ideal model delta sigma weight residual 112.70 127.16 -14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CG ARG I1034 " pdb=" CD ARG I1034 " pdb=" NE ARG I1034 " ideal model delta sigma weight residual 112.00 122.32 -10.32 2.20e+00 2.07e-01 2.20e+01 angle pdb=" C PHE H 8 " pdb=" CA PHE H 8 " pdb=" CB PHE H 8 " ideal model delta sigma weight residual 115.79 110.33 5.46 1.19e+00 7.06e-01 2.10e+01 angle pdb=" C PHE P 130 " pdb=" N THR P 131 " pdb=" CA THR P 131 " ideal model delta sigma weight residual 122.08 116.44 5.64 1.53e+00 4.27e-01 1.36e+01 angle pdb=" CA GLN K 75 " pdb=" CB GLN K 75 " pdb=" CG GLN K 75 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 ... (remaining 39350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.24: 16170 29.24 - 58.47: 1248 58.47 - 87.71: 122 87.71 - 116.95: 6 116.95 - 146.19: 3 Dihedral angle restraints: 17549 sinusoidal: 7856 harmonic: 9693 Sorted by residual: dihedral pdb=" CA ARG I 994 " pdb=" C ARG I 994 " pdb=" N ASP I 995 " pdb=" CA ASP I 995 " ideal model delta harmonic sigma weight residual -180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PRO I 993 " pdb=" C PRO I 993 " pdb=" N ARG I 994 " pdb=" CA ARG I 994 " ideal model delta harmonic sigma weight residual -180.00 -161.00 -19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" C4' DC A 39 " pdb=" C3' DC A 39 " pdb=" O3' DC A 39 " pdb=" P DC A 40 " ideal model delta sinusoidal sigma weight residual 220.00 73.81 146.19 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 17546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3292 0.036 - 0.072: 801 0.072 - 0.109: 318 0.109 - 0.145: 79 0.145 - 0.181: 5 Chirality restraints: 4495 Sorted by residual: chirality pdb=" CB ILE P 117 " pdb=" CA ILE P 117 " pdb=" CG1 ILE P 117 " pdb=" CG2 ILE P 117 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA MET I 488 " pdb=" N MET I 488 " pdb=" C MET I 488 " pdb=" CB MET I 488 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ILE H 107 " pdb=" N ILE H 107 " pdb=" C ILE H 107 " pdb=" CB ILE H 107 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 4492 not shown) Planarity restraints: 4843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP P 106 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO P 107 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO P 107 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO P 107 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 137 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C ASN G 137 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN G 137 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA G 138 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU J 925 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" CD GLU J 925 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU J 925 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU J 925 " 0.012 2.00e-02 2.50e+03 ... (remaining 4840 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 274 2.60 - 3.18: 23617 3.18 - 3.75: 46241 3.75 - 4.33: 60553 4.33 - 4.90: 99606 Nonbonded interactions: 230291 Sorted by model distance: nonbonded pdb=" OP1 U R 17 " pdb="MG MG J1503 " model vdw 2.027 2.170 nonbonded pdb=" P U R 17 " pdb="MG MG J1503 " model vdw 2.031 2.530 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.072 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.087 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG J1503 " model vdw 2.091 2.170 ... (remaining 230286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 4 through 218 or resid 220 through 233)) selection = (chain 'H' and (resid 4 through 218 or resid 220 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=0.50 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: 2.730 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: 1.220 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 93.170 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.002 0.043 28843 Z= 0.147 Angle : 0.527 14.462 39355 Z= 0.272 Chirality : 0.039 0.181 4495 Planarity : 0.004 0.054 4843 Dihedral : 18.805 146.185 11311 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 0.10 % Allowed : 24.54 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 3354 helix: 2.08 (0.16), residues: 1161 sheet: 0.24 (0.23), residues: 518 loop : -0.16 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 183 HIS 0.007 0.000 HIS I1023 PHE 0.012 0.001 PHE G 231 TYR 0.006 0.001 TYR J 140 ARG 0.014 0.000 ARG I 473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 476 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 127 GLN cc_start: 0.7905 (pm20) cc_final: 0.7642 (pm20) REVERT: I 515 MET cc_start: 0.7628 (ttm) cc_final: 0.7058 (ttp) REVERT: I 516 ASP cc_start: 0.7910 (p0) cc_final: 0.7414 (p0) REVERT: I 1188 ASP cc_start: 0.7901 (t0) cc_final: 0.7618 (t0) REVERT: I 1273 MET cc_start: 0.8710 (mtt) cc_final: 0.8352 (mtt) REVERT: J 329 ASP cc_start: 0.8162 (m-30) cc_final: 0.7729 (m-30) REVERT: J 485 MET cc_start: 0.8770 (tpp) cc_final: 0.8322 (tpt) REVERT: J 724 MET cc_start: 0.8329 (ttm) cc_final: 0.8039 (ttp) REVERT: J 878 ASP cc_start: 0.7725 (p0) cc_final: 0.7241 (p0) REVERT: K 61 ASN cc_start: 0.9346 (t0) cc_final: 0.9130 (t0) REVERT: K 79 GLU cc_start: 0.8548 (pt0) cc_final: 0.8287 (pt0) REVERT: H 65 LEU cc_start: 0.9409 (tp) cc_final: 0.9145 (tt) REVERT: H 66 HIS cc_start: 0.8096 (m170) cc_final: 0.7669 (m170) REVERT: H 182 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7611 (tpt-90) outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.4895 time to fit residues: 349.3618 Evaluate side-chains 250 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 311 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 53 ASN I 273 HIS ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN I1111 GLN I1257 GLN J 206 ASN J 266 ASN J 488 ASN J 792 ASN J1279 GLN K 43 ASN K 73 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28843 Z= 0.289 Angle : 0.583 9.102 39355 Z= 0.307 Chirality : 0.042 0.209 4495 Planarity : 0.004 0.038 4843 Dihedral : 15.705 150.104 4706 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 2.75 % Allowed : 23.25 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 3354 helix: 1.98 (0.15), residues: 1167 sheet: 0.28 (0.22), residues: 515 loop : -0.26 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP I 183 HIS 0.016 0.001 HIS I 273 PHE 0.018 0.002 PHE I1144 TYR 0.017 0.001 TYR J 631 ARG 0.009 0.001 ARG I 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 253 time to evaluate : 3.250 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: P 37 LYS cc_start: 0.8003 (mppt) cc_final: 0.7739 (mptt) REVERT: P 127 GLN cc_start: 0.7918 (pm20) cc_final: 0.7560 (pm20) REVERT: I 516 ASP cc_start: 0.7978 (p0) cc_final: 0.7671 (p0) REVERT: I 1188 ASP cc_start: 0.8139 (t0) cc_final: 0.7732 (t0) REVERT: I 1273 MET cc_start: 0.8677 (mtt) cc_final: 0.8404 (mtt) REVERT: J 42 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: J 301 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8224 (mm-30) REVERT: J 322 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.8290 (mtm-85) REVERT: K 43 ASN cc_start: 0.8753 (t0) cc_final: 0.8270 (t0) REVERT: H 10 LYS cc_start: 0.8551 (mmmm) cc_final: 0.8320 (mmtm) REVERT: H 25 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8252 (tttm) REVERT: H 65 LEU cc_start: 0.9443 (tp) cc_final: 0.9199 (tp) REVERT: H 182 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8103 (tpt90) REVERT: H 205 MET cc_start: 0.8323 (ptm) cc_final: 0.8109 (ptm) outliers start: 76 outliers final: 34 residues processed: 311 average time/residue: 0.4249 time to fit residues: 206.4108 Evaluate side-chains 256 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 219 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 312 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 309 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 250 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 24 GLN P 94 HIS ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 ASN J 921 GLN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28843 Z= 0.248 Angle : 0.527 8.484 39355 Z= 0.277 Chirality : 0.040 0.192 4495 Planarity : 0.004 0.037 4843 Dihedral : 15.684 147.331 4706 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 2.88 % Allowed : 23.18 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 3354 helix: 2.07 (0.15), residues: 1174 sheet: 0.35 (0.23), residues: 495 loop : -0.35 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 183 HIS 0.004 0.001 HIS P 77 PHE 0.014 0.001 PHE I 385 TYR 0.013 0.001 TYR J 140 ARG 0.007 0.000 ARG I 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 224 time to evaluate : 3.003 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: P 24 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8113 (mm-40) REVERT: P 127 GLN cc_start: 0.7938 (pm20) cc_final: 0.7578 (pm20) REVERT: P 140 MET cc_start: 0.8744 (tmm) cc_final: 0.7841 (tmm) REVERT: P 151 LYS cc_start: 0.8623 (tptp) cc_final: 0.8029 (tppt) REVERT: I 516 ASP cc_start: 0.8073 (p0) cc_final: 0.7872 (p0) REVERT: I 1188 ASP cc_start: 0.8136 (t0) cc_final: 0.7666 (t0) REVERT: I 1273 MET cc_start: 0.8584 (mtt) cc_final: 0.8372 (mtt) REVERT: J 1100 PHE cc_start: 0.8121 (m-80) cc_final: 0.7799 (t80) REVERT: K 43 ASN cc_start: 0.8601 (t0) cc_final: 0.8094 (t0) REVERT: H 10 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8372 (mmtm) REVERT: H 25 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8162 (tttm) REVERT: H 65 LEU cc_start: 0.9366 (tp) cc_final: 0.9020 (tp) REVERT: H 165 GLU cc_start: 0.4256 (OUTLIER) cc_final: 0.3550 (tm-30) REVERT: H 182 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8296 (tpt90) outliers start: 81 outliers final: 42 residues processed: 291 average time/residue: 0.4145 time to fit residues: 190.7378 Evaluate side-chains 255 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 209 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 182 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 2.9990 chunk 234 optimal weight: 0.0670 chunk 161 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 313 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 28843 Z= 0.317 Angle : 0.551 8.168 39355 Z= 0.290 Chirality : 0.041 0.174 4495 Planarity : 0.004 0.045 4843 Dihedral : 15.729 148.322 4706 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.22 % Favored : 96.75 % Rotamer: Outliers : 3.13 % Allowed : 23.25 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3354 helix: 2.05 (0.15), residues: 1169 sheet: 0.22 (0.23), residues: 497 loop : -0.40 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 183 HIS 0.005 0.001 HIS P 65 PHE 0.015 0.001 PHE I 385 TYR 0.017 0.001 TYR J 140 ARG 0.005 0.000 ARG I 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 213 time to evaluate : 3.207 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: P 127 GLN cc_start: 0.7882 (pm20) cc_final: 0.7535 (pm20) REVERT: P 138 ARG cc_start: 0.9335 (mtp-110) cc_final: 0.8952 (ttp-110) REVERT: P 140 MET cc_start: 0.8993 (tmm) cc_final: 0.8337 (tmm) REVERT: P 151 LYS cc_start: 0.8665 (tptp) cc_final: 0.8170 (tppt) REVERT: I 465 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7723 (tpt170) REVERT: I 1188 ASP cc_start: 0.8162 (t0) cc_final: 0.7647 (t0) REVERT: I 1273 MET cc_start: 0.8604 (mtt) cc_final: 0.8362 (mtt) REVERT: K 43 ASN cc_start: 0.8592 (t0) cc_final: 0.8015 (t0) REVERT: H 25 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8185 (tttm) REVERT: H 65 LEU cc_start: 0.9373 (tp) cc_final: 0.9052 (tp) REVERT: H 165 GLU cc_start: 0.4423 (OUTLIER) cc_final: 0.3768 (tm-30) outliers start: 88 outliers final: 59 residues processed: 292 average time/residue: 0.4203 time to fit residues: 194.3220 Evaluate side-chains 258 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 196 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 chunk 282 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1114 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 28843 Z= 0.334 Angle : 0.552 8.293 39355 Z= 0.292 Chirality : 0.041 0.146 4495 Planarity : 0.004 0.037 4843 Dihedral : 15.765 147.245 4706 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 3.16 % Allowed : 23.25 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3354 helix: 1.97 (0.15), residues: 1176 sheet: 0.20 (0.23), residues: 495 loop : -0.46 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I 183 HIS 0.004 0.001 HIS P 77 PHE 0.017 0.001 PHE I 385 TYR 0.013 0.001 TYR J 631 ARG 0.006 0.000 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 201 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 111 TYR cc_start: 0.8813 (m-10) cc_final: 0.8533 (m-10) REVERT: P 127 GLN cc_start: 0.7856 (pm20) cc_final: 0.7493 (pm20) REVERT: I 142 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: I 465 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7713 (tpt170) REVERT: I 1188 ASP cc_start: 0.8147 (t0) cc_final: 0.7630 (t0) REVERT: J 1046 ILE cc_start: 0.4753 (OUTLIER) cc_final: 0.4505 (pt) REVERT: H 65 LEU cc_start: 0.9369 (tp) cc_final: 0.9056 (tp) REVERT: H 182 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8721 (tpt90) REVERT: H 196 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.7973 (m) outliers start: 89 outliers final: 67 residues processed: 280 average time/residue: 0.4068 time to fit residues: 183.5274 Evaluate side-chains 262 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 190 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 95 GLN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 626 GLU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 196 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 111 optimal weight: 8.9990 chunk 298 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 194 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 331 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28843 Z= 0.161 Angle : 0.508 10.061 39355 Z= 0.267 Chirality : 0.040 0.148 4495 Planarity : 0.003 0.038 4843 Dihedral : 15.690 147.433 4706 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 2.57 % Allowed : 24.05 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 3354 helix: 2.14 (0.15), residues: 1170 sheet: 0.17 (0.23), residues: 502 loop : -0.43 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I 183 HIS 0.003 0.000 HIS P 77 PHE 0.013 0.001 PHE I1025 TYR 0.011 0.001 TYR J 140 ARG 0.007 0.000 ARG P 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 210 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 111 TYR cc_start: 0.8850 (m-10) cc_final: 0.8634 (m-10) REVERT: I 465 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7522 (tpt170) REVERT: I 488 MET cc_start: 0.8562 (mmm) cc_final: 0.8358 (tpt) REVERT: I 1188 ASP cc_start: 0.8036 (t0) cc_final: 0.7523 (t0) REVERT: I 1304 MET cc_start: 0.8964 (tpp) cc_final: 0.8761 (tpt) REVERT: J 1370 MET cc_start: 0.8685 (tpp) cc_final: 0.8479 (ttm) REVERT: K 72 GLN cc_start: 0.9252 (tp40) cc_final: 0.9052 (tp40) REVERT: K 73 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8150 (mt0) REVERT: H 10 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8441 (mmtm) REVERT: H 65 LEU cc_start: 0.9332 (tp) cc_final: 0.9103 (tp) REVERT: H 182 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8543 (tpt-90) outliers start: 72 outliers final: 52 residues processed: 268 average time/residue: 0.4153 time to fit residues: 175.7876 Evaluate side-chains 251 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 197 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 95 GLN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 151 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 626 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 182 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 242 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 279 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 330 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28843 Z= 0.295 Angle : 0.541 10.796 39355 Z= 0.285 Chirality : 0.041 0.155 4495 Planarity : 0.004 0.056 4843 Dihedral : 15.746 147.461 4706 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.28 % Favored : 96.69 % Rotamer: Outliers : 2.71 % Allowed : 23.98 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3354 helix: 2.08 (0.15), residues: 1175 sheet: 0.10 (0.23), residues: 514 loop : -0.44 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP J1193 HIS 0.005 0.001 HIS P 77 PHE 0.016 0.001 PHE I 385 TYR 0.011 0.001 TYR I 123 ARG 0.007 0.000 ARG J1194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 198 time to evaluate : 2.919 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: P 111 TYR cc_start: 0.8947 (m-10) cc_final: 0.8740 (m-10) REVERT: I 465 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7674 (tpt170) REVERT: I 488 MET cc_start: 0.8582 (mmm) cc_final: 0.8339 (tpt) REVERT: I 1188 ASP cc_start: 0.8105 (t0) cc_final: 0.7587 (t0) REVERT: J 1193 TRP cc_start: 0.9285 (p-90) cc_final: 0.8687 (p90) REVERT: H 65 LEU cc_start: 0.9339 (tp) cc_final: 0.9097 (tp) outliers start: 76 outliers final: 62 residues processed: 261 average time/residue: 0.4092 time to fit residues: 170.4696 Evaluate side-chains 253 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 190 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 95 GLN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 151 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 626 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 204 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 chunk 210 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 300 optimal weight: 0.1980 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 465 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28843 Z= 0.169 Angle : 0.510 11.038 39355 Z= 0.268 Chirality : 0.040 0.148 4495 Planarity : 0.003 0.038 4843 Dihedral : 15.684 147.437 4706 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 2.40 % Allowed : 24.37 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3354 helix: 2.12 (0.15), residues: 1176 sheet: 0.15 (0.23), residues: 518 loop : -0.41 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP J1193 HIS 0.003 0.000 HIS P 77 PHE 0.013 0.001 PHE I 385 TYR 0.011 0.001 TYR J 140 ARG 0.005 0.000 ARG J 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 202 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 465 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7518 (tpt170) REVERT: I 488 MET cc_start: 0.8583 (mmm) cc_final: 0.8349 (tpt) REVERT: I 1188 ASP cc_start: 0.8034 (t0) cc_final: 0.7504 (t0) REVERT: I 1304 MET cc_start: 0.8988 (tpp) cc_final: 0.8782 (tpt) REVERT: J 1189 MET cc_start: 0.8504 (mmp) cc_final: 0.8081 (tpp) REVERT: K 43 ASN cc_start: 0.8449 (t0) cc_final: 0.7734 (t0) REVERT: K 73 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8153 (mt0) REVERT: H 65 LEU cc_start: 0.9351 (tp) cc_final: 0.9020 (tp) REVERT: H 182 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8520 (tpt-90) outliers start: 67 outliers final: 58 residues processed: 259 average time/residue: 0.4093 time to fit residues: 169.6611 Evaluate side-chains 256 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 196 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 95 GLN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 151 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 308 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 291 optimal weight: 0.0470 chunk 306 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28843 Z= 0.195 Angle : 0.508 11.595 39355 Z= 0.267 Chirality : 0.040 0.147 4495 Planarity : 0.003 0.037 4843 Dihedral : 15.677 147.562 4706 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 2.33 % Allowed : 24.50 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 3354 helix: 2.20 (0.15), residues: 1170 sheet: 0.10 (0.23), residues: 520 loop : -0.41 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP J1193 HIS 0.004 0.000 HIS P 77 PHE 0.013 0.001 PHE I 385 TYR 0.010 0.001 TYR J 140 ARG 0.004 0.000 ARG J 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 198 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 465 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7529 (tpt170) REVERT: I 488 MET cc_start: 0.8579 (mmm) cc_final: 0.8324 (tpt) REVERT: I 1188 ASP cc_start: 0.8065 (t0) cc_final: 0.7540 (t0) REVERT: J 1189 MET cc_start: 0.8526 (mmp) cc_final: 0.8069 (tpp) REVERT: K 73 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8153 (mt0) REVERT: H 65 LEU cc_start: 0.9311 (tp) cc_final: 0.8989 (tp) REVERT: H 182 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8420 (tpt-90) outliers start: 65 outliers final: 58 residues processed: 252 average time/residue: 0.4514 time to fit residues: 183.3770 Evaluate side-chains 253 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 193 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 95 GLN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 151 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 626 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 325 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 154 optimal weight: 0.0470 chunk 226 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 314 optimal weight: 0.0040 chunk 272 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 210 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 216 optimal weight: 0.6980 overall best weight: 0.4690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28843 Z= 0.148 Angle : 0.500 11.399 39355 Z= 0.262 Chirality : 0.040 0.192 4495 Planarity : 0.003 0.039 4843 Dihedral : 15.626 147.688 4706 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 2.02 % Allowed : 24.92 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3354 helix: 2.20 (0.15), residues: 1176 sheet: 0.23 (0.23), residues: 504 loop : -0.40 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP J1193 HIS 0.003 0.000 HIS P 77 PHE 0.014 0.001 PHE I 188 TYR 0.009 0.001 TYR J 140 ARG 0.007 0.000 ARG I 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 213 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 488 MET cc_start: 0.8553 (mmm) cc_final: 0.8323 (tpt) REVERT: I 1188 ASP cc_start: 0.7964 (t0) cc_final: 0.7371 (t0) REVERT: I 1230 MET cc_start: 0.8377 (ttm) cc_final: 0.8027 (ttt) REVERT: J 1189 MET cc_start: 0.8565 (mmp) cc_final: 0.8134 (tpp) REVERT: K 73 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8140 (mt0) REVERT: H 65 LEU cc_start: 0.9286 (tp) cc_final: 0.9022 (tp) REVERT: H 182 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8636 (tpt-90) outliers start: 56 outliers final: 49 residues processed: 259 average time/residue: 0.4228 time to fit residues: 175.5788 Evaluate side-chains 249 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 199 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 151 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 626 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 182 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 250 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 272 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 279 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 239 optimal weight: 0.0270 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.070803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.049245 restraints weight = 101622.785| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.16 r_work: 0.2691 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28843 Z= 0.264 Angle : 0.533 11.627 39355 Z= 0.280 Chirality : 0.041 0.238 4495 Planarity : 0.004 0.039 4843 Dihedral : 15.720 147.737 4706 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 2.19 % Allowed : 24.82 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3354 helix: 2.24 (0.15), residues: 1170 sheet: 0.19 (0.23), residues: 503 loop : -0.38 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP J1193 HIS 0.007 0.001 HIS J1227 PHE 0.015 0.001 PHE I 385 TYR 0.011 0.001 TYR J 140 ARG 0.013 0.000 ARG I 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5930.86 seconds wall clock time: 106 minutes 51.71 seconds (6411.71 seconds total)