Starting phenix.real_space_refine on Thu Jul 25 21:41:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pil_17685/07_2024/8pil_17685_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pil_17685/07_2024/8pil_17685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pil_17685/07_2024/8pil_17685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pil_17685/07_2024/8pil_17685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pil_17685/07_2024/8pil_17685_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pil_17685/07_2024/8pil_17685_neut.cif" } resolution = 3.2 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= 0.010 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 83 5.49 5 Mg 1 5.21 5 S 116 5.16 5 C 18823 2.51 5 N 5389 2.21 5 O 6026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ASP 160": "OD1" <-> "OD2" Residue "I GLU 415": "OE1" <-> "OE2" Residue "I ASP 446": "OD1" <-> "OD2" Residue "I PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 562": "OE1" <-> "OE2" Residue "I TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 813": "OE1" <-> "OE2" Residue "I ASP 930": "OD1" <-> "OD2" Residue "I GLU 1089": "OE1" <-> "OE2" Residue "I GLU 1279": "OE1" <-> "OE2" Residue "I GLU 1340": "OE1" <-> "OE2" Residue "J ASP 413": "OD1" <-> "OD2" Residue "J ASP 460": "OD1" <-> "OD2" Residue "J GLU 827": "OE1" <-> "OE2" Residue "J PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 1239": "OD1" <-> "OD2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "G GLU 163": "OE1" <-> "OE2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H GLU 261": "OE1" <-> "OE2" Residue "F PHE 24": "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: 30440 Number of models: 1 Model: "" Number of chains: 11 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: 10604 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1342, 10585 Classifications: {'peptide': 1342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1285} Conformer: "B" Number of residues, atoms: 1342, 10585 Classifications: {'peptide': 1342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1285} bond proxies already assigned to first conformer: 10732 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: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2299 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "A" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 733 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "B" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 740 Classifications: {'DNA': 36} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 35} 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: "F" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1605 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} 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 12347 SG CYS J 70 37.176 71.372 91.436 1.00116.29 S ATOM 12361 SG CYS J 72 36.058 67.868 90.486 1.00116.32 S ATOM 12469 SG CYS J 85 34.292 69.564 93.247 1.00115.34 S ATOM 12493 SG CYS J 88 37.812 68.495 93.894 1.00112.63 S ATOM 18181 SG CYS J 814 71.028 125.865 100.007 1.00 95.84 S ATOM 18746 SG CYS J 888 73.003 123.151 98.573 1.00 95.46 S ATOM 18797 SG CYS J 895 71.736 126.014 96.256 1.00 89.23 S ATOM 18818 SG CYS J 898 74.623 126.536 98.574 1.00 89.44 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE I 156 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE I 156 " occ=0.50 Time building chain proxies: 23.08, per 1000 atoms: 0.76 Number of scatterers: 30440 At special positions: 0 Unit cell: (153.92, 170.56, 163.904, 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 116 16.00 P 83 15.00 Mg 1 11.99 O 6026 8.00 N 5389 7.00 C 18823 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: 13.27 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " 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 ZN J1501 " - pdb=" SG CYS J 70 " 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 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6786 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 52 sheets defined 39.2% alpha, 17.6% beta 32 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 10.37 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 71 Processing helix chain 'P' and resid 89 through 99 removed outlier: 4.111A pdb=" N VAL P 98 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.711A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.632A pdb=" N ASP I 33 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.728A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) removed outlier: 3.610A 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: 3.837A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 4.090A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 3.886A 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 328 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: 3.959A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.580A pdb=" N MET I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.556A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.819A 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: 3.882A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 3.568A 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 Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.811A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.799A 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: 3.702A pdb=" N HIS I 628 " --> pdb=" O GLU I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.117A 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 864 removed outlier: 4.143A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 895 through 902 Processing helix chain 'I' and resid 942 through 982 Processing helix chain 'I' and resid 985 through 991 Processing helix chain 'I' and resid 993 through 1000 Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 4.158A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 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 1160 through 1164 removed outlier: 3.801A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 removed outlier: 3.700A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.557A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1239 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 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.731A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 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 181 through 192 removed outlier: 3.701A 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 484 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.811A 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: 4.008A 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: 3.598A pdb=" N VAL J 618 " --> pdb=" O LEU J 614 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.217A 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: 4.070A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 875 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 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.878A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.356A 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: 3.611A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1360 through 1375 removed outlier: 4.168A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA J1375 " --> pdb=" O ARG J1371 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.597A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.740A pdb=" N GLY G 40 " --> pdb=" O GLY G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.663A 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: 3.501A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.104A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.528A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 159 Processing helix chain 'H' and resid 161 through 166 removed outlier: 4.076A pdb=" N ASP H 164 " --> pdb=" O SER H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'H' and resid 228 through 233 removed outlier: 4.005A pdb=" N ASP H 233 " --> pdb=" O GLU H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 255 Processing helix chain 'H' and resid 256 through 260 Processing helix chain 'H' and resid 263 through 273 Processing helix chain 'H' and resid 277 through 284 removed outlier: 3.794A pdb=" N LEU H 281 " --> pdb=" O TYR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 311 removed outlier: 3.863A pdb=" N LYS H 304 " --> pdb=" O LEU H 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 19 through 39 Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'F' and resid 103 through 128 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 34 Processing sheet with id=AA3, first strand: chain 'P' and resid 150 through 154 removed outlier: 8.345A pdb=" N MET P 140 " --> pdb=" O THR P 131 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR P 131 " --> pdb=" O MET P 140 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE P 129 " --> pdb=" O LEU P 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.349A 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: 5.864A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (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 451 through 454 removed outlier: 6.206A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 154 through 159 removed outlier: 5.351A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB1, first strand: chain 'I' and resid 239 through 240 removed outlier: 3.566A pdb=" N MET I 239 " --> pdb=" O ILE I 285 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE I 285 " --> pdb=" O MET I 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 255 through 257 removed outlier: 3.823A pdb=" N VAL I 263 " --> pdb=" O ILE I 255 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.614A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.527A pdb=" N LYS I 593 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.539A pdb=" N ASP I 654 " --> pdb=" O ALA I 617 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.629A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.373A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 755 through 758 Processing sheet with id=AB9, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.701A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.826A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.859A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL I 887 " --> pdb=" O GLU I 849 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.256A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.744A pdb=" N HIS I1244 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC7, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.605A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.778A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.985A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD2, first strand: chain 'J' and resid 706 through 709 Processing sheet with id=AD3, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD4, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD5, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.144A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 842 through 843 removed outlier: 3.803A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.301A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AD9, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 6.267A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE2, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.145A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.675A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.628A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 97 through 105 removed outlier: 6.293A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AE7, first strand: chain 'G' and resid 108 through 111 removed outlier: 4.081A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AE9, first strand: chain 'H' and resid 15 through 18 removed outlier: 6.596A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N THR H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL H 192 " --> pdb=" O THR H 196 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 97 through 105 removed outlier: 3.634A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AF3, first strand: chain 'H' and resid 109 through 111 removed outlier: 6.752A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AF5, first strand: chain 'F' and resid 60 through 61 Processing sheet with id=AF6, first strand: chain 'F' and resid 137 through 138 removed outlier: 3.571A pdb=" N SER F 185 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 141 through 144 removed outlier: 6.830A pdb=" N SER F 151 " --> pdb=" O LYS F 143 " (cutoff:3.500A) 1239 hydrogen bonds defined for protein. 3479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 14.40 Time building geometry restraints manager: 14.40 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: 10054 1.34 - 1.46: 4848 1.46 - 1.58: 15809 1.58 - 1.70: 164 1.70 - 1.82: 201 Bond restraints: 31076 Sorted by residual: bond pdb=" C ASP P 106 " pdb=" N PRO P 107 " ideal model delta sigma weight residual 1.333 1.357 -0.023 1.01e-02 9.80e+03 5.20e+00 bond pdb=" CB LYS J 87 " pdb=" CG LYS J 87 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" CG ARG I 996 " pdb=" CD ARG I 996 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CG ASP J 460 " pdb=" OD1 ASP J 460 " ideal model delta sigma weight residual 1.249 1.224 0.025 1.90e-02 2.77e+03 1.70e+00 bond pdb=" CB ASP J 460 " pdb=" CG ASP J 460 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.67e+00 ... (remaining 31071 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.36: 874 105.36 - 112.53: 16301 112.53 - 119.69: 10502 119.69 - 126.85: 14205 126.85 - 134.01: 470 Bond angle restraints: 42352 Sorted by residual: angle pdb=" CA ARG I 996 " pdb=" CB ARG I 996 " pdb=" CG ARG I 996 " ideal model delta sigma weight residual 114.10 123.16 -9.06 2.00e+00 2.50e-01 2.05e+01 angle pdb=" CA GLU I 908 " pdb=" CB GLU I 908 " pdb=" CG GLU I 908 " ideal model delta sigma weight residual 114.10 122.82 -8.72 2.00e+00 2.50e-01 1.90e+01 angle pdb=" C GLY I 907 " pdb=" N GLU I 908 " pdb=" CA GLU I 908 " ideal model delta sigma weight residual 121.54 129.53 -7.99 1.91e+00 2.74e-01 1.75e+01 angle pdb=" CG ARG I 996 " pdb=" CD ARG I 996 " pdb=" NE ARG I 996 " ideal model delta sigma weight residual 112.00 120.82 -8.82 2.20e+00 2.07e-01 1.61e+01 angle pdb=" CA GLU I 813 " pdb=" CB GLU I 813 " pdb=" CG GLU I 813 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 ... (remaining 42347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.59: 17263 27.59 - 55.19: 1485 55.19 - 82.78: 201 82.78 - 110.37: 13 110.37 - 137.96: 2 Dihedral angle restraints: 18964 sinusoidal: 8431 harmonic: 10533 Sorted by residual: dihedral pdb=" CA MET F 125 " pdb=" C MET F 125 " pdb=" N VAL F 126 " pdb=" CA VAL F 126 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ASP I 995 " pdb=" C ASP I 995 " pdb=" N ARG I 996 " pdb=" CA ARG I 996 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASN I 314 " pdb=" C ASN I 314 " pdb=" N MET I 315 " pdb=" CA MET I 315 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 18961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3615 0.038 - 0.076: 827 0.076 - 0.114: 353 0.114 - 0.152: 47 0.152 - 0.191: 4 Chirality restraints: 4846 Sorted by residual: chirality pdb=" CA GLU I 908 " pdb=" N GLU I 908 " pdb=" C GLU I 908 " pdb=" CB GLU I 908 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" CB ILE P 38 " pdb=" CA ILE P 38 " pdb=" CG1 ILE P 38 " pdb=" CG2 ILE P 38 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA MET F 125 " pdb=" N MET F 125 " pdb=" C MET F 125 " pdb=" CB MET F 125 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 4843 not shown) Planarity restraints: 5251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP J 460 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" CG ASP J 460 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASP J 460 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP J 460 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 464 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" CG ASP J 464 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP J 464 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP J 464 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG H 166 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO H 167 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO H 167 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 167 " 0.031 5.00e-02 4.00e+02 ... (remaining 5248 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 15 2.28 - 2.93: 12795 2.93 - 3.59: 46076 3.59 - 4.24: 70506 4.24 - 4.90: 117844 Nonbonded interactions: 247236 Sorted by model distance: nonbonded pdb=" CB ASP J 460 " pdb="MG MG J1503 " model vdw 1.621 2.570 nonbonded pdb=" OD2 ASP J 460 " pdb=" OP1 U R 17 " model vdw 2.008 3.040 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.049 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb=" OD2 ASP J 462 " model vdw 2.115 3.040 nonbonded pdb=" CG ASP J 460 " pdb="MG MG J1503 " model vdw 2.130 2.400 ... (remaining 247231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.940 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: 0.030 Extract box with map and model: 1.130 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 105.250 Find NCS groups from input model: 0.540 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 0.042 31076 Z= 0.136 Angle : 0.497 11.077 42352 Z= 0.260 Chirality : 0.039 0.191 4846 Planarity : 0.003 0.055 5251 Dihedral : 18.896 137.964 12178 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.19 % Allowed : 25.44 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 1.07 (0.14), residues: 3641 helix: 2.08 (0.15), residues: 1258 sheet: 0.31 (0.23), residues: 522 loop : -0.08 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 183 HIS 0.003 0.000 HIS J 430 PHE 0.013 0.001 PHE J 461 TYR 0.011 0.001 TYR P 99 ARG 0.017 0.000 ARG I 996 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 221 time to evaluate : 6.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 32 MET cc_start: 0.7991 (mmm) cc_final: 0.7762 (mmm) REVERT: I 856 ASN cc_start: 0.7852 (p0) cc_final: 0.7646 (p0) REVERT: J 822 MET cc_start: 0.8460 (tpp) cc_final: 0.8196 (mtp) REVERT: K 69 ARG cc_start: 0.8740 (ttm110) cc_final: 0.8222 (ptp90) REVERT: K 72 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8691 (tm-30) REVERT: F 141 VAL cc_start: 0.0367 (OUTLIER) cc_final: 0.0156 (m) REVERT: F 167 MET cc_start: 0.5697 (mmt) cc_final: 0.4913 (mmp) outliers start: 5 outliers final: 2 residues processed: 225 average time/residue: 0.4589 time to fit residues: 166.8042 Evaluate side-chains 205 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 202 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain F residue 141 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 4.9990 chunk 280 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 336 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 2 GLN I 193 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 435 GLN J 910 ASN G 41 ASN H 137 ASN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31076 Z= 0.318 Angle : 0.534 7.569 42352 Z= 0.281 Chirality : 0.041 0.149 4846 Planarity : 0.004 0.054 5251 Dihedral : 14.859 138.807 4988 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.14 % Allowed : 24.64 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 1.03 (0.14), residues: 3641 helix: 2.01 (0.15), residues: 1297 sheet: 0.25 (0.23), residues: 524 loop : -0.10 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 62 HIS 0.004 0.001 HIS J1252 PHE 0.015 0.001 PHE J1325 TYR 0.015 0.001 TYR F 39 ARG 0.004 0.000 ARG I 996 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 207 time to evaluate : 6.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 856 ASN cc_start: 0.7919 (p0) cc_final: 0.7705 (p0) REVERT: J 857 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8083 (mt) REVERT: J 895 CYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8138 (p) REVERT: J 1189 MET cc_start: 0.8429 (mmt) cc_final: 0.8179 (mmt) REVERT: K 69 ARG cc_start: 0.8776 (ttm110) cc_final: 0.8261 (ptp90) REVERT: K 72 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8670 (tm-30) REVERT: F 167 MET cc_start: 0.5574 (mmt) cc_final: 0.4913 (mmt) outliers start: 66 outliers final: 30 residues processed: 259 average time/residue: 0.4147 time to fit residues: 174.9854 Evaluate side-chains 226 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 194 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 279 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 336 optimal weight: 0.9980 chunk 363 optimal weight: 40.0000 chunk 299 optimal weight: 1.9990 chunk 333 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 270 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 193 ASN J 164 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31076 Z= 0.213 Angle : 0.491 7.223 42352 Z= 0.261 Chirality : 0.040 0.192 4846 Planarity : 0.003 0.056 5251 Dihedral : 14.889 140.002 4984 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.01 % Allowed : 25.15 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 1.04 (0.14), residues: 3641 helix: 2.08 (0.15), residues: 1299 sheet: 0.18 (0.23), residues: 533 loop : -0.12 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 62 HIS 0.003 0.001 HIS J 430 PHE 0.010 0.001 PHE I 405 TYR 0.012 0.001 TYR J 631 ARG 0.003 0.000 ARG J1123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 211 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 813 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7300 (tm-30) REVERT: J 172 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.6669 (p90) REVERT: J 1167 LYS cc_start: 0.8321 (tptp) cc_final: 0.7947 (tmtt) REVERT: J 1189 MET cc_start: 0.8442 (mmt) cc_final: 0.8226 (mmt) REVERT: K 69 ARG cc_start: 0.8796 (ttm110) cc_final: 0.8190 (ptp90) REVERT: K 72 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8707 (tm-30) REVERT: F 38 LYS cc_start: 0.6671 (tmmt) cc_final: 0.5496 (mttm) REVERT: F 167 MET cc_start: 0.5361 (mmt) cc_final: 0.4991 (mmp) outliers start: 62 outliers final: 42 residues processed: 259 average time/residue: 0.4686 time to fit residues: 197.4632 Evaluate side-chains 244 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 201 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 156 ASN Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 23 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 0.7980 chunk 253 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 337 optimal weight: 2.9990 chunk 357 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 320 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 24 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN H 137 ASN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31076 Z= 0.189 Angle : 0.482 8.647 42352 Z= 0.254 Chirality : 0.040 0.150 4846 Planarity : 0.003 0.056 5251 Dihedral : 14.873 141.683 4984 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.81 % Allowed : 24.48 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 1.04 (0.14), residues: 3641 helix: 2.12 (0.15), residues: 1294 sheet: 0.16 (0.23), residues: 532 loop : -0.15 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 62 HIS 0.003 0.001 HIS J 430 PHE 0.009 0.001 PHE J 988 TYR 0.013 0.001 TYR P 99 ARG 0.004 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 207 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 813 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7201 (tm-30) REVERT: J 172 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.6673 (p90) REVERT: J 192 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8039 (ttm) REVERT: J 298 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8321 (mpp) REVERT: J 1167 LYS cc_start: 0.8282 (tptp) cc_final: 0.7969 (tmtt) REVERT: J 1189 MET cc_start: 0.8452 (mmt) cc_final: 0.8227 (mmt) REVERT: K 69 ARG cc_start: 0.8789 (ttm110) cc_final: 0.8169 (ptp90) REVERT: K 72 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8709 (tm-30) REVERT: H 66 HIS cc_start: 0.7922 (m170) cc_final: 0.7697 (m90) REVERT: F 38 LYS cc_start: 0.6595 (tmmt) cc_final: 0.5606 (mttm) REVERT: F 167 MET cc_start: 0.5382 (mmt) cc_final: 0.4983 (mmp) outliers start: 87 outliers final: 56 residues processed: 277 average time/residue: 0.4035 time to fit residues: 182.2675 Evaluate side-chains 262 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 203 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 156 ASN Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 297 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 266 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 305 optimal weight: 1.9990 chunk 247 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 182 optimal weight: 0.9990 chunk 321 optimal weight: 0.7980 chunk 90 optimal weight: 0.0980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31076 Z= 0.135 Angle : 0.470 8.354 42352 Z= 0.248 Chirality : 0.040 0.285 4846 Planarity : 0.003 0.057 5251 Dihedral : 14.821 142.177 4984 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.52 % Allowed : 24.90 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 1.07 (0.14), residues: 3641 helix: 2.14 (0.15), residues: 1302 sheet: 0.15 (0.23), residues: 547 loop : -0.12 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 62 HIS 0.003 0.000 HIS J 430 PHE 0.009 0.001 PHE I 405 TYR 0.011 0.001 TYR J 631 ARG 0.004 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 210 time to evaluate : 3.347 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: I 813 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7145 (tm-30) REVERT: J 172 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.6714 (p90) REVERT: J 1167 LYS cc_start: 0.8275 (tptp) cc_final: 0.8019 (tmtt) REVERT: J 1189 MET cc_start: 0.8453 (mmt) cc_final: 0.8230 (mmt) REVERT: K 69 ARG cc_start: 0.8775 (ttm110) cc_final: 0.8143 (ptp90) REVERT: K 72 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8708 (tm-30) REVERT: H 66 HIS cc_start: 0.7865 (m170) cc_final: 0.7648 (m90) REVERT: F 167 MET cc_start: 0.5303 (mmt) cc_final: 0.5026 (mmp) outliers start: 78 outliers final: 57 residues processed: 274 average time/residue: 0.4489 time to fit residues: 201.6495 Evaluate side-chains 261 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 203 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 156 ASN Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 120 optimal weight: 0.8980 chunk 322 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 357 optimal weight: 10.0000 chunk 297 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 193 ASN I 798 GLN ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 31076 Z= 0.457 Angle : 0.600 8.113 42352 Z= 0.313 Chirality : 0.043 0.200 4846 Planarity : 0.004 0.054 5251 Dihedral : 14.970 141.665 4984 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.36 % Allowed : 24.42 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 0.77 (0.14), residues: 3641 helix: 1.86 (0.15), residues: 1294 sheet: -0.01 (0.23), residues: 527 loop : -0.27 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 62 HIS 0.004 0.001 HIS J1252 PHE 0.021 0.002 PHE I 385 TYR 0.016 0.001 TYR J 631 ARG 0.007 0.001 ARG J 838 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 191 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 32 MET cc_start: 0.8013 (mmm) cc_final: 0.7718 (mmm) REVERT: I 492 MET cc_start: 0.8952 (tpp) cc_final: 0.8553 (ttm) REVERT: I 813 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7249 (tm-30) REVERT: I 814 ASP cc_start: 0.7947 (m-30) cc_final: 0.7687 (m-30) REVERT: J 172 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.6833 (p90) REVERT: J 298 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8370 (mpp) REVERT: J 709 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7264 (ptm160) REVERT: J 762 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7455 (m-40) REVERT: J 857 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8063 (mt) REVERT: J 933 ARG cc_start: 0.7507 (mtp-110) cc_final: 0.7267 (mtp85) REVERT: J 985 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7374 (tt) REVERT: J 1167 LYS cc_start: 0.8330 (tptp) cc_final: 0.8060 (tmtt) REVERT: J 1189 MET cc_start: 0.8407 (mmt) cc_final: 0.8177 (mmt) REVERT: K 69 ARG cc_start: 0.8843 (ttm110) cc_final: 0.8254 (ptp90) REVERT: K 72 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8591 (tm-30) REVERT: H 66 HIS cc_start: 0.7969 (m170) cc_final: 0.7760 (m90) REVERT: F 167 MET cc_start: 0.5407 (mmt) cc_final: 0.5103 (mmp) outliers start: 104 outliers final: 71 residues processed: 279 average time/residue: 0.4023 time to fit residues: 182.9100 Evaluate side-chains 261 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 184 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 156 ASN Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 345 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 356 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 193 ASN I 798 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31076 Z= 0.179 Angle : 0.502 7.556 42352 Z= 0.264 Chirality : 0.040 0.166 4846 Planarity : 0.003 0.055 5251 Dihedral : 14.917 142.447 4984 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.81 % Allowed : 24.67 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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 (0.14), residues: 3641 helix: 1.96 (0.15), residues: 1301 sheet: 0.06 (0.23), residues: 527 loop : -0.24 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 62 HIS 0.004 0.000 HIS J 430 PHE 0.010 0.001 PHE I 828 TYR 0.018 0.001 TYR I 62 ARG 0.004 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 202 time to evaluate : 3.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 492 MET cc_start: 0.8764 (tpp) cc_final: 0.8514 (ttm) REVERT: I 813 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7253 (tm-30) REVERT: I 814 ASP cc_start: 0.7849 (m-30) cc_final: 0.7572 (m-30) REVERT: J 172 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.6718 (p90) REVERT: J 298 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8314 (mpp) REVERT: J 985 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7354 (tt) REVERT: J 1167 LYS cc_start: 0.8271 (tptp) cc_final: 0.8034 (tmtt) REVERT: J 1189 MET cc_start: 0.8441 (mmt) cc_final: 0.8192 (mmt) REVERT: K 69 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8188 (ptp90) REVERT: K 72 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8564 (tm-30) REVERT: H 66 HIS cc_start: 0.7855 (m170) cc_final: 0.7627 (m90) REVERT: F 167 MET cc_start: 0.5330 (mmt) cc_final: 0.5082 (mmp) outliers start: 87 outliers final: 66 residues processed: 278 average time/residue: 0.4148 time to fit residues: 189.6039 Evaluate side-chains 267 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 198 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 156 ASN Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 173 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 220 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 280 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 798 GLN ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31076 Z= 0.226 Angle : 0.509 7.852 42352 Z= 0.267 Chirality : 0.040 0.143 4846 Planarity : 0.003 0.054 5251 Dihedral : 14.901 143.198 4984 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.62 % Allowed : 24.99 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 0.85 (0.14), residues: 3641 helix: 1.93 (0.15), residues: 1300 sheet: 0.06 (0.23), residues: 523 loop : -0.24 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 183 HIS 0.003 0.001 HIS J 430 PHE 0.011 0.001 PHE J1325 TYR 0.020 0.001 TYR I 62 ARG 0.004 0.000 ARG P 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 194 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 813 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7284 (tm-30) REVERT: I 814 ASP cc_start: 0.7881 (m-30) cc_final: 0.7606 (m-30) REVERT: I 1327 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8717 (mp) REVERT: J 172 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.6720 (p90) REVERT: J 298 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8309 (mpp) REVERT: J 857 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8025 (mt) REVERT: J 895 CYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7914 (p) REVERT: J 1167 LYS cc_start: 0.8288 (tptp) cc_final: 0.8056 (tmtt) REVERT: J 1189 MET cc_start: 0.8471 (mmt) cc_final: 0.8238 (mmt) REVERT: K 69 ARG cc_start: 0.8822 (ttm110) cc_final: 0.8163 (ptp90) REVERT: K 72 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8574 (tm-30) REVERT: H 66 HIS cc_start: 0.7842 (m170) cc_final: 0.7637 (m90) REVERT: F 38 LYS cc_start: 0.6661 (tmmt) cc_final: 0.5411 (mtmm) REVERT: F 167 MET cc_start: 0.5334 (mmt) cc_final: 0.5083 (mmp) outliers start: 81 outliers final: 66 residues processed: 263 average time/residue: 0.4116 time to fit residues: 179.2008 Evaluate side-chains 266 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 195 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 156 ASN Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 173 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 324 optimal weight: 8.9990 chunk 341 optimal weight: 7.9990 chunk 311 optimal weight: 0.6980 chunk 332 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 300 optimal weight: 0.2980 chunk 314 optimal weight: 0.9980 chunk 331 optimal weight: 5.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31076 Z= 0.290 Angle : 0.537 9.612 42352 Z= 0.280 Chirality : 0.041 0.149 4846 Planarity : 0.004 0.053 5251 Dihedral : 14.949 142.728 4984 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.78 % Allowed : 25.09 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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 (0.14), residues: 3641 helix: 1.90 (0.15), residues: 1294 sheet: 0.06 (0.23), residues: 523 loop : -0.28 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 62 HIS 0.003 0.001 HIS J1252 PHE 0.014 0.001 PHE I 385 TYR 0.023 0.001 TYR I 62 ARG 0.008 0.000 ARG J 838 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 190 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 813 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7392 (tm-30) REVERT: I 814 ASP cc_start: 0.7883 (m-30) cc_final: 0.7614 (m-30) REVERT: I 1327 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8724 (mp) REVERT: J 172 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6763 (p90) REVERT: J 298 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8330 (mpp) REVERT: J 857 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8030 (mt) REVERT: J 895 CYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8016 (p) REVERT: J 985 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7384 (tt) REVERT: J 1167 LYS cc_start: 0.8314 (tptp) cc_final: 0.8073 (tmtt) REVERT: J 1189 MET cc_start: 0.8486 (mmt) cc_final: 0.8247 (mmt) REVERT: K 69 ARG cc_start: 0.8797 (ttm110) cc_final: 0.8171 (ptp90) REVERT: K 72 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8676 (tm-30) REVERT: F 167 MET cc_start: 0.5233 (mmt) cc_final: 0.5003 (mmp) outliers start: 86 outliers final: 71 residues processed: 262 average time/residue: 0.4039 time to fit residues: 175.0328 Evaluate side-chains 265 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 188 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 156 ASN Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 173 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 218 optimal weight: 2.9990 chunk 351 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 166 optimal weight: 0.2980 chunk 244 optimal weight: 9.9990 chunk 368 optimal weight: 30.0000 chunk 339 optimal weight: 50.0000 chunk 293 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 179 optimal weight: 0.0570 overall best weight: 1.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 798 GLN ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31076 Z= 0.170 Angle : 0.499 8.913 42352 Z= 0.261 Chirality : 0.040 0.146 4846 Planarity : 0.003 0.055 5251 Dihedral : 14.896 143.482 4984 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.36 % Allowed : 25.31 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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 (0.14), residues: 3641 helix: 1.98 (0.15), residues: 1294 sheet: 0.06 (0.23), residues: 533 loop : -0.22 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 62 HIS 0.004 0.000 HIS J 430 PHE 0.010 0.001 PHE J 988 TYR 0.021 0.001 TYR F 39 ARG 0.004 0.000 ARG K 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 200 time to evaluate : 3.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 813 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7286 (tm-30) REVERT: I 814 ASP cc_start: 0.7811 (m-30) cc_final: 0.7505 (m-30) REVERT: I 1327 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8668 (mp) REVERT: J 172 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6725 (p90) REVERT: J 821 MET cc_start: 0.8449 (tpt) cc_final: 0.8227 (tpt) REVERT: J 857 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8025 (mt) REVERT: J 985 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7353 (tt) REVERT: J 1189 MET cc_start: 0.8506 (mmt) cc_final: 0.8269 (mmt) REVERT: K 69 ARG cc_start: 0.8721 (ttm110) cc_final: 0.8278 (ptp90) REVERT: K 72 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8652 (tm-30) REVERT: F 38 LYS cc_start: 0.6380 (tmmt) cc_final: 0.5730 (mtmm) outliers start: 73 outliers final: 65 residues processed: 261 average time/residue: 0.4395 time to fit residues: 187.1343 Evaluate side-chains 264 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 195 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1197 ASN Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 173 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 233 optimal weight: 9.9990 chunk 312 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 270 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 293 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 301 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.081671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.054072 restraints weight = 148927.145| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.23 r_work: 0.2787 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31076 Z= 0.150 Angle : 0.493 9.876 42352 Z= 0.256 Chirality : 0.040 0.145 4846 Planarity : 0.003 0.055 5251 Dihedral : 14.853 143.645 4984 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.40 % Allowed : 25.25 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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 (0.14), residues: 3641 helix: 2.02 (0.15), residues: 1291 sheet: 0.08 (0.23), residues: 542 loop : -0.19 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 62 HIS 0.003 0.000 HIS J 430 PHE 0.008 0.001 PHE J1325 TYR 0.016 0.001 TYR I 62 ARG 0.004 0.000 ARG J1174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6734.20 seconds wall clock time: 123 minutes 42.15 seconds (7422.15 seconds total)